KEGG   VARIANT: 4005v1
Entry
4005v1                      Variant                                
Name
LMO2 rearrangement
Gene
LMO2  LIM domain only 2 [KO:K15612]
Organism
hsa_var Human gene variants (Homo sapiens)
Variation
translocation t(11;14) (p13;q11)
Variation
translocation t(7;11)(q35;p13)
Variation
deletion del(11)(p12p13)
Network
nt06240  Transcription (cancer)
Disease
H00002  T-cell acute lymphoblastic leukemia
Reference
PMID:26108219
  Authors
Chambers J, Rabbitts TH
  Title
LMO2 at 25 years: a paradigm of chromosomal translocation proteins.
  Journal
Open Biol 5:150062 (2015)
DOI:10.1098/rsob.150062
Reference
PMID:23904235
  Authors
Larmonie NS, Dik WA, Meijerink JP, Homminga I, van Dongen JJ, Langerak AW
  Title
Breakpoint sites disclose the role of the V(D)J recombination machinery in the formation of T-cell receptor (TCR) and non-TCR associated aberrations in T-cell acute lymphoblastic leukemia.
  Journal
Haematologica 98:1173-84 (2013)
DOI:10.3324/haematol.2012.082156
Reference
PMID:16873670
  Authors
Van Vlierberghe P, van Grotel M, Beverloo HB, Lee C, Helgason T, Buijs-Gladdines J, Passier M, van Wering ER, Veerman AJ, Kamps WA, Meijerink JP, Pieters R
  Title
The cryptic chromosomal deletion del(11)(p12p13) as a new activation mechanism of LMO2 in pediatric T-cell acute lymphoblastic leukemia.
  Journal
Blood 108:3520-9 (2006)
DOI:10.1182/blood-2006-04-019927
LinkDB

KEGG   Homo sapiens (human): 8861
Entry
8861              CDS       T01001                                 
Symbol
LDB1, CLIM-2, CLIM2, LDB-1, NLI
Name
(RefSeq) LIM domain binding 1
  KO
K15617  LIM domain-binding protein 1
Organism
hsa  Homo sapiens (human)
Pathway
hsa05202  Transcriptional misregulation in cancer
Network
nt06240  Transcription (cancer)
  Element
N00121  LMO2-rearrangement to transcriptional activation
N00122  LMO2-rearrangement to transcriptional repression
Brite
KEGG Orthology (KO) [BR:hsa00001]
 09160 Human Diseases
  09161 Cancer: overview
   05202 Transcriptional misregulation in cancer
    8861 (LDB1)
 09180 Brite Hierarchies
  09183 Protein families: signaling and cellular processes
   04990 Domain-containing proteins not elsewhere classified [BR:hsa04990]
    8861 (LDB1)
Domain-containing proteins not elsewhere classified [BR:hsa04990]
 LIM domain-containing proteins
  Lim domain binding proteins
   8861 (LDB1)
SSDB
Motif
Pfam: LIM_bind LID
Other DBs
NCBI-GeneID: 8861
NCBI-ProteinID: NP_001106878
OMIM: 603451
HGNC: 6532
Ensembl: ENSG00000198728
UniProt: Q86U70
Structure
LinkDB
Position
10:complement(102102088..102121442)
AA seq 411 aa
MSVGCACPGCSSKSFKLYSPKEPPNGNAFPPFHPGTMLDRDVGPTPMYPPTYLEPGIGRH
TPYGNQTDYRIFELNKRLQNWTEECDNLWWDAFTTEFFEDDAMLTITFCLEDGPKRYTIG
RTLIPRYFRSIFEGGATELYYVLKHPKEAFHSNFVSLDCDQGSMVTQHGKPMFTQVCVEG
RLYLEFMFDDMMRIKTWHFSIRQHRELIPRSILAMHAQDPQMLDQLSKNITRCGLSNSTL
NYLRLCVILEPMQELMSRHKTYSLSPRDCLKTCLFQKWQRMVAPPAEPTRQQPSKRRKRK
MSGGSTMSSGGGNTNNSNSKKKSPASTFALSSQVPDVMVVGEPTLMGGEFGDEDERLITR
LENTQFDAANGIDDEDSFNNSPALGANSPWNSKPPSSQESKSENPTSQASQ
NT seq 1236 nt   +upstreamnt  +downstreamnt
atgtcagtgggctgtgcctgtcctggttgttcctcaaagtcattcaagctgtactcgccg
aaggagcccccgaacggcaacgcctttccccccttccatcccggcaccatgctggatagg
gatgtgggcccaactcccatgtatccgcctacatacctggagccagggattgggaggcac
acaccatatggcaaccaaactgactacagaatatttgagcttaacaaacggcttcagaac
tggacagaggagtgtgacaatctctggtgggatgcattcacgactgagttctttgaggat
gatgccatgttgaccatcactttctgcctggaggatggaccaaagagatataccattggc
cggaccctgatcccacgctacttccgcagcatctttgaggggggtgctacggagctgtac
tatgttcttaagcaccccaaggaggcattccacagcaactttgtgtccctcgactgtgac
cagggcagcatggtgacccagcatggcaagcccatgttcacccaggtgtgtgtggagggc
cggttgtacctggagttcatgtttgacgacatgatgcggataaagacgtggcacttcagc
atccggcagcaccgagagctcatcccccgcagcatccttgccatgcatgcccaagacccc
cagatgttggatcagctctccaaaaacatcactcggtgtgggctgtccaattccactctc
aactacctccgactctgtgtgatactcgagcccatgcaagagctcatgtcacgccacaag
acctacagcctcagcccccgcgactgcctcaagacctgccttttccagaagtggcagcgc
atggtagcaccccctgcggagcccacacgtcagcagcccagcaaacggcggaaacggaag
atgtcagggggcagcaccatgagctctggtggtggcaacaccaacaacagcaacagcaag
aagaagagcccagctagcaccttcgccctctccagccaggtacctgatgtgatggtggtg
ggggagcccaccctgatgggcggggagttcggggacgaggacgagaggctcatcacccgg
ctggagaacacccagtttgacgcagccaacggcattgacgacgaggacagctttaacaac
tcccctgcactgggcgccaacagcccctggaacagcaagcctccgtccagccaagaaagc
aaatcggagaaccccacgtcacaggcctcccagtaa

KEGG   Homo sapiens (human): 4066
Entry
4066              CDS       T01001                                 
Symbol
LYL1, bHLHa18
Name
(RefSeq) LYL1 basic helix-loop-helix family member
  KO
K15604  protein lyl-1
Organism
hsa  Homo sapiens (human)
Pathway
hsa05202  Transcriptional misregulation in cancer
Network
nt06240  Transcription (cancer)
  Element
N00121  LMO2-rearrangement to transcriptional activation
N00122  LMO2-rearrangement to transcriptional repression
Disease
H00002  T-cell acute lymphoblastic leukemia
Brite
KEGG Orthology (KO) [BR:hsa00001]
 09160 Human Diseases
  09161 Cancer: overview
   05202 Transcriptional misregulation in cancer
    4066 (LYL1)
 09180 Brite Hierarchies
  09182 Protein families: genetic information processing
   03000 Transcription factors [BR:hsa03000]
    4066 (LYL1)
Transcription factors [BR:hsa03000]
 Eukaryotic type
  Basic helix-loop-helix (bHLH)
   Tal/Twist/Atonal/Hen, Lymphoid factors
    4066 (LYL1)
SSDB
Motif
Pfam: HLH
Other DBs
NCBI-GeneID: 4066
NCBI-ProteinID: NP_005574
OMIM: 151440
HGNC: 6734
Ensembl: ENSG00000104903
UniProt: P12980
LinkDB
Position
19:complement(13099033..13102858)
AA seq 280 aa
MCPPQAQAEVGPTMTEKAEMVCAPSPAPAPPPKPASPGPPQVEEVGHRGGSSPPRLPPGV
PVISLGHSRPPGVAMPTTELGTLRPPLLQLSTLGTAPPTLALHYHPHPFLNSVYIGPAGP
FSIFPSSRLKRRPSHCELDLAEGHQPQKVARRVFTNSRERWRQQNVNGAFAELRKLLPTH
PPDRKLSKNEVLRLAMKYIGFLVRLLRDQAAALAAGPTPPGPRKRPVHRVPDDGARRGSG
RRAEAAARSQPAPPADPDGSPGGAARPIKMEQTALSPEVR
NT seq 843 nt   +upstreamnt  +downstreamnt
atgtgcccgcctcaggcacaggcagaggtgggccccaccatgactgagaaggcagagatg
gtgtgtgcccccagcccagcgcctgccccaccccctaagcctgcctcgcctgggcccccg
caggtggaggaggtgggccaccgaggaggctcctcgccccccaggctgccacctggtgta
ccagtgatcagcctgggccacagcaggcccccaggggtagccatgcccaccacagagctg
ggcactctgcggcccccgctgctgcaactctccaccctgggaactgccccgcccactttg
gccctgcactaccaccctcaccccttcctcaacagtgtctacattgggccagcaggacct
tttagcatcttccctagcagccggttgaagcggagaccaagccactgtgagctggacctg
gctgaggggcaccagccccagaaggtggcccggcgcgtgttcaccaacagccgggagcgc
tggcggcagcagaacgttaacggcgccttcgccgagctgaggaagctgctgccgacgcac
ccgcccgaccggaagctgagcaagaacgaggtgctccgcctagccatgaagtacatcggc
ttcctggtgcggctgctgcgcgaccaagccgcagctctggccgcaggccccacccctccc
gggcctcgcaaacggccggtgcaccgggtcccagacgacggcgcccgccggggatccgga
cgcagggccgaggcggcagcgcgctcgcagcccgcgcccccggccgaccccgacggcagc
cccggtggagcggcccggcccatcaagatggagcaaaccgctttgagcccagaggtgcgg
tga

KEGG   Homo sapiens (human): 6929
Entry
6929              CDS       T01001                                 
Symbol
TCF3, AGM8, AGM8A, AGM8B, E2A, E47, ITF1, TCF-3, VDIR, bHLHb21, p75
Name
(RefSeq) transcription factor 3
  KO
K09063  transcription factor E2-alpha
Organism
hsa  Homo sapiens (human)
Pathway
hsa04550  Signaling pathways regulating pluripotency of stem cells
hsa05166  Human T-cell leukemia virus 1 infection
hsa05202  Transcriptional misregulation in cancer
Network
nt06160  Human T-cell leukemia virus 1 (HTLV-1)
nt06240  Transcription (cancer)
  Element
N00117  E2A-PBX1 fusion to transcriptional activation
N00121  LMO2-rearrangement to transcriptional activation
N00122  LMO2-rearrangement to transcriptional repression
N00511  HTLV-1 Tax to E47-mediated transcription
Disease
H00001  B-cell acute lymphoblastic leukemia
H00085  Agammaglobulinemias
Brite
KEGG Orthology (KO) [BR:hsa00001]
 09140 Cellular Processes
  09144 Cellular community - eukaryotes
   04550 Signaling pathways regulating pluripotency of stem cells
    6929 (TCF3)
 09160 Human Diseases
  09161 Cancer: overview
   05202 Transcriptional misregulation in cancer
    6929 (TCF3)
  09172 Infectious disease: viral
   05166 Human T-cell leukemia virus 1 infection
    6929 (TCF3)
 09180 Brite Hierarchies
  09182 Protein families: genetic information processing
   03000 Transcription factors [BR:hsa03000]
    6929 (TCF3)
Transcription factors [BR:hsa03000]
 Eukaryotic type
  Basic helix-loop-helix (bHLH)
   Ubiquitous (class A) factors
    6929 (TCF3)
SSDB
Motif
Pfam: HLH Response_reg_2
Other DBs
NCBI-GeneID: 6929
NCBI-ProteinID: NP_003191
OMIM: 147141
HGNC: 11633
Ensembl: ENSG00000071564
UniProt: P15923
Structure
LinkDB
Position
19:complement(1609292..1652615)
AA seq 654 aa
MNQPQRMAPVGTDKELSDLLDFSMMFPLPVTNGKGRPASLAGAQFGGSGLEDRPSSGSWG
SGDQSSSSFDPSRTFSEGTHFTESHSSLSSSTFLGPGLGGKSGERGAYASFGRDAGVGGL
TQAGFLSGELALNSPGPLSPSGMKGTSQYYPSYSGSSRRRAADGSLDTQPKKVRKVPPGL
PSSVYPPSSGEDYGRDATAYPSAKTPSSTYPAPFYVADGSLHPSAELWSPPGQAGFGPML
GGGSSPLPLPPGSGPVGSSGSSSTFGGLHQHERMGYQLHGAEVNGGLPSASSFSSAPGAT
YGGVSSHTPPVSGADSLLGSRGTTAGSSGDALGKALASIYSPDHSSNNFSSSPSTPVGSP
QGLAGTSQWPRAGAPGALSPSYDGGLHGLQSKIEDHLDEAIHVLRSHAVGTAGDMHTLLP
GHGALASGFTGPMSLGGRHAGLVGGSHPEDGLAGSTSLMHNHAALPSQPGTLPDLSRPPD
SYSGLGRAGATAAASEIKREEKEDEENTSAADHSEEEKKELKAPRARTSPDEDEDDLLPP
EQKAEREKERRVANNARERLRVRDINEAFKELGRMCQLHLNSEKPQTKLLILHQAVSVIL
NLEQQVRERNLNPKAACLKRREEEKVSGVVGDPQMVLSAPHPGLSEAHNPAGHM
NT seq 1965 nt   +upstreamnt  +downstreamnt
atgaaccagccgcagaggatggcgcctgtgggcacagacaaggagctcagtgacctcctg
gacttcagcatgatgttcccgctgcctgtcaccaacgggaagggccggcccgcctccctg
gccggggcgcagttcggaggttcaggtcttgaggaccggcccagctcaggctcctggggc
agcggcgaccagagcagctcctcctttgaccccagccggaccttcagcgagggcacccac
ttcactgagtcgcacagcagcctctcttcatccacattcctgggaccgggactcggaggc
aagagcggtgagcggggcgcctatgcctccttcgggagagacgcaggcgtgggcggcctg
actcaggctggcttcctgtcaggcgagctggccctcaacagccccgggcccctgtcccct
tcgggcatgaaggggacctcccagtactacccctcctactccggcagctcccggcggaga
gcggcagacggcagcctagacacgcagcccaagaaggtccggaaggtcccgccgggtctt
ccatcctcggtgtacccacccagctcaggtgaggactacggcagggatgccaccgcctac
ccgtccgccaagacccccagcagcacctatcccgcccccttctacgtggcagatggcagc
ctgcacccctcagccgagctctggagtcccccgggccaggcgggcttcgggcccatgctg
ggtgggggctcatccccgctgcccctcccgcccggtagcggcccggtgggcagcagtgga
agcagcagcacgtttggtggcctgcaccagcacgagcgtatgggctaccagctgcatgga
gcagaggtgaacggtgggctcccatctgcatcctccttctcctcagcccccggagccacg
tacggcggcgtctccagccacacgccgcctgtcagcggggccgacagcctcctgggctcc
cgagggaccacagctggcagctccggggatgccctcggcaaagcactggcctcgatctac
tccccggatcactcaagcaataacttctcgtccagcccttctacccccgtgggctccccc
cagggcctggcaggaacgtcacagtggcctcgagcaggagcccccggtgccttatcgccc
agctacgacgggggtctccacggcctgcagagtaagatagaagaccacctggacgaggcc
atccacgtgctccgcagccacgccgtgggcacagccggcgacatgcacacgctgctgcct
ggccacggggcgctggcctcaggtttcaccggccccatgtcactgggcgggcggcacgca
ggcctggttggaggcagccaccccgaggacggcctcgcaggcagcaccagcctcatgcac
aaccacgcggccctccccagccagccaggcaccctccctgacctgtctcggcctcccgac
tcctacagtgggctagggcgagcaggtgccacggcggccgccagcgagatcaagcgggag
gagaaggaggacgaggagaacacgtcagcggctgaccactcggaggaggagaagaaggag
ctgaaggccccccgggcccggaccagcccagacgaggacgaggacgaccttctcccccca
gagcagaaggccgagcgggagaaggagcgccgggtggccaataacgcccgggagcggctg
cgggtccgtgacatcaacgaggcctttaaggagctggggcgcatgtgccaactgcacctc
aacagcgagaagccccagaccaaactgctcatcctgcaccaggctgtctcggtcatcctg
aacttggagcagcaagtgcgagagcggaacctgaatcccaaagcagcctgtttgaaacgg
cgagaagaggaaaaggtgtcaggtgtggttggagacccccagatggtgctttcagctccc
cacccaggcctgagcgaagcccacaaccccgccgggcacatgtga

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