RetrogeneDB ID: | retro_ecab_403 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 17:737192..738400(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSECAG00000000155 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PEX13 | ||
| Ensembl ID: | ENSECAG00000019622 | ||
| Aliases: | None | ||
| Description: | peroxisomal biogenesis factor 13 [Source:HGNC Symbol;Acc:8855] |
Retrocopy-Parental alignment summary:
>retro_ecab_403
ATGGCATCCCAGCCGCCACAGCCCCCGATACCCGGGGAGACCCACCGAATTCCGGGGGCTGGTCCGGGACCAGGACCCGG
CCCCACTTTCCAATCTGCTGATTTGGGTCCTACTTTATTGACAAGACCTGGACAACCAACACTTACCAGAGTGCCGCCAC
CTATTCTTCCAAGGCCATCACAGCAGACAGGAAGCAGCAGTGTGAACACTTTTAGACCTACTTACAGTTCATTTTCTTCT
GGATATGGTGCCTATGGAAATTCATTTTATGGAAGCTATAGCCCTTATAGTTATGGATATAATGGGTTGGGCTATAACCG
CATCCGTGTGGATGATCTTCCACCTAGTAGATTTGTTCAGCAAGCTGAAGAAAGCAGCAGAGGTGCATTTCACTCCATTG
AAAGTATTGTGCATGCATTTGCCTCTGTCAGTATGATGATGGATGCTACCTTTCCAGCTGTCTATAACAGTTTCAGGGCT
GTATTGCATGTAGCAAATCACTTTTCCCGATTAAAAATACACTTCACAAAGGTCTTTTCAGCTTTTGCATTAGTTGGGAC
TATAAGGTATCTTTATAGACGGTTACAGCAGATGATAGGTTTAAGAGGAGGCTCTGAGAATGAGGACTTATGGGCAGAAA
GTGAAGGAACTGTGGCTTGCCTTGGTGCCGAGGACAGAGCAGCTAATTCAGCAAAATCTTGGCCAATATTCTTATTCTTT
GCTGTTATCCTTGGTGGTCCTTATCTCATCTGGAAACTGCTGTCTATCCACACTGATGAAGTAACAGACAACACCAACTG
GGCAAGTGGTGAGGATGACCATGTAGTTGCTAGGGCAGAATATGATTTTACTGCTGCATCTGAAGAAGAAATTTCTTTCC
GTGCTGGTGATATGCTACATTTAGCTCTCAAAGAACAGCAACCCAAGTGCGTGGTTGGCTTCTGGCTAGTCTTGATGGTC
AAACAACAGGACTTATACCTGCTAATTATGTCAAAATTCTTGGTAAAAGAAGAGGTAGAAAAACAGTGGAATCCAGTAAA
ATTCCCAAGCAGCAACAATCTTTTACCAACACAACACTAATTAAAGGAGTCACGGCCACTGATTCTTTGGATGAACAGGA
AGCTGCCTTTGAATCTGTTTTTGTTGAAACTTGTAAGGTTCCAGTTGCACCTGATTCCACTGGGAAAAGTGGAGATAAAC
AAGTTCTT
ORF - retro_ecab_403 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 95.79 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MASQPPPPPKPWETRRIPGAGPGPGPGPTFQSADLGPTLLTRPGQPTLTRVPPPILPRPSQQTGSSSVNT |
| MASQPP.PP.P.ET.RIPGAGPGPGPGPTFQSADLGPTLLTRPGQPTLTRVPPPILPRPSQQTGSSSVNT | |
| Retrocopy | MASQPPQPPIPGETHRIPGAGPGPGPGPTFQSADLGPTLLTRPGQPTLTRVPPPILPRPSQQTGSSSVNT |
| Parental | FRPAYSSFSSGYGAYGNSFYGSYSPYSYGYNGLGYNRLRLDDLPPSRFVQQAEESSRGAFQSIESIVHAF |
| FRP.YSSFSSGYGAYGNSFYGSYSPYSYGYNGLGYNR.R.DDLPPSRFVQQAEESSRGAF.SIESIVHAF | |
| Retrocopy | FRPTYSSFSSGYGAYGNSFYGSYSPYSYGYNGLGYNRIRVDDLPPSRFVQQAEESSRGAFHSIESIVHAF |
| Parental | ASVSMMMDATFSAVYNSFRAVLDVANHFSRLKIHFTKVFSAFALVRTIRYLYRRLQRMIGLRGGSENEDL |
| ASVSMMMDATF.AVYNSFRAVL.VANHFSRLKIHFTKVFSAFALV.TIRYLYRRLQ.MIGLRGGSENEDL | |
| Retrocopy | ASVSMMMDATFPAVYNSFRAVLHVANHFSRLKIHFTKVFSAFALVGTIRYLYRRLQQMIGLRGGSENEDL |
| Parental | WAESEGTVACLGAEDRAANSAKSWPIFLFFAVILGGPYLIWKLLSTHTDEVTDNTNWASGEDDHVVARAE |
| WAESEGTVACLGAEDRAANSAKSWPIFLFFAVILGGPYLIWKLLS.HTDEVTDNTNWASGEDDHVVARAE | |
| Retrocopy | WAESEGTVACLGAEDRAANSAKSWPIFLFFAVILGGPYLIWKLLSIHTDEVTDNTNWASGEDDHVVARAE |
| Parental | YDFTAASEEEISFRAGDMLHLALKEQQPK-VRGWLLASLDGQTTGLIPANYVKILGKRRGRKTVESSKIP |
| YDFTAASEEEISFRAGDMLHLALKEQQPK.VRGWLLASLDGQTTGLIPANYVKILGKRRGRKTVESSKIP | |
| Retrocopy | YDFTAASEEEISFRAGDMLHLALKEQQPK<VRGWLLASLDGQTTGLIPANYVKILGKRRGRKTVESSKIP |
| Parental | KQQQSFTNTTLIKGATAADSLDEQEAAFESVFVETCKVPVAPDSTGKSGDKQDL |
| KQQQSFTNTTLIKG.TA.DSLDEQEAAFESVFVETCKVPVAPDSTGKSGDKQ.L | |
| Retrocopy | KQQQSFTNTTLIKGVTATDSLDEQEAAFESVFVETCKVPVAPDSTGKSGDKQVL |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP021940_articular_cartilage | 0 .00 RPM | 3 .25 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 2 .75 RPM |
| SRP021940_embryo | 0 .05 RPM | 4 .55 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 4 .33 RPM |
| SRP021940_synovial_membrane | 0 .03 RPM | 2 .61 RPM |
| SRP021940_testis | 0 .13 RPM | 12 .34 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_403 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_403 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_403 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000012871 | 1 retrocopy | |
| Equus caballus | ENSECAG00000019622 | 1 retrocopy |
retro_ecab_403 ,
|
| Felis catus | ENSFCAG00000028969 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000020283 | 1 retrocopy |