RNA id: TCONS_00028348


Basic Information

Item Value
RNA id TCONS_00028348
length 1501
RNA type mRNA
GC content 0.46
exon number 7
gene id XLOC_014268
representative True

Chromosome Information

Item Value
chromosome id NC_007130.7
NCBI id CM002903.2
chromosome length 48449771
location 42609132 ~ 42617723 (+)
genome version GRCz11_2017_zebrafish_Genome
species zebrafish
(Danio rerio)

Sequence

CCATAAGCCACCATGGCTTCCTCATTCCATTGCATCCGAATTGCATTATTAATAATCTCCTTTTCCGTTTGCGTCCTCGCGCAGTATGAGAAATATAACTTTCGCAGTTTCCCACGACACGAGCTGATGCCGCTGGACTCCGCGTACCGACATGCGTTAGACCTGTACAGTGAGGAGAAGTGGAAGGAGAGCGTGGAGTTTCTGGAGGTCAGTCTGCGGCTCTACCGGCTGCTCCGGGACAGCGAGGCCTTCTGTAACCTCAACTGCAGCTCGGTCAGACTCGACGATGAGACCCGTTTCAGCGACTTTCCCGAGCTGCAGGCCTTCGGTAATGTGATGAAGAGAGCTCAGTGTTTGAAGAGGTGCAAACAGGGGCTACCAGCCTTCAGACAGACCCTCCCCAGCCGGGACACCGTCGATGAGTTTGATAAACGGGAGCCATACAAGTACCTGCAGTTCGCCTACTTCAAAAGTGATAATTTGGCCAAAGCGGTATCCGCTGCACACACATTCCTGCTGAAGCATCCTGATGATGAGATGATGCAGAGAAACATGAACTACTACAAGAGTTTACCAGGAGCTGAGGACCATCTGAAAGACCTGGAGACCAAATCATACGAGATGCTGTTCATTCGGGCCGTGCGAGCGTATAATGGAGATAATTTCCGAACGTCGGTGTCAGATATGGAGCTGGCACTGAGAGACTTTTTTAAGGTATACGATGAATGTATCGCCGCATCAGAAGGATCCAGACAGATTAAAGACTTTAAAGACTTTTACCCGTCCATCGCAGATCATTACTCGGAGGTTCTGGAGAGGAAGGTTCGCTGTGAGAGCGAGCTTACGCCGGTTGTTGGAGGATTTGTTGTTGAGAAATTTGTGGCGACTATGTATCACTACCTGCAGTTTGCCTATTATAAATTGAATGACCTGAAGAACGCAGTGCCGTGTGTGTCCAGCTACATGCTCTTTGACCCCAGTGATGAGGTGATGAGGAATAACGTGGAATATTATCGCTTCCACAGAGAAAAATTTGGCCTCGACGATGAGGACTTCTTACCTAGAGCGGAAGCAGTGCGGTATCATAATCAGACGACGCTACAAATGCAGATGCTGGAATTCGCCAAACAGAAGTTCATGCCAGATGATGAGGGTGAAGTTGTAGAGTTTCTTGATGAATATCTGGATGCTGGGGATGAATAACTGATTGTGTGAGTttgaaataaatgtgaaaaagacCAGAAAGGTATTCCTCGTCCTGTAGTGTTGTTGCTGTTGTATTTATTTAGGGTTTGGTGATTGGAATTGttgatatttttagtttttactcattattttaaaaaacgtCCTAGCACAGCACAGTCTAAACTCGTGCACCACAAGCCAAAAGATAATATATCTGAATCTCAGTCCCTGTCAACTTACTGTATCTCAGAGAAAACAAtgttctgtgtttttattttctcagATTGCTTTAATAAAGACTTGAATACAGTAAAAA

Function

GO:

id name namespace
GO:0018400 peptidyl-proline hydroxylation to 3-hydroxy-L-proline biological_process
GO:0030199 collagen fibril organization biological_process
GO:0005783 endoplasmic reticulum cellular_component
GO:0005518 collagen binding molecular_function

KEGG:

id description
ko03110 Chaperones and folding catalysts

ZFIN:

id description
ZDB-GENE-040426-2619 Predicted to contribute to collagen binding activity. Predicted to be involved in collagen fibril organization and peptidyl-proline hydroxylation to 3-hydroxy-L-proline. Predicted to be active in endoplasmic reticulum. Is expressed in notochord; otic vesicle; pectoral fin; periderm; and pharyngeal arch. Human ortholog(s) of this gene implicated in osteogenesis imperfecta type 7. Orthologous to human CRTAP (cartilage associated protein).

Ensembl:

ensembl_id ENSDART00000010104

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TCONS_00028347 lncRNA upstream 5843 42560956 ~ 42603289 (+) True XLOC_014266
TCONS_00030036 lncRNA upstream 36005 42565358 ~ 42573127 (+) True XLOC_014267
TCONS_00029731 lncRNA upstream 61928 42518577 ~ 42547204 (+) True XLOC_014265
TCONS_00028346 lncRNA upstream 92998 42505974 ~ 42516134 (+) False XLOC_014264
TCONS_00030034 lncRNA upstream 100955 42505975 ~ 42508177 (+) False XLOC_014264
TCONS_00028356 lncRNA downstream 144223 42761946 ~ 42764766 (+) False XLOC_014270
TCONS_00028357 lncRNA downstream 148984 42766707 ~ 42773579 (+) False XLOC_014270
TCONS_00028359 lncRNA downstream 175642 42793365 ~ 42798406 (+) True XLOC_014270
TCONS_00028372 lncRNA downstream 406964 43024687 ~ 43027483 (+) True XLOC_014277
TCONS_00028377 lncRNA downstream 454970 43072693 ~ 43079678 (+) False XLOC_014278
TCONS_00028344 mRNA upstream 124068 42469058 ~ 42485064 (+) False XLOC_014263
TCONS_00028345 mRNA upstream 124130 42470396 ~ 42485002 (+) True XLOC_014263
TCONS_00028343 mRNA upstream 153131 42432625 ~ 42456001 (+) True XLOC_014262
TCONS_00028340 mRNA upstream 267317 42328423 ~ 42341815 (+) False XLOC_014260
TCONS_00028341 mRNA upstream 268247 42336523 ~ 42340885 (+) True XLOC_014260
TCONS_00028349 mRNA downstream 42435 42660158 ~ 42682947 (+) True XLOC_014269
TCONS_00028350 mRNA downstream 76132 42693855 ~ 42802298 (+) False XLOC_014270
TCONS_00028351 mRNA downstream 76488 42694211 ~ 42744977 (+) False XLOC_014270
TCONS_00028352 mRNA downstream 98819 42716542 ~ 42802298 (+) False XLOC_014270
TCONS_00028354 mRNA downstream 117488 42735211 ~ 42802298 (+) False XLOC_014270
TCONS_00028342 other upstream 271701 42337317 ~ 42337431 (+) True XLOC_014261
TCONS_00028333 other upstream 420028 42188990 ~ 42189104 (+) True XLOC_014257
TCONS_00028303 other upstream 1650516 40958500 ~ 40958616 (+) True XLOC_014238
TCONS_00028293 other upstream 2264395 40337554 ~ 40344737 (+) False XLOC_014231
TCONS_00028276 other upstream 2482368 40116262 ~ 40126764 (+) False XLOC_014226
TCONS_00028353 other downstream 114965 42732688 ~ 42735285 (+) False XLOC_014270
TCONS_00028365 other downstream 297696 42915419 ~ 42915541 (+) True XLOC_014274
TCONS_00028379 other downstream 460021 43077744 ~ 43077879 (+) True XLOC_014279
TCONS_00028380 other downstream 463202 43080925 ~ 43081060 (+) True XLOC_014280
TCONS_00028401 other downstream 821678 43439401 ~ 43451947 (+) False XLOC_014288

Expression Profile

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Homologous

species RNA id representative length rna type GC content exon number chromosome id location
grasscarp (Ctenopharyngodon idella) CI01000054_01550659_01554963.mRNA True 1375 mRNA 0.46 7 CI01000054 1550475 ~ 1554963 (-)
grasscarp (Ctenopharyngodon idella) TU272189 True 500 lncRNA 0.34 1 CI01000055 4482291 ~ 4482790 (+)
bowfin (Amia calva) AMCG00002463 True 3517 mRNA 0.44 7 CM030136.1 15607041 ~ 15616265 (-)
mexican tetra (Astyanax mexicanus) TU272189 True 1459 lncRNA 0.49 7 NC_035919.1 28747108 ~ 28755442 (-)