RetrogeneDB ID: retro_fcat_618

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:61630816..61631442(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GRPEL2
• Ensembl ID: ENSFCAG00000003624
• Aliases: None
• Description: GrpE-like 2, mitochondrial (E. coli) [Source:HGNC Symbol;Acc:21060]

Sequence

>retro_fcat_618
ATGGCTGTGTGGTCAGTGTGAGCAATCCAGCCACTGGTGCAGTGCCTTCCGGCCTTCAGTGCTGTGTTGGAAGGCAGGGG
ATCGCTGCATCCTTTCAGTACTGCCACTCAGAGAACTGCCGAAGAGGACTGCGTTCTGAGGACCCTCCTGATGCACTTGG
ACCCTCTCTTGCAGAACGAGCCTTAAACCTTAAAGCTGTGAAACGGGAGAAGGAAGTCCAGGACTTAACAATGAGATACC
AGAGAGCTGTGGCTGATGATGAAAACATAAGGTGGCAAACCCACATATATGTAGAAGATGCCAAGATATTGGAATCCAGA
GTTTCTGTACGGACTTGGTAGAGGTGGCAGACGTTTTGGAAAGGACTGCAGAGTACATTTCTGAAGAAACAGAGCCCGGG
GACCAGAAGCTTACACTGGAGAATATCTTCCAAGAGTTATCACTTTTAGAAGTAAAGCTAAAGAGTGTTTGCCAAACATG
GCCTGGAGAAGATGACATCCATGGATGACAAACATGACCCTCATGAGTATGAACTCATCTGTCATGTGCCCACTGGCATT
GGGGTACAGCCTGGCACAGTGGCATTAGCAAGACAAGATGGCTATAAGCTTCATGGCCACACCATT

Alignment

ORF - retro_fcat_618 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.04 %
• Parental protein coverage: 93.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAARSVWAVRRLVQRLLASSAASEGRGRLHPFSTATQRTAGEDC-SSEDPPDDLGPSLAERALKLKAVKL
          MA..SV.A...LVQ.L.A.SA..EGRG.LHPFSTATQRTA.EDC..SEDPPD.LGPSLAERAL.LKAVK.
Retrocopy MAVWSV*AIQPLVQCLPAFSAVLEGRGSLHPFSTATQRTAEEDC<RSEDPPDALGPSLAERALNLKAVKR

Parental  EKEVQDLTMRYQRAVADGENIRRRTQRCVEDAKIF-GIQSFCKDLVEVADILEKTTEYISEETEPGDQKL
          EKEVQDLTMRYQRAVAD.ENIR..T...VEDAKI..GIQSFC.DLVEVAD.LE.T.EYISEETEPGDQKL
Retrocopy EKEVQDLTMRYQRAVADDENIRWQTHIYVEDAKIL<GIQSFCTDLVEVADVLERTAEYISEETEPGDQKL

Parental  TLEKIFRGLSLLE-AKLKS-VFAKHGLEKMTPIGDKYDPHEHELICHVPAGVGVQPGTVALVRQDGYKLH
          TLE.IF..LSLLE..K.K..VFAKHGLEKMT...DK.DPHE.ELICHVP.G.GVQPGTVAL.RQDGYKLH
Retrocopy TLENIFQELSLLE<SKAKE<VFAKHGLEKMTSMDDKHDPHEYELICHVPTGIGVQPGTVALARQDGYKLH

Parental  GRTI
          G.TI
Retrocopy GHTI

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	5.39 RPM
SRP017611_kidney	0.00 RPM	2.16 RPM
SRP017611_liver	0.00 RPM	1.62 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_618 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_618 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 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004070	1 retrocopy	retro_chof_1984,
Dipodomys ordii	ENSDORG00000011142	1 retrocopy	retro_dord_353,
Felis catus	ENSFCAG00000003624	1 retrocopy	retro_fcat_618 ,
Homo sapiens	ENSG00000164284	2 retrocopies	retro_hsap_1284, retro_hsap_4842,
Gorilla gorilla	ENSGGOG00000005410	2 retrocopies	retro_ggor_1008, retro_ggor_3021,
Macaca mulatta	ENSMMUG00000021662	1 retrocopy	retro_mmul_1317,
Nomascus leucogenys	ENSNLEG00000010160	1 retrocopy	retro_nleu_710,
Oryctolagus cuniculus	ENSOCUG00000016138	3 retrocopies	retro_ocun_89, retro_ocun_905, retro_ocun_943,
Otolemur garnettii	ENSOGAG00000014326	1 retrocopy	retro_ogar_791,
Pongo abelii	ENSPPYG00000015933	2 retrocopies	retro_pabe_1063, retro_pabe_3764,
Pan troglodytes	ENSPTRG00000017396	2 retrocopies	retro_ptro_3226, retro_ptro_877,
Sorex araneus	ENSSARG00000005467	2 retrocopies	retro_sara_320, retro_sara_511,