XLOC_002497 (pdlim5b)


Basic Information

Item Value
gene id XLOC_002497
gene name pdlim5b
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007121.7
NCBI id CM002894.2
chromosome length 45420867
location 1187653 ~ 1276046 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00004665
TTGGCAGTATTCACCATGAGCAGCAGCTACAGCGTGTCCCTGATCGGACCTTCCCCGTGGGGCTTCAGACTTCAGGGCGGCAAGGACTTCAGCATGCCGCTAACCATCTCCAAAtTGACAGATGGAGGAAAGGCGGCTAAAGCCAAGATCAGTGTTGGTGATGTGGTTCTGTCCATCGACGGCATCCACACTGAGAGAATGACACACCTGGAGGCCCAGAACAAGATCAAAGCCTGCAGCGGGAACCTCAACCTCTCACTCAtgagacCTTCCAGTGTCATTAAAGTGGAGACACCAAAGGAGGAGCCGCTGGAGATCATAAAGCCGGTTCCTATCAGCCAAACCCCTGCGTCCGCCAGCAGCCCTGTCGGTCTGACCCCTGCCTATAATAAGACGGCTCGTCCCTTCGGCGGGGCCACAAACACTGTCCGATCCGTCAGTCCATCCCCCGCTGCACCCAAAGCCTCCATCCCATCAGCCTCTTCTGCTTTCACTCCTGCTGCTCCCTCCCAGCAGCCGCCGCAGCCTCCATTCCCTCTTGCTGGCTCCGCCCAGCGCTCACAGCCCTCCCCTAATTCCATATCTAGCCCTGCCTCTAACTCCGCCCCCAAACCATCATCCGGCCGCTCCCCATTTGCCAACTCCTCCTCCGCATCATCTTCCGGCTCCTCCTCCCCTGCAAGAGTGACAGCTCCGGCTCCGGCTCCGCCCCCAGCCTCAGCCACGCCTCATTCGTCTGTTTATAACACGCCCATAAGCCTGTACTCCAATCAGAACGCATGTGAGGTTGCTATGGGCCAGAGGCGTGGCCTAATGGAGAGCAAAGGGGAGCAGCAGAACGGaaCGGCCCGTAAGCCTGTGCTGGAGACGGAGGTGAACCATGTTTCTCCACTCAGCGACGCCAGTAAGAAGCGTCTGATTGAGGACACAGAGGACTGGCATCCACGAACCGGCACCACTCAGTCCCGCTCCTTCAGGATCCTGGCACAGATCACCGGCACAGAGAACGATCAAGCTCAGGAGAGCCGGCCTGGAAAGAAtgaggCGGTGGAGGATCTTCAGCCCAGCTCTCACTCCTCATCTTCAGTGTTCACCATGAGCAAGAGTCCTGCTGGAGCGACTCGACAGGGAAACGGCATCAGTGCAGCTCCAGCCAAACACTGGCAGACCTCCAGCAGCAGCGGCGCAgGGTTTCCTAGATCAGGTGGTGCAGGTGTGGCCCCGACGGGACCCTCAGCTGGACGGGGGGTCAGCAGCAGTGTTCCCAAGGGCCCTGAGCGGCCCGTGCCTCAGCCGCACCCCAGAGACCAGGACGAGTCTGTGGTGCAGAGAGCTGAACACATGCCGGCCGGGACACGCACACCCATGTGTGCTCACTGCAACACCGTCATCAGGGGTCCGTTCCTGGTGGCGATGGGTAAGTCGTGGCACAAGGATGAGTTCACCTGCTCTCACTGCCGCAGCTCTCTGGCAGACGTGGGCTTCGTGGAGGAGCGGGGGTCCGTGTACTGTGTGCTCTGCTATGAGGAGTTCCTCGCTCCCACCTGCTTTCAGTGCCACAAGAAGATCATCGGAGAAGTCATCAATGCCCTGAAGCAAACCTGGCATGTGAACTGCTTCCTGTGTGCGTCCTGCAAACAACCCATCGGCAACAACACCTTCCACCTGGAGGACGGACAGCCGTACTGCGAGAAAGATTATTACTCCCTCTTCGGCACCGGCTGTCATGGATGTGACTTTCCCATTGAAGCAGGAGACAAGTTTCTGGAGGCTCTGGGCTTTACCTGGCATGACACCTGCTTTGTCTGCGCGGTTTGCAGCACGAGTCTGGAGGGTCAAACTTTCTTCTCCAAGAAAGACAAGCCACTGTGCAAGAAACACGCTCACACCGTCCAGTTCTGA
>TCONS_00004666
aaactttataaatgctttggcaatacatttgtaacatttgtcatgcaaataaagcaattgattttaatagagagagagagagagagagagagagagagagagagagagagagacagagagagagagagagagagagagagagagagagagagagagagagagagagagagagtaaattgTGTTCATCGTCGGTGACGTCAGCGAGCGCGGCACagtgagtgggtttcctccagcgcGTGTTAAAGGGGCGGAAGTCAGTCAGACAGCAGAGTTCAGTTGCCGGAGTTTCTCAGCTCTACTTCCTAAAGTTCCTCATTCTCAGTTTGACTTTCCAGCAGCTCACAGGCAGTGAATTGGACGTTGGCAGTATTCACCATGAGCAGCAGCTACAGCGTGTCCCTGATCGGACCTTCCCCGTGGGGCTTCAGACTTCAGGGCGGCAAGGACTTCAGCATGCCGCTAACCATCTCCAAAtTGACAGATGGAGGAAAGGCGGCTAAAGCCAAGATCAGTGTTGGTGATGTGGTTCTGTCCATCGACGGCATCCACACTGAGAGAATGACACACCTGGAGGCCCAGAACAAGATCAAAGCCTGCAGCGGGAACCTCAACCTCTCACTCAtgagacCTTCCAGTGTCATTAAAGTGGAGACACCAAAGGAGGAGCCGCTGGAGATCATAAAGCCGGTTCCTATCAGCCAAACCCCTGCGTCCGCCAGCAGCCCTGTCGGTCTGACCCCTGCCTATAATAAGACGGCTCGTCCCTTCGGCGGGGCCACAAACACTGTCCGATCCGTCAGTCCATCCCCCGCTGCACCCAAAGCCTCCATCCCATCAGCCTCTTCTGCTTTCACTCCTGCTGCTCCCTCCCAGCAGCCGCCGCAGCCTCCATTCCCTCTTGCTGGCTCCGCCCAGCGCTCACAGCCCTCCCCTAATTCCATATCTAGCCCTGCCTCTAACTCCGCCCCCAAACCATCATCCGGCCGCTCCCCATTTGCCAACTCCTCCTCCGCATCATCTTCCGGCTCCTCCTCCCCTGCAAGAGTGACAGCTCCGGCTCCGGCTCCGCCCCCAGCCTCAGCCACGCCTCATTCGTCTGTTTATAACACGCCCATAAGCCTGTACTCCAATCAGAACGCATGTGAGGTTGCTATGGGCCAGAGGCGTGGCCTAATGGAGAGCAAAGGGGAGCAGCAGAACGGaaCGGCCCGTAAGCCTGTGCTGGAGACGGAGGTGAACCATGTTTCTCCACTCAGCGACGCCAGTAAGAAGCGTCTGATTGAGGACACAGAGGACTGGCATCCACGAACCGGCACCACTCAGTCCCGCTCCTTCAGGATCCTGGCACAGATCACCGGCACAGAGAACGATCAAGCTCAGGAGAGCCGGCCTGGAAAGAAtgaggCGGTGGAGGATCTTCAGCCCAGCTCTCACTCCTCATCTTCAGTGTTCACCATGAGCAAGAGTCCTGCTGGAGCGACTCGACAGGGAAACGGCATCAGTGCAGCTCCAGCCAAACACTGGCAGACCTCCAGCAGCAGCGGCGCAgGGTTTCCTAGATCAGGTGGTGCAGGTGTGGCCCCGACGGGACCCTCAGCTGGACGGGGGGTCAGCAGCAGTGTTCCCAAGGGCCCTGAGCGGCCCGTGCCTCAGCCGCACCCCAGAGACCAGGACGAGTCTGTGGTGCAGAGAGCTGAACACATGCCGGCCGGGACACGCACACCCATGTGTGCTCACTGCAACACCGTCATCAGGGGTCCGTTCCTGGTGGCGATGGGTAAGTCGTGGCACAAGGATGAGTTCACCTGCTCTCACTGCCGCAGCTCTCTGGCAGACGTGGGCTTCGTGGAGGAGCGGGGGTCCGTGTACTGTGTGCTCTGCTATGAGGAGTTCCTCGCTCCCACCTGCTTTCAGTGCCACAAGAAGATCATCGGAGAAGTCATCAATGCCCTGAAGCAAACCTGGCATGTGAACTGCTTCCTGTGTGCGTCCTGCAAACAACCCATCGGCAACAACACCTTCCACCTGGAGGACGGACAGCCGTACTGCGAGAAAGATTATTACTCCCTCTTCGGCACCGGCTGTCATGGATGTGACTTTCCCATTGAAGCAGGAGACAAGTTTCTGGAGGCTCTGGGCTTTACCTGGCATGACACCTGCTTTGTCTGCGCGGTTTGCAGCACGAGTCTGGAGGGTCAAACTTTCTTCTCCAAGAAAGACAAGCCACTGTGCAAGAAACACGCTCACACCGTCCAGTTCTGA
>TCONS_00004667
ATGAGCAGCAGCTACAGCGTGTCCCTGATCGGACCTTCCCCGTGGGGCTTCAGACTTCAGGGCGGCAAGGACTTCAGCATGCCGCTAACCATCTCCAAAtTGACAGATGGAGGAAAGGCGGCTAAAGCCAAGATCAGTGTTGGTGATGTGGTTCTGTCCATCGACGGCATCCACACTGAGAGAATGACACACCTGGAGGCCCAGAACAAGATCAAAGCCTGCAGCGGGAACCTCAACCTCTCACTCAtgagacCTTCCAGTGTCATTAAAGTGGAGACACCAAAGgaGGAGCCAATGACAAAaaCGGCCCGTAAGCCTGTGCTGGAGACGGAGGTGAACCATGTTTCTCCACTCAGCGACGCCAGTAAGAAGCGTCTGATTGAGGACACAGAGGACTGGCATCCACGAACCGGCACCACTCAGTCCCGCTCCTTCAGGATCCTGGCACAGATCACCGGCACAGAGAACGATCAAGCTCAGGAGAGCCGGCCTGGAAAGAAGGTGAATAAAGTGGACCCAGAGGTTTTGCGGCCTCAGTACAACAAGCTGAGAGACTGGCATCATGGGGTCTCTGCCCGCGTGCTCAATGTCTGA

Function

symbol description
pdlim5b Predicted to enable actin binding activity and muscle alpha-actinin binding activity. Predicted to be involved in actin cytoskeleton organization; heart development; and muscle structure development. Predicted to be part of filamentous actin. Predicted to be active in Z disc; adherens junction; and stress fiber. Is expressed in digestive system; epidermis; musculature system; and periderm. Orthologous to human PDLIM5 (PDZ and LIM domain 5).

GO:

id name namespace
GO:0007507 heart development biological_process
GO:0030036 actin cytoskeleton organization biological_process
GO:0061061 muscle structure development biological_process
GO:0001725 stress fiber cellular_component
GO:0005912 adherens junction cellular_component
GO:0031941 filamentous actin cellular_component
GO:0030018 Z disc cellular_component
GO:0046872 metal ion binding molecular_function
GO:0003779 actin binding molecular_function
GO:0051371 muscle alpha-actinin binding molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-040426-908 Predicted to enable actin binding activity and muscle alpha-actinin binding activity. Predicted to be involved in actin cytoskeleton organization; heart development; and muscle structure development. Predicted to be part of filamentous actin. Predicted to be active in Z disc; adherens junction; and stress fiber. Is expressed in digestive system; epidermis; musculature system; and periderm. Orthologous to human PDLIM5 (PDZ and LIM domain 5).

Ensembl:

ensembl_id ENSDARG00000027600

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00004665 False 1902 mRNA 0.58 12 1187653 1258405
TCONS_00004666 False 2262 mRNA 0.56 13 1187653 1276046
TCONS_00004667 True 594 mRNA 0.55 7 1204745 1258390

Neighbor

gene id symbol gene type direction distance location
XLOC_002496 bmpr1bb coding downstream 7339 1082961 ~ 1180314 (-)
XLOC_002494 glis3 coding downstream 497483 644574 ~ 690170 (-)
XLOC_002495 NA coding downstream 530247 657051 ~ 657406 (-)
XLOC_002493 rfx3 coding downstream 546044 600164 ~ 641609 (-)
XLOC_002492 NA coding downstream 639452 546202 ~ 548201 (-)
XLOC_002498 opn4xa coding upstream 18417 1294463 ~ 1320114 (-)
XLOC_002499 NA coding upstream 147195 1423241 ~ 1433140 (-)
XLOC_002500 WDR70 coding upstream 158910 1434956 ~ 1523289 (-)
XLOC_002501 CABZ01066320.2 coding upstream 265217 1541263 ~ 1544095 (-)
XLOC_002502 CABZ01066320.1 coding upstream 268117 1544163 ~ 1552789 (-)
XLOC_002491 NA non-coding downstream 766000 415997 ~ 421653 (-)
XLOC_002489 NA non-coding downstream 828946 356555 ~ 358707 (-)
XLOC_002488 NA non-coding downstream 832996 354093 ~ 354657 (-)
XLOC_002504 NA non-coding upstream 390296 1666342 ~ 1667630 (-)
XLOC_002505 NA non-coding upstream 393098 1669144 ~ 1718637 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
tiger barb (Puntius tetrazona) G182418 NA non-coding NW_025048054.1 JAEQBD010000399.1 569026 ~ 570332 (-)