CI01000006_10211545_10223229 (SMARCB1A, SMARCB1B, SMARCB1, SMARCB1.S)


Basic Information

Item Value
gene id CI01000006_10211545_10223229
gene name SMARCB1A, SMARCB1B, SMARCB1, SMARCB1.S
gene type coding
species grasscarp (Ctenopharyngodon idella)
category of species economic fish

Chromosome Information

Item Value
chromosome id CI01000006
NCBI id null
chromosome length 13024002
location 10211431 ~ 10223836 (-)
genome version v1_2015/06_NatureGenetics_grasscarp_Genome

Sequence

>CI01000006_10211545_10223229.mRNA
ACAGTATTTGTTCATGTTCCAGCAAGCAATGGCAAACAAATTATGACTATATAAAATGTATATTAAATATACAGCCTGCTAAATAACTCTGAAGTTGCCTCAGAGCATAAAGTTCAGTGTTATTTTAGTTTTTATTTTAGATTTATTATAGTTATTTTTAAAATATATTTTATATTTTTATTTTTTATGTTAGTTTTATATTAATTTTTAGTAATTCTGTGCGTTTTTGTATTACTTGTTTAATTTATTTTTTAGTTAGTTTTAGTTTTACTTATTTCCAGGTAATAATTTTAGTGCTTCAACTTAAACTTATTTCAGTTTATTGCCAACTGGCCATCATTTCTCATTTTTGTTTAGTTTTAAGTTTATAATCATTTATAATAAATAGCCTACTGCATTATTCCGTAGAAAAGTAGAATTGTCAGTACTGATTTTTAAGTTATTGAAAATGTTTTTAGGGCTTCCTAGTATTGTAACATCCAGCGAGGTGTCCTCCAACAGCAGGCATTACTGCACGCCTGCAGCGTGTCGCCCCAGAGCATGAGCTCTTCCCACCTCGCCGCTTCCTTTATACGCATGCGCGTTGACGCTCATTGTGTTCGCAAAGATGGCGTTGAGTAAAACATTTGGACAAAAACCAATAAAATTTCAACTCGAGCAAGATGGGGATTTTTACATGATAGGTTCAGAGGTTGGCAATTACCTGCGTATGTTCAGAGGCTCTCTGTATAAGCGGTACCCATCACTATGGAGACGCCTTGCATCCGTGGAGGAGCGGAAGAAGATTGTAGCATCATCACACGATCATGGTTACACAACTTTAGCCACCAGTGTGACCCTGCTGAAGGCGTCTGAGTGTGAGGAGATCTTCGAGGGGAATGATGAGAAGTACAAGGCAGTGTCCATCAGCACAGAGCCTCCGGCGTATCTCAGGGAGCAGAAGGCGAAGAGGAACAGTCAGTGGGTGCCCACCCTACCCAACAGCTCCCACCACCTGGATGCAGTGCCTTGTTCCACCACTATCAACAGAAACCGAATGGGACGTGACAAGAAAAGGACCTTTCCATTATGTTTCGATGACCATGACCCTGCAGTCATCCACGAAAATGCATCCCAGGCAGAGGTCCTGGTGCCTATCCGCCTGGACATGGAGATTGATGGGCAGAAGCTCAGAGATGCCTTCACCTGGAACATGAACGAGAAACTTATGACTCCAGAGATGTTTGCTGAGATCCTGTGTGACGACCTAGACCTGAATCCTCTCACCTTCGTCCCTGCCATCGCCTCAGCCATTAGACAGCAGATCGAGTCCTACCCTACCGACAGCATTCTGGATGAGCAGACAGACCAGAGAGTCATCATTAAGCTAAACATTCATGTGGGGAACATCTCTCTGGTGGACCAGTTTGAATGGGACATGTCAGAGAAGGAGAACTCGCCAGAAACGTTTGCTTTGAAGCTCTGCTCTGAGTTGGGCCTCGGAGGAGAGTTCGTCACCACCATCGCCTACAGCATCCGCGGACAGCTCAGCTGGCACCAGAGGACGTACGCCTTCAGTGAGAACCCATTACCAACGGTGGAGATTGCCATTCGGAACACAGGTGATGCCGACCAGTGGTGCCCTCTGCTGGAGACCCTGACAGACGCAGAGATGGAGAAGAAAATCAGAGACCAGGACAGAAACACAAGGCGTATGCGACGACTTGCCAACACCGCCCCTGCCTGGCTTTACAGCGCTCATAGAGGCTGTTCGGGATGTCTCGTTAGAATGCCTGTCATTGCCGATTCTCTGGTCTCCAGTTATAGGGACATCTGTCTAGTCTGGTTGTAAGAACAGGACATTGTTGAGAATGTTTGATTGAGTGTTGTGTTTTTCGTTAAAGGTGCTAATGCATACTATGAACTTGAATTGCTTCTTTTTTTTCTTTTTTTTTTTTTAAATAAA

Function

symbol description
smarcb1b Predicted to enable transcription coactivator activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within chromatin remodeling. Predicted to be located in nuclear chromosome. Predicted to be part of chromatin. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 3; atypical teratoid rhabdoid tumor; neurilemmomatosis; and rhabdoid cancer. Orthologous to human SMARCB1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1).
smarcb1a Predicted to enable DNA binding activity and transcription coactivator activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within chromatin remodeling. Predicted to be located in nuclear chromosome. Predicted to be part of chromatin. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 3; atypical teratoid rhabdoid tumor; neurilemmomatosis; and rhabdoid cancer. Orthologous to human SMARCB1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1).
smarcb1 Enables several functions, including Tat protein binding activity; p53 binding activity; and transcription coactivator activity. Contributes to RNA polymerase I core promoter sequence-specific DNA binding activity. Involved in several processes, including chromatin organization; regulation of histone modification; and regulation of transcription, DNA-templated. Acts upstream of or within single stranded viral RNA replication via double stranded DNA intermediate. Located in fibrillar center and nucleoplasm. Part of SWI/SNF complex. Implicated in Coffin-Siris syndrome 3; atypical teratoid rhabdoid tumor; neurilemmomatosis; and rhabdoid cancer. Biomarker of colorectal adenocarcinoma; hepatocellular carcinoma; sinonasal undifferentiated carcinoma; and synovial sarcoma.

GO:

id name namespace
GO:0001824 blastocyst development biological_process

KEGG:

id description
K11648 SMARCB1, SNF5, INI1; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1

RNA

RNA id representative length rna type GC content exon number start site end site
CI01000006_10211545_10223229.mRNA True 1945 mRNA 0.44 10 10211431 10223836

Neighbor

gene id symbol gene type direction distance location
CI01000006_10157899_10159258 CHCHD10 coding downstream 52173 10157847 ~ 10159258 (-)
CI01000006_10156167_10157125 DDT coding downstream 54306 10155884 ~ 10157125 (-)
CI01000006_10152518_10154866 NA coding downstream 56565 10151961 ~ 10154866 (-)
CI01000006_10144817_10151330 P2RX4, P2RX4A coding downstream 60101 10144817 ~ 10151330 (-)
CI01000006_10137964_10143809 IDH3B.S, IDH3B coding downstream 67622 10137964 ~ 10143809 (-)
CI01000006_10349084_10362629 NA coding upstream 125137 10348973 ~ 10363587 (-)
CI01000006_10372387_10387314 NA coding upstream 148293 10372129 ~ 10387602 (-)
CI01000006_10402704_10447782 NA coding upstream 178859 10402695 ~ 10449101 (-)
CI01000006_10453630_10483241 NA coding upstream 229777 10453613 ~ 10484006 (-)
CI01000006_10499329_10508831 NA coding upstream 275459 10499240 ~ 10509655 (-)
G47024 NA non-coding downstream 16790 10194432 ~ 10194641 (-)
G46986 NA non-coding downstream 193582 10017583 ~ 10017849 (-)
CI01000006_10016544_10031947 FAM169AB non-coding downstream 194055 10016375 ~ 10031947 (-)
G46979 NA non-coding downstream 215689 9995539 ~ 9995742 (-)
G46973 NA non-coding downstream 221995 9989204 ~ 9989436 (-)
G47035 NA non-coding upstream 8343 10232179 ~ 10232399 (-)
G47053 NA non-coding upstream 40245 10264081 ~ 10264320 (-)
G47410 NA non-coding upstream 85044 10308880 ~ 10309101 (-)
CI01000006_07500281_07507754 NA other downstream 2700475 7500246 ~ 7507976 (-)
CI01000006_06974359_06976736 NA other downstream 3234559 6973224 ~ 6976872 (-)
CI01000006_04560607_04560993 NA other downstream 5649363 4559509 ~ 4562068 (-)
G43549 NA other downstream 5856003 4352510 ~ 4355428 (-)
G43102 NA other downstream 7277447 2908451 ~ 2933984 (-)
G47658 NA other upstream 807075 11030911 ~ 11033127 (-)
CI01000006_11651067_11653761 SMD3, SNRPD3, SNRPD3L, MGC52856 other upstream 1426527 11650363 ~ 11654424 (-)
CI01000006_12348300_12348961 GLRX other upstream 2110573 12347180 ~ 12349383 (-)
CI01000006_12569291_12581457 CELL, CEL.2, CEL.1 other upstream 2126923 12569205 ~ 12582487 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
bowfin (Amia calva) AMCG00018844 smarcb1,LOC107661349 coding CM030135.1 CM030135.1 22637693 ~ 22645367 (-)