XLOC_006639 (pdlim1)


Basic Information

Item Value
gene id XLOC_006639
gene name pdlim1
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007124.7
NCBI id CM002897.2
chromosome length 52186027
location 25762908 ~ 25774183 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00012821
GAATTCGACTGGATTTGGGAGTGGCACATACCAAATCCTAGGATTTGGCTCTTCCATACATGGTAAACTTAAATATGAGATGACGTAACGGTCCACCCCTAAACAAACATAGGAAATAAACTCTTATCAGCACAGAGACCTGACATTATTCGCTCCCTTTAGAGGAAGCTCCGCCCAGGTATCATTTCTTCAAAGTGAACGCCCCTGTCCTGCGACAGAAACTGCCCAGTTCTACAGTTTACGGTGCACTGCTCCAGGATTAAGTTTGCCTGTTGGAACTATAATGCCTCAGCGGGTTGTTTTACAAGGTCCCGGGCCATGGGGATTCCGTCTGGTCGGGGGTAAAGATTTCGAGCAGCCTCTGACTATCTCGAGGGTAACCCCAGGAAGTAAAGCAGCTCAGGCTGACCTCTGCATGGGGGACATGATCCTGGCCATAGATGGAGAGTCCACTGATGGCATGACCCATCTGGAGGCACAGAATAAAATCAAAGCCTGCGGGGATGAAATGGCACTTTCCATTGACAGATCAGAATCAAAAATGTGGTCGCCTCTAGTCACTGAAGACGGAAAGACGAATCCATACAAGATGAATCTGGCAAAAACCAACACACAGGAGGAGAAGCATATAGGCTCTGCTCATAACAGAAGTGCTATGCCATTTAATTCTGCCAGTCCTAGAGTCGTCACCAACCAGTACAACAACCCGGCTGGCCTGTACTCCTCTGAAAACATCAAGAACTTCAACAGCGCAGTGGATGAAGTCCAGACGACCGCTGCCTCCAGTGAAGCTAGCAGGAACTCAGATCCCAGTAAACCAGGCCACACAAAAGCTGCTATAGCTGCAGATTCAGAGGTGTACAAAATGCTGCAGGAGAATCAGGAATCCAATGAACCTCCTCGCCAGTCGGCCTCTTTTAAAGTTCTGCAGGAGATCCTGGAAACTGGTGATTCAGAGAAACCCTCAGGCTTCAGAAGCGTCAAGGCTCCTACCACAAAAATTGGAGCTTCCGTTGGGAATCCTGAAAAGCTCTCTCTTTGTGACAAATGTGGATCAGGGATTGTAGGAATGATTGTCAAACTTCGAGATAAGTTTCGTCACCCAGAATGCTACGTCTGCACAGACTGCGGGATCAATCTGAAGCAAAAAGGACACTTTTTTGTTGAGGACCAGATTTACTGCGAGAAGCACGCACGCGAACGCATCACTCCTCCAGAGGGTTATGATGTTGTCACCGTTTTTCCAAAATAGAGCATTTCCCCTGTGCCGCTTTACAACTGCACATTCCCTTATGAGGGAAATTCGTAACACTTAATTTGGATAGTATTCCAGTGAGGCTGCTCTGTTGCTAGCAAGGGTAGCGCATGGATTTAAAAGGACTTTGGCAACAATGATCATGAAATGTGAATACAGAGTCTGTCCACATAAAGTGCTGTCGTTGTCTTACATTCCATTTTCTTAATCATTCCATTCATGTATCGCATAAAAGGCTCAATTAACGGTGCTTGGGTATCTTCAGGCCGCTTATTGCATTTTCATTTTTCCgtaaaacgttttttatgaattGATCATTGAAATGTATGTAATCATGGTCATATTCCTCTCGCACAGTGATATGTAAAACTATTCAATGTATGTATGGTCTTTTGGAATctccatatttttttataaaaagaatGAATTTGTAtttgctataaaaaataaaatgtttcatatCCATTGT
>TCONS_00012822
ATAGGCTCTGCTCATAACAGAAGTGCTATGCCATTTAATTCTGCCAGTCCTAGAGTCGTCACCAACCAGTACAACAACCCGGCTGGCCTGTACTCCTCTGAAAACATCAAGAACTTCAACAGCGCAGTGGATGAAGTCCAGACGACCGCTGCCTCCAGTGAAGCTAGCAGGAACTCAGATCCCAGTAAACCAGGCCACACAAAAGCTGCTATAGCTGCAGATTCAGAGGTGTACAAAATGCTGCAGGAGAATCAGGAATCCAATGAACCTCCTCGCCAGTCGGCCTCTTTTAAAGTTCTGCAGGAGATCCTGGAAACTGgaactttgatgcggtggctgaagtatgagaaggagcgctatgctgctgaagaattttcc
>TCONS_00012823
ATTAAGTTTGCCTGTTGGAACTATAATGCCTCAGCGGGTTGTTTTACAAGGTCCCGGGCCATGGGGATTCCGTCTGGTCGGGGGTAAAGATTTCGAGCAGCCTCTGACTATCTCGAGGGTAACCCCAGGAAGTAAAGCAGCTCAGGCTGACCTCTGCATGGGGGACATGATCCTGGCCATAGATGGAGAGTCCACTGATGGCATGACCCATCTGGAGGCACAGAATAAAATCAAAGCCTGCGGGGATGAAATGGCACTTTCCATTGACAGATCAGAATCAAAAATGTGGTCGCCTCTAGTCACTGAAGACGGAAAGACGAATCCATACAAGATGAATCTGGCAAAAACCAACACACAGGTGTGTTTCAGATCTACTTAACTGAGAGCCGAGGGACTTTTCAGTGGCCCCCTGATCATTTTAATGCACTTTAAAGCTTTTCACATTGCTTGAGACTGTCATTCATAACGGAAGCATAGCCGCTAAACAAATAAAGGCACGGCACTATAGACTGCCAAAGTGAAGTCATTGTTTATGTCCTAACAAGCTTTATCCATGGAGACCAGGGAGTTTATCAGCCAGAGCCATGACGCAAGACTTGCATCCTGCGGGCTAAGTTTGAAATTTAAGGTCAGAATGTGAATGATCATAGGAAGTGTGTGGGGTTTGACTACATAGTTTGGGTGTTATAAATGTTTCCTGAAtcaagcagagagagagagagggagagaagaataataagaaaCAACTGCTAAATATGTTGTTAACCTAGGAAAGTTTCACAGTGTCATTAAAAGCTTGGTCATTAGTGTGGCAAAGCTTTTTCCATCTCTGTTTTTCTTCCTGCTGTTTAATGGCCAGTTTTCACATCAACTGGTTAAATAT

Function

symbol description
pdlim1 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 located in cytoskeleton. Predicted to be part of filamentous actin. Predicted to be active in Z disc; adherens junction; and stress fiber. Is expressed in several structures, including anterior axial hypoblast; digestive system; epidermis; nervous system; and yolk syncytial layer. Orthologous to human PDLIM1 (PDZ and LIM domain 1).

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:0005856 cytoskeleton 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-030131-5227 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 located in cytoskeleton. Predicted to be part of filamentous actin. Predicted to be active in Z disc; adherens junction; and stress fiber. Is expressed in several structures, including anterior axial hypoblast; digestive system; epidermis; nervous system; and yolk syncytial layer. Orthologous to human PDLIM1 (PDZ and LIM domain 1).

Ensembl:

ensembl_id ENSDARG00000019845

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00012821 False 1724 mRNA 0.44 7 25762908 25774183
TCONS_00012822 False 378 mRNA 0.49 3 25765474 25767210
TCONS_00012823 True 883 lncRNA 0.44 3 25769379 25773925

Neighbor

gene id symbol gene type direction distance location
XLOC_006638 sgpl1 coding downstream 11998 25725547 ~ 25750910 (-)
XLOC_006637 si:dkey-192p21.6 coding downstream 42001 25642050 ~ 25720907 (-)
XLOC_006636 ret coding downstream 130152 25584556 ~ 25632756 (-)
XLOC_006635 csgalnact2 coding downstream 181605 25569831 ~ 25581303 (-)
XLOC_006634 mcmbp coding downstream 214026 25531004 ~ 25548882 (-)
XLOC_006640 NA coding upstream 2206 25776389 ~ 25778815 (-)
XLOC_006641 rel coding upstream 21328 25795511 ~ 25819825 (-)
XLOC_006642 papolg coding upstream 50162 25824345 ~ 25842074 (-)
XLOC_006643 NA coding upstream 72349 25846532 ~ 25853311 (-)
XLOC_006644 NA coding upstream 235314 26009497 ~ 26703804 (-)
XLOC_006471 BX537274.2 misc downstream 15498003 10264741 ~ 10264905 (-)
XLOC_006338 rn7sk misc downstream 24936683 825904 ~ 826225 (-)
XLOC_006633 BX005252.1 non-coding downstream 232260 25530534 ~ 25530648 (-)
XLOC_006629 NA non-coding downstream 478192 25210158 ~ 25284716 (-)
XLOC_006619 NA non-coding downstream 1139683 24590420 ~ 24623225 (-)
XLOC_006620 AL831745.2 non-coding downstream 1156281 24602410 ~ 24606627 (-)
XLOC_006618 AL831745.1 non-coding downstream 1174688 24585224 ~ 24588220 (-)
XLOC_006645 NA non-coding upstream 759171 26533354 ~ 26544816 (-)
XLOC_006646 AL627132.1 non-coding upstream 792883 26567066 ~ 26567184 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) G76914 NA non-coding CI01000012 null 11897330 ~ 11900381 (-)
eurasian perch (Perca fluviatilis) G101464 NA non-coding NC_053120.1 CM020917.1 39278652 ~ 39278953 (+)
tiger barb (Puntius tetrazona) LOC122356835 NA non-coding NC_056711.1 CM032080.1 9570989 ~ 9583671 (+)