CI01000034_04431146_04446849 (SMARCA4A, SMARCA4)


Basic Information

Item Value
gene id CI01000034_04431146_04446849
gene name SMARCA4A, SMARCA4
gene type coding
species grasscarp (Ctenopharyngodon idella)
category of species economic fish

Chromosome Information

Item Value
chromosome id CI01000034
NCBI id null
chromosome length 5914002
location 4431146 ~ 4447168 (-)
genome version v1_2015/06_NatureGenetics_grasscarp_Genome

Sequence

>CI01000034_04431146_04446849.mRNA
AGCTTGTTTTGGCATGTTTCATGTGTTGTTGTTGTTGTTGTTTTTTAATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTATATATGTGTGTGTGTATATATGTGTGTGTATATATGTGTGTATATATATACACACATATAATATGTGCTGTTTTTAAGCTTGTTTTGGCATGTTTCATGTGTTGTTGTTGTTGTTGTTTTTTAATCAAGCTGCTGAAATTAATCTTATTTTTCATTTCCAGGCTTTCTGAAAACGGATACAGGACACTGTTTTTCTGCCTCTTACGTCTTCCGGCTCTGCTGAGAGATGTCCACCCCTGACCCACCTATGGGCGGGACCCCTCGGCCGGGCCCTTCCCCAGGCCCTGGGCCGTCTCCAGGGGCCATGTTAGGGCCTAGTCCTGGACCCTCACCTGGCTCTGCCCATGGCATGATGGGCCCTAGCCCTGGGCCCCCCTCCTCAGGACACCCACTACCTCCACAGGGCCCCTCAGGTTACCCCCAGGACAACATGCACATGCACAAGCCCATGGAAGGCATGCTCGAGAAAGGCATTCCCGAAGATCAACGCTACGGTCAAATGAAGGGTATGGGCATGAGACAGGGTGGGCACAGTGGCATGGGACCCCCACCCAGCCCTATGGACCAACACTCTCAAGGTTACCCCTCTCCTCTGGGTGGATCTGAACATGCCCCCAGCCCGGTACCTTCTAACGGGCCTCCGTCTGGCCCCATGATGCCTTCTGGTCCTGGTGCCGTCCCCATGGAGGGCGGTGACCTGCAGAACCGGAGCGGAGGTACAGGTGCTGTTGCAGGTTCGGGACCCAGCGGAGGACCTCCAAACGCAGGTGGGCCTGGTGGTGCCGGCGGACCCACTCCTTTCAACCAAAACCAGCTTCACCAGCTGCGGGCACAGATCATGGCCTATAAGATGCTGGCGCGTGGGCAGCCTCTACCTGACCACCTGCAGATGGCCGTGCAGGGAAAGCGGCCCATGCCAGGCATGCAACAGGGGATGCCCAACATGCCCCCCGCTTCAGGACAAGGAGCAGGACCGCCTGGACCTGGGGGTCCCGGTCCTGGAGGACCCAACTACAATCGACCAACTGGAATGGTCGGTCCAAACATGCCTCCTCCAGGACCCTCTGGTGTTCCTCCAGGCCTGCAGGGACAACCCACCAATGGACCACCTAAAGCTTGGCCTGAAGGGCCCATGGTGAACGCTGCCGCCCCTGCAAGTGCCCCACAGAAGCTGATACCTCCTCAGCCCACGGGCCGCCCTTCTCCAGCGCCACCTTCAGTTCCTCCCGCTGCCTCTCCCGTCATGCCCCCTCAGACCCAGTCTCCAGGACAACCGGCCCAGCCGCCCATGATGTTGCATCAGAAGCAGAACCGCATCACACCCATCCAGAAACCTCGGGGTCTGGACCCAGTGGAGATCCTCCAGGAGAGAGAGTACAGGTTACAAGCTCGTATTGCTCATCGTATTCAGGAACTGGAGAACCTTCCAGGCTCTCTGGCTGGAGACTTGAGGACCAAAGCCAACATCGAGCTCAAGGCACTTAGGCTCCTGAACTTTCAGAGACAGCTCCGGCAGGAAGTCGTAGTGTGTATGCGGCGTGATACGGCTCTGGAGACTGCACTGAATGGCAAGGCCTACAAACGCAGCAAGAGGCAGTCCCTGCGTGAAGCTCGTATCACTGAGAAACTGGAGAAACAGCAGAAGATTGAGCAGGAACGGAAGCGCCGACAGAAACATCAGGAGTATCTCAACAGCATCCTGCAGCATGCTAAAGACTTCAAGGAATACCATCGCTCCATCACCGCAAAGATGCAGAAGTTGACCAAAGCCGTAGCCACGTACCATGCCAACACTGAGAGAGAGCAGAAGAAGGAGAATGAGCGTATCGAGAAGGAGAGAATGAGAAGGCTGATGGCTGAAGATGAAGAGGGTTACAGGAAGCTGATCGATCAGAAGAAAGACAAACGTCTGGCTTACTTGCTGCAGCAGACGGACGAGTATGTGGCCAACCTCACAGAGCTCAAGCCAGAGAATGCAGAGGGTGGAGTTCCTGCTCTGGGTCCAGATGGAGAGCCTCTCGATGAAACCAGTCAAATGAGTGACTTACCGGTGAAGGTGATTCACGTGGACAGTGGGAAGATCCTCACTGGCATGGATGCTCCTAAAGCTGGACAACTGGATACTTGGCTGGAGATGAATCCAGGGTACGAGGTTGCCCCGCGGTCAGATAGTGAAGATAGTGGCTCAGAGGACGAAGAGGAGGATGATGATGAGCCTCAGTCCTCTCAGGCCCTAACAGAGGAGAAGAAGATTATTCCAGATCCAGACAGTGAGGATGTGTCTGAGGTGGACGCCCGTCACATCATTGAGCATGCCAAGCAGGATGTTGATGATGAATACGGTAACGCAGCGTTCGCTCGCGGCCTGCAGTCTTACTACGCCGTGGCTCACGCCGTCACGGAGAAGGTGGACAGACAGTCGAGCCTGCTAGTCAACGGACAGCTCAAACAGTACCAGATCAAAGGTCTAGAGTGGCTGGTGTCTCTGTATAACAATAACTTGAATGGCATTCTGGCTGATGAAATGGGTTTGGGAAAAACCATCCAGACCATCGCACTCATCACCTACCTCATGGAGTACAAACGCCTCAACGGACCCTTCCTTATTATCGTCCCCCTCTCGACTCTGTCGAACTGGGTGTACGAGTTTGATAAGTGGGCTCCATCTGTGGTGAAAGTATCTTACAAGGGCTCTCCTGCTGCTCGCCGCGCATTCGTTCCCATTTTGCGCAGCGGCAAGTTCAACGTGCTGGTCACCACTTACGAGTACATCATCAAAGACAAGCAAGTGCTGGCCAAGCTCCGCTGGAAGTACATGATAGTGGACGAAGGTCACCGTATGAAGAACCACCACTGTAAACTCACTCAGGTGTTGAACACACATTACCTGGCGCCCCGGCGTCTGCTGCTCACCGGCACGCCACTGCAGAACAAGCTGCCCGAGCTGTGGGCACTGCTCAACTTCCTGCTGCCCACCATCTTCAAGAGCTGCAGCACCTTCGAGCAGTGGTTCAACGCTCCGTTCGCCATGACTGGAGAGAAGGTGGACCTGAATGAAGAAGAGACCATTCTGATCATCCGTCGTCTGCACAAAGTGCTCCGCCCCTTCCTGCTCAGGAGACTCAAAAAGGAAGTTGAGGCTCAACTGCCGGAGAAGGTGGAATATGTGATCAAGTGCGACATGTCGGCTCTACAGAGAGTGCTGTACAGACACATGCAGGCTAAAGGAGTGCTGCTCACTGACGGCTCTGAAAAAGACAAGAAGGGTAAAGGAGGCACCAAGACTCTGATGAACACTATTATGCAGTTGAGGAAGATTTGTAACCACCCTTACATGTTCCAGCACATTGAGGTGATTATTTGTTTCACATATTCCGCATATGAGGTCATATTTATCCCTGAATCTTTCTCTGAGCACTTGGGCTTCACTGGAGGCATTGTTCAGGGGTACGTAGAACAAAAAGTTTGCATTCATAACTTTGCATTTTTATTGGTTTTCTCTGTGACTTACTATATTCTGTATCACCTCAATTTAGACCTGATTTGTACCGTGCCTCTGATGACCTCGCTCATGACCATCATGGAGGACTACTTCGCCTACCGCAACTTCAAATACCTGCGCTTGGACGGAACCACTAAGGCTGAGGATCGTGGCATGCTGCTGAAGAACTTTAATGATCCATCCTTTCAGTACTTCATCTTCCTGCTGAGCACCAGAGCAGGAGGTCTGGGGCTGAACCTGCAGTCTGCTGATACTGTTATCATCTTTGACAGCGACTGGAACCCTCACCAGGATCTGCAGGCCCAGGATCGTGCCCATCGTATTGGGCAGCAGAACGAGGTGCGTGTGCTGCGTCTGTGTACTGTGAACAGCGTGGAGGAGAAGATCCTGGCCGCTGCCAAATACAAACTGAACGTGGACCAAAAGGTCATCCAGGCTGGTATGTTCGACCAGAAATCCTCCAGTCATGAGCGCAAAGCTTTCCTGCAGGCCATCCTGGAGCACGAAGAGCAGGATGAGGAGGAAGATGAAGTACCCGATGACGAGACCGTTAATCAGATGATTGCTAGAAGCGAGGAAGAGTTTGATCACTTCATGCGCATGGATCTCGACCGCCGTCGTGAAGAAGCTCGTAACCCGAAGCGCAGACCCCGGCTGATGGAGGAGGATGAGCTGCCCACCTGGATCATGAAGGACGACGCGGAGGTGGAGAGACTCACCTGCGAAGAAGAAGAGGAGAAGATGTTCGGCCGCGGCTCCCGTCAGAGGAAGGAGGTGGACTACAGTGACTCCCTCACGGAGAAACAGTGGCTGAAGGCCATCGAGGAAGGCACCCTTGATGAGATTGAGGAGGACGTGCGGCACAAGAAAACAACCCGGAAGAGGAAGCGTGACCGTGACCTCGACCTTCCAGGCCCGGCCACGCCCAGCTCCAGTGGGCGGAGCAGAGATAAAGATGATGACAGTAAGAAGCAGAAGAAGCGCGGCCGTCCTCCTGCTGAAAAACTCTCTCCCAACCCTCCCACTCTCACCAAGAAGATGAAGAAGGTTGTGGATGCTGTAATCAAATACAAGGATGGCAATGGGAGACAACTGAGTGAGGTGTTTATTCAGCTGCCGTCTCGTAAAGAGCTGCCAGAATATTATGAACTCATTCGCAAACCTGTGGACTTCAGGAAGATCAAGGAGCGCATCAGGAGCCACAAGTACCGAAGTCTGAACGACCTGGAGAAAGACGTCATGCTGCTTTGTCAGAACGCTCAGACCTTCAACCTCGAGGGATCACTGATCTATGAGGACTCTATCGTGCTGCAGTCTGTGTTCACCACTCGCTCAGTGAAGGTGAAGATAAAGCTGAGTCGAAAGGACAAGGTGGAGAGAGGGAAGGGAAGACGCCGGACTGGACGCAGCTCGCGCCCTAAACCTGTCGTTAGTGACGATGACAGTGAGGAGGACCAGGAGGAG

Function

symbol description
smarca4a Predicted to enable ATPase, acting on DNA and DNA binding activity. Acts upstream of or within animal organ development; fin regeneration; and nervous system development. Predicted to be part of SWI/SNF complex. Predicted to be active in nucleus. Is expressed in head; mesoderm; nervous system; pectoral fin; and presumptive neural retina. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 4; hepatocellular carcinoma; lung non-small cell carcinoma; and rhabdoid cancer. Orthologous to human SMARCA4 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4).
smarca4 Enables several functions, including DNA polymerase binding activity; RNA polymerase II-specific DNA-binding transcription factor binding activity; and lysine-acetylated histone binding activity. Contributes to RNA polymerase I core promoter sequence-specific DNA binding activity. Involved in several processes, including chromatin organization; regulation of signal transduction; and regulation of transcription, DNA-templated. Located in chromatin and nucleolus. Part of SWI/SNF complex and npBAF complex. Implicated in Coffin-Siris syndrome 4; hepatocellular carcinoma; lung non-small cell carcinoma; and rhabdoid cancer. Biomarker of prostate cancer.

GO:

id name namespace
GO:0000185 activation of MAPKKK activity biological_process

KEGG:

id description
K11647 SMARCA2_4; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2/4

RNA

RNA id representative length rna type GC content exon number start site end site
CI01000034_04431146_04446849.mRNA True 5059 mRNA 0.53 32 4431146 4447168

Neighbor

gene id symbol gene type direction distance location
CI01000034_04392399_04400096 LDLR, LDLRA coding downstream 31050 4392200 ~ 4400096 (-)
CI01000034_04376314_04386958 NA coding downstream 44188 4376314 ~ 4386958 (-)
CI01000034_04370706_04374491 SPC24 coding downstream 55733 4370626 ~ 4375413 (-)
CI01000034_04350907_04363668 NA coding downstream 67463 4350606 ~ 4363683 (-)
CI01000034_04318823_04319740 FOXD3, FOXD1 coding downstream 111019 4318544 ~ 4320127 (-)
CI01000034_04451917_04454531 NA coding upstream 4291 4451459 ~ 4454531 (-)
CI01000034_04466151_04467388 RLN3A coding upstream 18684 4465852 ~ 4467480 (-)
CI01000034_04630595_04640739 NA coding upstream 183373 4630541 ~ 4640987 (-)
CI01000034_04652096_04678983 TMEM104 coding upstream 204766 4651934 ~ 4679037 (-)
CI01000034_04690669_04706837 NA coding upstream 243319 4690487 ~ 4706959 (-)
G172456 NA non-coding downstream 21909 4405635 ~ 4409237 (-)
G172480 NA non-coding downstream 74592 4356313 ~ 4356554 (-)
G172475 NA non-coding downstream 96373 4334149 ~ 4334773 (-)
G172422 NA non-coding downstream 139400 4291531 ~ 4291746 (-)
G172421 NA non-coding downstream 140292 4290653 ~ 4290854 (-)
G172488 NA non-coding upstream 21766 4468934 ~ 4469211 (-)
G172504 NA non-coding upstream 51836 4499004 ~ 4499747 (-)
G172507 NA non-coding upstream 68703 4515871 ~ 4516396 (-)
G172508 NA non-coding upstream 69325 4516493 ~ 4516717 (-)
G172509 NA non-coding upstream 69735 4516903 ~ 4517633 (-)
CI01000034_04216451_04218876 NA other downstream 213404 4216212 ~ 4221881 (-)
CI01000034_04165535_04172272 KCTD13 other downstream 258976 4165373 ~ 4172272 (-)
G172151 NA other downstream 1033333 3391144 ~ 3451802 (-)
G172016 NA other downstream 1194531 3234963 ~ 3236615 (-)
CI01000034_02510595_02511512 NA other downstream 1919625 2510061 ~ 2511521 (-)
G172593 NA other upstream 545792 4992960 ~ 4994943 (-)
G172800 NA other upstream 1341864 5789032 ~ 5789738 (-)
CI01000034_05795972_05811363 NA other upstream 1350402 5795835 ~ 5811781 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
zebrafish (Danio rerio) XLOC_025239 smarca4a coding NC_007114.7 CM002887.2 19245804 ~ 19282525 (+)