RetrogeneDB ID: retro_fcat_1706

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: E2:19741622..19742441(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: HCCS
• Ensembl ID: ENSFCAG00000022393
• Aliases: None
• Description: holocytochrome c synthase [Source:HGNC Symbol;Acc:4837]

Sequence

>retro_fcat_1706
TTGTCTGCATCTACCCCCACTGTTACAGTTCAGACCTCACATGCTTCAGATCATCGGATGGCGTCCCCACCATCAGGATG
TCCCATGCATGAAGGGAAAATGAAAGGCTGTCCAGTGCAGAGCATGTGACCCATCTTGTGAGAACAAAATGAGCCCTGTG
GCTGCTCGCCAGGGCAGGATCGCGTGTGTGAGTCCATGGGAAGTCCTGTTACGGGCGCTGTGGCCGAGAATAAGGAGCAC
CTAGATTCTCATCTGATGCCACCACCTGATCGGACACTGCCCCCCCCCCCCCCCACCGATCAGCCATTTGCACTGTTTAC
TGTGAGAGAGGACTCATCCATTCCGAGAGCAGATTCGGAGAATAAGTGCGTTTATCCTTCAGAACAGATGCTCTGGAATG
CGATGGTACGGGAAGGGTGGAAATGGAAGGATGAGGCTATGAGTCACAAAGACAGCATAATATCATCAGAATTCACAATC
AGAATAATGAGCAAGCCCGGAAGGAGATCCAGAAGTAGGAAGCCATTCATGCCGCCAAACATCCTTCGTGCTCCATCACT
CATCCGGTTCGGAGGTAAAGAGAAAGAGTATTCACCAAGGGCGAGAATTCATTCCTGGATGGGGTACAAGTTGCCTTTTG
ACAGGCACGATTGGAACATCCACCCTTGTGGGCCAGAAGTCAGATAGGTCATCGGCTACTGCGATGGCGGTGAGGTCAAA
CAGGACTACCAGTTCACCACCCTGGACGCCCGGCCCGCTCTGGACCCTCTCTCGTGAATGGGGGACAGAATGGAGGCTGC
ATGGTGGCGCTGGACCTCA

Alignment

ORF - retro_fcat_1706 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.55 %
• Parental protein coverage: 99.26 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LSASTPAVAVQTSNASDHQTASPPSGCPMHEGKMKGCPVSAEPPEPTCENKTSSVPTHQDRAYEYVECPV
          LSASTP.V.VQTS.ASDH..ASPPSGCPMHEGKMKGCPV....P.....N........QDR..E....PV
Retrocopy LSASTPTVTVQTSHASDHRMASPPSGCPMHEGKMKGCPVQSM*PIL*EQNEPCGCSPGQDRVCESMGSPV

Parental  TGAVAGSKEDLDPSNLMPPPNQMPAP---DQPFALSTVREESSIPRADSDKKWVYPSEQMFWNAMLRKGW
          TGAVA..KE.LD.....PP..........DQPFAL.TVRE.SSIPRADS..K.VYPSEQM.WNAM.R.GW
Retrocopy TGAVAENKEHLDSHLMPPPDRTLXXXXXTDQPFALFTVREDSSIPRADSENKCVYPSEQMLWNAMVREGW

Parental  KWKDDDISQRD-MYNIIKIHNQNNEQAWKEILKWEALHAAECPC-GPSLIRFGGKAKEYSPRARIRSWMG
          KWKD...S..D...NII.IHNQNNEQA.KEI.K.EA.HAA..P...PSLIRFGGK.KEYSPRARI.SWMG
Retrocopy KWKDEAMSHKD<QHNIIRIHNQNNEQARKEIQK*EAIHAAKHPS>APSLIRFGGKEKEYSPRARIHSWMG

Parental  YELPFDRHDWIINRCGTEVRYVIDYYDGGEVNQDYQFTILDVRPALDSFSAVWDRMKVAWWRWTS
          Y.LPFDRHDW.I..CG.EVR.VI.Y.DGGEV.QDYQFT.LD.RPALD..S...DRM..AWWRWTS
Retrocopy YKLPFDRHDWNIHPCGPEVR*VIGYCDGGEVKQDYQFTTLDARPALDPLS*MGDRMEAAWWRWTS

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	21.92 RPM
SRP017611_kidney	0.00 RPM	19.58 RPM
SRP017611_liver	0.00 RPM	10.31 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1706 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1706 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 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000022393	1 retrocopy	retro_fcat_1706 ,
Myotis lucifugus	ENSMLUG00000003569	1 retrocopy	retro_mluc_1621,
Ictidomys tridecemlineatus	ENSSTOG00000014037	6 retrocopies	retro_itri_1277, retro_itri_1462, retro_itri_1594, retro_itri_1700, retro_itri_242, retro_itri_745,
Tupaia belangeri	ENSTBEG00000002670	1 retrocopy	retro_tbel_1503,