RetrogeneDB ID: | retro_fcat_976 | ||
Retrocopy location | Organism: | Cat (Felis catus) | |
| Coordinates: | B4:84487753..84488471(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PCOLCE | ||
| Ensembl ID: | ENSFCAG00000006843 | ||
| Aliases: | None | ||
| Description: | procollagen C-endopeptidase enhancer [Source:HGNC Symbol;Acc:8738] |
Retrocopy-Parental alignment summary:
>retro_fcat_976
TACAGCTCCCTCAGCATGTTCATCGGAGCAGCCAGCGATGAGGCCAAGAGGCAAATCTCTGCTGTGACACAGCCTCAGGT
CCCATCTCCTCCACAGGGAATAAGCTCCTCCTCCAGCTCATCTCTGACCTCAATGTCATGGCCAACAGCTTCTCCATCTC
TTACAAGACACTTGCCTCTTTGTGCTGCCAAAGAAGGGCAGGCCCAGGGCCGGGGGAGGATGCCCCACTCCCCACCTCTG
ACTCCAAGCCAAGACTCCCACTGAGGAGAAACTGAAAGTCCTCGTCTGAGACCCAGGCAGCTCCAGGGGAGCCCCAATGC
ACCCCGTGTCCCCTGTCCAAAGCAGTGCTGATAGATAGGCACCTTGCAGAGCAACTTTTGAACCAGCAACCTGGTGGTGA
CTGCCAACAGCACAGTCCATGGTTCGGTGCCCAGGGGAGGGCCTCACTTCTCTGTCAGTCTCATTGGTGCTGACAAAACT
GGAGGCCTGAACATGCCCTCAGCACTCACTGACACTCCCCTCAAGTTTTGCCTGCCCTGCAAGCAGTGCCCCCGGCATGA
AGAAAGGAGCCAGTTATCTGACGATGGGCCAGGTGGAAGAGAACAGAGGTCCTATCCTTCCTCCAGAGAACTTCATGGCT
CTCTACTGATCCAACCAGGCCCAGACCCTCACCAACCTCAGCAAGAAAAAGTGCCTCTCCCAGCCTGTTCAGGCTGCT
ORF - retro_fcat_976 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.14 % |
| Parental protein coverage: | 53.28 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 7 |
Retrocopy - Parental Gene Alignment:
| Parental | YDSVSVFNGAASDDAKRL-GKFCGDTAPGTISSEGNELLVQFVSDLSVTADGFSASYKTL-PRGAAKEAQ |
| Y.S.S.F.G.A..D........C.DTA.G.ISS.GN.LL.Q..SDL.V.A..FS.SYKTL.P..AAKE.Q | |
| Retrocopy | YSSLSMFIG-AASDEAKR<ANLCCDTASGPISSTGNKLLLQLISDLNVMANSFSISYKTL>PLCAAKEGQ |
| Parental | AQSAG-EDARSGTPILSPGPKPGLPSEEKPKASSEAQATPG-GPDVPSVPCPKQCRRTGTLQSNFCTSNL |
| AQ..G.EDA....P......KP.LP.....K.SSE.QA.PG..P..P.VPCPKQC...GTLQSNF.TSNL | |
| Retrocopy | AQGRG<EDA----PLPTSDSKPRLPLRRN*KSSSETQAAPG>SPNAPRVPCPKQC**IGTLQSNF*TSNL |
| Parental | VVTA-TVKSMVRGPGEGLT-VTVSLIGAYKTGGLDLPSPLTDTPLKFYVPCKQCPP-MKKGVSYLMMGQV |
| VVTA.T..SMVR.PGEGLT...VSLIGA.KTGGL..PS.LTDTPLKF..PCKQCP..MKKG.SYL.MGQV | |
| Retrocopy | VVTA>TAQSMVRCPGEGLT<FSVSLIGADKTGGLNMPSALTDTPLKFCLPCKQCPR>MKKGASYLTMGQV |
| Parental | EENRGPTLPPESFVVLYRSNQDQILTNLSKRKCPSQPVRAA |
| EENRGP.LPPE.F..LY.SNQ.Q.LTNLSK.KC.SQPV.AA | |
| Retrocopy | EENRGPILPPENFMALY*SNQAQTLTNLSKKKCLSQPVQAA |
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 |
|---|---|---|
| SRP017611_brain | 0 .00 RPM | 7 .12 RPM |
| SRP017611_kidney | 0 .00 RPM | 34 .11 RPM |
| SRP017611_liver | 0 .00 RPM | 11 .42 RPM |
Felis catus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_fcat_976 retrocopy.
Felis catus was not studied using FANTOM5 data.
retro_fcat_976 was not experimentally validated.
Retrocopy orthology:
Felis catus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Felis catus | ENSFCAG00000006843 | 1 retrocopy |
retro_fcat_976 ,
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