RetrogeneDB ID: retro_fcat_1648

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: E1:16512061..16512497(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS8
• Ensembl ID: ENSFCAG00000013789
• Aliases: None
• Description: COP9 signalosome subunit 8 [Source:HGNC Symbol;Acc:24335]

Sequence

>retro_fcat_1648
ATAGAATCTGTAAATTCTGAACTTGGGGGAATTTGGTCAGTAGGACAAAGAATCTGGAGAGAGATTTTCCTGGAATCTAC
ATGACCTTCAACGCACACCAGTGGTCTGAGATGGTCTGGCCAATCATAGAAGCACTTAGAGATGCCACAAAGAGAAGAGC
CTTCACCCTAGTCTCTCAAGCCTACACTTCCATAAAGAGCCAACGACTTTGCAGCTGTTGTCAGGCTCCTGTGGAAGAGG
CTGTGAAAGGTACATTAGAACAAGGATGGCAAGCTCACTTCACCACAAGAATGTTATGCCCAAAAAACCAGTTGCAGGAG
CCCTGGATGTTTCCTTCAACTGGATCATTCCCTCATCAGAACCTGCCCCAATTACACCAATCCCCAACAAGCAGCAGTTA
GCCAGACTGACCAATTATGTGGCTTTCATCAAAAGC

Alignment

ORF - retro_fcat_1648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 69.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IKSANSELGGIWSVGQRIW-QRDFPGIYSTINAHQWSETVQPIMEALRDATRRRAFALVSQAYTSI-IAD
          I.S.NSELGGIWSVGQRIW..RDFPGIY.T.NAHQWSE.V.PI.EALRDAT.RRAF.LVSQAYTSI..A.
Retrocopy IESVNSELGGIWSVGQRIW<ERDFPGIYMTFNAHQWSEMVWPIIEALRDATKRRAFTLVSQAYTSI>RAN

Parental  DFAAFVGL-PVEEAVKGILEQGWQADSTTRM-VMPKKPVAGALDVSFNRFIPLSACAEPAPVPPIPNEQQ
          DFAA.V.L.PVEEAVKG.LEQGWQA..TTRM.VMPKKPVAGALDVSFN..IP.S...EPAP..PIPN.QQ
Retrocopy DFAAVVRL<PVEEAVKGTLEQGWQAHFTTRM<VMPKKPVAGALDVSFNWIIPSS---EPAPITPIPNKQQ

Parental  LARLTDYVAFLEN
          LARLT.YVAF...
Retrocopy LARLTNYVAFIKS

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	16.53 RPM
SRP017611_kidney	0.00 RPM	10.10 RPM
SRP017611_liver	0.00 RPM	5.86 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1648 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1648 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 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005854	3 retrocopies	retro_btau_1315, retro_btau_1401, retro_btau_1402,
Canis familiaris	ENSCAFG00000030168	1 retrocopy	retro_cfam_1327,
Dasypus novemcinctus	ENSDNOG00000015309	5 retrocopies	retro_dnov_1157, retro_dnov_1306, retro_dnov_149, retro_dnov_1701, retro_dnov_527,
Felis catus	ENSFCAG00000013789	1 retrocopy	retro_fcat_1648 ,
Loxodonta africana	ENSLAFG00000008617	1 retrocopy	retro_lafr_928,
Macropus eugenii	ENSMEUG00000008189	3 retrocopies	retro_meug_583, retro_meug_609, retro_meug_701,
Monodelphis domestica	ENSMODG00000007474	1 retrocopy	retro_mdom_1295,
Mustela putorius furo	ENSMPUG00000000068	1 retrocopy	retro_mputfur_176,
Mus musculus	ENSMUSG00000034432	1 retrocopy	retro_mmus_1812,
Oryctolagus cuniculus	ENSOCUG00000007341	4 retrocopies	retro_ocun_1549, retro_ocun_1579, retro_ocun_428, retro_ocun_550,
Pongo abelii	ENSPPYG00000013308	1 retrocopy	retro_pabe_3787,
Rattus norvegicus	ENSRNOG00000019635	3 retrocopies	retro_rnor_1005, retro_rnor_1078, retro_rnor_975,
Tupaia belangeri	ENSTBEG00000015944	1 retrocopy	retro_tbel_4315,