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 symbol: PCOLCE
• Ensembl ID: ENSFCAG00000006843
• Aliases: None
• Description: procollagen C-endopeptidase enhancer [Source:HGNC Symbol;Acc:8738]

Sequence

>retro_fcat_976
TACAGCTCCCTCAGCATGTTCATCGGAGCAGCCAGCGATGAGGCCAAGAGGCAAATCTCTGCTGTGACACAGCCTCAGGT
CCCATCTCCTCCACAGGGAATAAGCTCCTCCTCCAGCTCATCTCTGACCTCAATGTCATGGCCAACAGCTTCTCCATCTC
TTACAAGACACTTGCCTCTTTGTGCTGCCAAAGAAGGGCAGGCCCAGGGCCGGGGGAGGATGCCCCACTCCCCACCTCTG
ACTCCAAGCCAAGACTCCCACTGAGGAGAAACTGAAAGTCCTCGTCTGAGACCCAGGCAGCTCCAGGGGAGCCCCAATGC
ACCCCGTGTCCCCTGTCCAAAGCAGTGCTGATAGATAGGCACCTTGCAGAGCAACTTTTGAACCAGCAACCTGGTGGTGA
CTGCCAACAGCACAGTCCATGGTTCGGTGCCCAGGGGAGGGCCTCACTTCTCTGTCAGTCTCATTGGTGCTGACAAAACT
GGAGGCCTGAACATGCCCTCAGCACTCACTGACACTCCCCTCAAGTTTTGCCTGCCCTGCAAGCAGTGCCCCCGGCATGA
AGAAAGGAGCCAGTTATCTGACGATGGGCCAGGTGGAAGAGAACAGAGGTCCTATCCTTCCTCCAGAGAACTTCATGGCT
CTCTACTGATCCAACCAGGCCCAGACCCTCACCAACCTCAGCAAGAAAAAGTGCCTCTCCCAGCCTGTTCAGGCTGCT

Alignment

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

Expression

RNA-Seq

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

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_976 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_976 was not experimentally validated.

Homology

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.

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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 ,