XLOC_004236 (col6a1)


Basic Information

Item Value
gene id XLOC_004236
gene name col6a1
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007122.7
NCBI id CM002895.2
chromosome length 45484837
location 33996526 ~ 34065718 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00008089
GCTGAAAGGCGTTTCATTCTGCTGCGCGCTCGGAGCGGACGCGCTACTGTCCGCCACTGCATCCCACAGACCCTCATTTCATAATTCATCTGTATTTATATCACTCATTCTGTATTGTGTGTTCCCCCCACCGCCACTTTGCACGGTTAACGTGCAGTTAAATCAGGATCTATGGCGCTTAATGGATATATATTGACCGCTCTGTGCGCTCTTTGGGCAGGGATCTTCGCTCAGGATGTCTCCAGATCCTCCTTCAGAGAGTGTCCTGTGGACCTGTTCTTTGTGCTGGACACGTCTGAAAGTGTGGCTCTCAGAGCCAAACCTCCAGAGTTTTACATCAACCAGATTAAGACCTTCACAAAGCTGTTCATCGATGAGCTCAAAGACCTACGCCAGCCCTGTGATCGCGATGTGACATGGAACTCGGGAGCGCTGCACTACAGTGATGACACAGAGCTGGTCATGGGATTAGTCGACCTCAACACAAAACGTGCTGACCTTAAAGCTGCCATCGACAGAATCAAATACATCGGCAAGGGAACGTACACCGACTGCGCCATCAAGGAGGGCATCGCTGAGCTGCTCAGAGCGGGTTCGCATTATCATGAGAATAAATACATTGTGGTGGTGACGGATGGTCATCCTATAACCGGATATAAGGAACCATGCGGTGGCATTCAGGAGGCCGCCAATGAGGCTCGACAACATGCCATTAAAGTGTTTGCTGTGGCCATCTCACCTGACCAGGAGGACACCAGACTGTCTGTCATTGCCACAGATATAAACTACAGACAGAACTTCACCGCTGCAGACAACTCCCGCTCCACACAAATGAGCACTATACGCTCCATCATCCACATGATTACAAACGAAACAAAGGATGTGTGCTGCTCCTTTGACTGCATCGCTGATGGAGGCCCTCAAGGACCCCCTGGAGATCCAGGTCAAAGGGGAGAGACCGGGAGACCAGGCATGCCAGGAGAAAAAGGAGACTTTGGGGCTCAGGGAAATCCTGGTGATCCCGGTCCAGTCGGTTACCAAGGAATGAAGgGAGACCAGGGAATAAAAGGTGATAAGGGAGAGAGAGGTCATAAAGGCTTCAAGGGAGACAAAGGTCATCATGGTCTCGATGGCACGGATGGACGTAAGGGCGAGCCGGGATTCCCTGGACTTCCAGGCTGTAAAGGGTCACCAGGGCCAGATGGTTTGCAAGGAGAATCAGGGCCTAAAGGAGACCCCGGACAATATGGACGCAAAGGAGAACGAGGAGATCCTGGCAGAGATGGTGAGCCAGGAAGACCTGGAAACTACGGACCATCTGGGGCCAAGGGAGACAGGGGTCCTCGTGGGGCTAACGGCGATAAAGGCGAGAGAGGAGATGATGGACCACCAGGACCAGATGGCCCAAGAGGAGAAAGAGGCCAAGGTGGTGAGAAGGGTGAACAAGGGTCTCGAGGTAACAGAGGTCCCAGAGGCGAGCCTGGTGAACCCGGGCCAAGGGGTGAGCAAGGACGTGAAGGATCATCCGGAGCAAATGGAGAGCCGGGTGAGCAAGGAAGAGCAGGGCAGCCAGGTTATCGTGGCGATGAGGGTCCTGCTGGGCCAGAGGGAGATAAAGGGCCCAGAGGAATCAAAGGGGCTCCAGGAGACAGAGGCCTGATGGGAGAGAGGGGTGAAGACGGACCTCCAGGAAACGGGACGGAGGGTTGTGCTGGCTTTCAGGGTTATCCTGGTCCAAGGGGAGATCCTGGAGCACCTGGTGGAAAAGGAACCCCAGGACCCAAGGGAGATGATGGAGAGCCGGGTGACACTGGATTAGATAATGACAGACTTGGACCACCTGGGACAAAAGGAGCCAAAGGTCACAGAGGACCTGAAGGAAAACCTGGACCCCCAGGACCACCCGGACCTCAAGGAGCTGATGAATGTGAGATTCTGGATATCATCATGAAGATGTGCTcttGCTGTGAATGCACATGTGGACCCTTGGATATTGCCTTTATCGTGGACAGCTCTGAGAGTATTGGAGCTTCTAACTTTGCCATCTCTAAAGAATTCATCGTGACAATAATGGACAGACTCAAGTTAAGACAGtttggTGCCAATGAGTCTCGTATTGGTGTGGTGCAGTACAGTGGTGAAAAATCTCAAGAGGTGGTACAGCTTGGTGACCCCAACATCAAGACCCTGACCGACCTAAAACAAGCTGTGAAAGACTTGCGCTGGCTGGCTGAGGCCACATACACTGGAGAAGCTCTTCAGTACTCGCTAAGAAACATGCTCAGCAAGCTTATCACGGAGAGGAGTGTGGTCCTTGTTCTTACTGATGGACGCTCAGACACTATTAGGGATAAAGTGCCATTAAACGTGCTGTGCGGCAAAGGATTTAAGGTTGGTGGGGTTGGAGTGACGGATTACGCAGAGAGGAAACCCAATCCGGAACAGCTTGATGAGGTTGTGTGTAAAGATGATCCTAGAAAAGGCTTCTCCTTTGTCCTAAACAACTTTGGCCTACTTCTGGATGACAACTTCCTGCAAAACCTGACTGAGAAAATCTGTGAAGATAAGAAGTGTCCCACATATACTTGTCCAAtTTCATTTAATGACAACACCGATGTCCTCATCATGATGGACAGCTCGGCCAGCGTTGGCGCCAAGAACTTCGAGATGACCAAGGACTTCTCACGGATGCTAGCTAAGCGCTTTTTGTCAGCAGAAAGAGGAAATTTCCAGGTTCGAATTGGTGTTGGCCAATACAGCAACAATGCCAACTTGGAGGCCGAATTTTCCACAAACGCCACTCAGGTGGTCGCTCAAATCGCAGACGCCAAGTTCCAGAATGCAGGTACACAGGTAACAAACGCTCTCAACTTCGCCATCGAGCGCTTCAGAGGCGGTAGGACGAGGAAGAAGAAGCTGCTGGTGTTTTCTGATGGTCGTTCTCAAGGTGTTAACTCCATTCAGATTGAGAAAGCCGTGGAGCAGGTGAGCAACGCAGGAATTGAGCTGTATGTTCTTGCTGTTGGAAATCAGGTGAATGAAGCGCATTTACGCACCTTAGTGAGCCGAGGCCGGCCTTACGACAACACCTACGCCTACCGCCATCTTTTCAAAGTACCCGACTACCGCTCATTGGTCACTGGGGTATTTTACCAAACTGTGTCCCGCAAGATTTCCCTGGAGACGAGAGGGTGATTGGATAATGGGAGGGGGTGAGGAATAAAGGGCATGGGTGGCATTATAGCACAAGCTTTAATTGTTTTAGGGTTTTTATTTTGTCTACGTTTTTCATGTGAACGATGTATCTGAACCTGAAAGGTTTTTCATAGTCATTTTGTAAAAGACAGTAAATGATTGTGTCAgaattctttaaaacattagtatttttatGTCACTTATGTCTTAAAACTTAGGGGATTACTCAAGAGATGTTTCACAGTTGTTGGAGGGGGTATTAGGGCTTTGACTAGGTATATGGCTGCATTCGTTTTGCTGTCCATGAAATTTTTCAACACTCAATCATTCAACACTCAATCATATGTGTATTATCTAATGTCGAGagcacagaattttttttttctccagtggTGAATAGATAGAATCTGTATAATTCAGACTTAAGCCCCTTTCATATAGGCATatcggtaaatatccggaaaatttccagaacaactttaccgttaaattcaaaaaagcactgttcacacaggcaaggatgttccggaatttttccggaaaagagcattcacacatctattccaaaataccggtaaattctgacatcattaaccagaaattatctctaaacagctgcgcttgtatttgtaaacatttgactacattacaaactctttggatggagaagcattgtgaacaacttcgatgaaaacatatgagggaacactttcgcatgtcgaaatgtttatattatgtgtgtgtgccgATTCTTGCTGGCTGCTTCACatgcacacgcgtcaagcaactgaaagAAGCAGAgcctgaaggtaaacaaacagcggcttatcataagcattttatcaataattttgtacacagttggcattaagaaggaacatagaaacgttgtctgactaacatctagcagctaaatgtgtctggaaaaatattcaaaggcttttttttttcataaacagcgcgacaatgtgtctgaatgttctgattggttggagtagacgtctcacgtcagtgtGTTCTATTAGTGAAcatgctctttccggcaattttccttctgcgttcacacagtgcagaattccagcaaattaccagtaatgctACAagttctctttctggaaaattgccagaacaaaattactggtattttcaaaaaaggcctgttcacacatacagacctttccgaaaAATTGCCGAAATTTCCAAAATtttaattttccagaaaggtctatCTGTGAAATGAGCCTTAGTATCTTTAAAGTAATAATtcgcccaaaaataaaaaatgtactctCTAGTTACGTGACCTTAAGTCCATTTAAACCTTTTTCTTCggttgaaaacaaaagaatatattttgaagaaagctgaaaactcatagccattgacatctataataaaaaaagcaaatcctatggatgtcaatggttacaggtttccatcattttttcaaagtatattaatttgcgttcaacagaagaaataaactcaaataggttttaaacaaaaggagggagagtaaatgatcacaaaatgttcatttttgaaaatgttcataCCTTTAACGACCGTTCATGCTGAGATACATATCTATAAAGATAATCACTGGGATAATAATATCCATGTCAATGTACTATTAACGGAAATTGTGATGCCTGCCACTTTGAATGCACACACTTGTTAAAGCAGgatggattgtgattggctgcttTTATCATTCATAAGCAGAAAGAAATAGAACTGTATCTTTATCTTTATAGTTATCCTTTGTATGAATGGTGCTTTAGGCACTTTTAAGGCTCATTCACACCAAGAATGATAACTACTGTTTTACAATAACTATATTTGTGTCCACATAAACATaaagaaatgtcatttttatcCTTGTGTTAAGTGCAAACTTCAGTTTTGTCATCTGCTTCTTAAAATGCATGAAATTGACAAATAGGATGGGTTCCAACTGAAAGTGTTTTCAGTGATGTTTTCTATGCTGTTATTATTACAGCTGTGGTGTCTCTTATTCTTTTATATCTGTTTCTTTATTGTTATCACTAAAGTTGCTTTTCTTGGATTGAATGAGCCTTTATAAATAAAAGTAGTGTAATGCAACATAAACAAATATTGCTAAGAGGGTTCAAAATCAACATCTATCTTGCCTTTATTTTGGACCCTGCTTGCAACAAAATctgagcaattaaaaaaaaaaaagttttgtttttttcattagtTTGTGATACACTTATAGCATTGACAGTAAAACTTGAATATAAATTTGGTGCTACCGATGTAAACACTACACTAGCTCCTTTAGCTACTCAAATGCAGGTTTCTTCAGAAGTATTCTTTACACCTTAAGCCAAAGAGTTTATCGATGGGTTTCTTGTGTCAGAAATGTATTTGAAACTTTGTAAAGGTATTTGAAATAAAGGACGCTACACCCCACCA

Function

symbol description
col6a1 Acts upstream of or within locomotory behavior and skeletal muscle tissue development. Predicted to be active in collagen-containing extracellular matrix and extracellular space. Is expressed in caudal fin; dermis; mandibular arch skeleton; muscle; and pleuroperitoneal region. Used to study Bethlem myopathy and congenital muscular dystrophy. Human ortholog(s) of this gene implicated in Ullrich congenital muscular dystrophy. Orthologous to human COL6A1 (collagen type VI alpha 1 chain).

GO:

id name namespace
GO:0007519 skeletal muscle tissue development biological_process
GO:0007626 locomotory behavior biological_process
GO:0061061 muscle structure development biological_process
GO:0062023 collagen-containing extracellular matrix cellular_component
GO:0005615 extracellular space cellular_component

KEGG: NA

ZFIN:

id description
ZDB-GENE-070501-6 Acts upstream of or within locomotory behavior and skeletal muscle tissue development. Predicted to be active in collagen-containing extracellular matrix and extracellular space. Is expressed in caudal fin; dermis; mandibular arch skeleton; muscle; and pleuroperitoneal region. Used to study Bethlem myopathy and congenital muscular dystrophy. Human ortholog(s) of this gene implicated in Ullrich congenital muscular dystrophy. Orthologous to human COL6A1 (collagen type VI alpha 1 chain).

Ensembl:

ensembl_id ENSDARG00000074908

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00008089 True 5637 mRNA 0.44 35 33996526 34065718

Neighbor

gene id symbol gene type direction distance location
XLOC_004235 NA coding downstream 3379 33992033 ~ 33993147 (-)
XLOC_004234 CR925698.1 coding downstream 30254 33966158 ~ 33966272 (-)
XLOC_004233 col6a2 coding downstream 36208 33921358 ~ 33960318 (-)
XLOC_004232 phka2 coding downstream 77217 33870357 ~ 33919309 (-)
XLOC_004231 si:ch211-227n13.3 coding downstream 127618 33861177 ~ 33868908 (-)
XLOC_004237 tdo2b coding upstream 18814 34084532 ~ 34097437 (-)
XLOC_004238 atp13a3 coding upstream 51016 34116734 ~ 34147205 (-)
XLOC_004239 atp13a3 coding upstream 85459 34151177 ~ 34151487 (-)
XLOC_004240 atp13a3 coding upstream 88875 34154593 ~ 34188346 (-)
XLOC_004241 tmem44 coding upstream 135465 34201183 ~ 34219211 (-)
XLOC_004063 CR854846.1 misc downstream 17868848 16127382 ~ 16127678 (-)
XLOC_004019 CR450764.8 misc downstream 21304835 12691395 ~ 12691691 (-)
XLOC_004015 CR450764.4 misc downstream 21374759 12621518 ~ 12621767 (-)
XLOC_004013 CABZ01022569.1 misc downstream 21405230 12590999 ~ 12591296 (-)
XLOC_004008 BX000700.19 misc downstream 21483264 12512966 ~ 12513262 (-)
XLOC_004229 NA non-coding downstream 307577 33676834 ~ 33688949 (-)
XLOC_004227 NA non-coding downstream 595050 33305132 ~ 33401476 (-)
XLOC_004226 BX530032.2 non-coding downstream 797922 33190658 ~ 33198604 (-)
XLOC_004243 FO681390.1 non-coding upstream 183738 34249456 ~ 34255220 (-)
XLOC_004244 NA non-coding upstream 249807 34315525 ~ 34358689 (-)
XLOC_004245 BX548160.1 non-coding upstream 289826 34355544 ~ 34355662 (-)
XLOC_004247 BX548160.2 non-coding upstream 400677 34466395 ~ 34466513 (-)
XLOC_004249 NA non-coding upstream 485129 34550847 ~ 34577106 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) G434940 NA non-coding CI01000306 null 7744774 ~ 7781940 (+)
rainbow trout (Oncorhynchus mykiss) G441109 NA non-coding NC_048569.1 CM023223.2 76704659 ~ 76707911 (+)