RetrogeneDB ID: retro_fcat_464

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A3:35542677..35543167(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000006586
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000025737
• Aliases: None
• Description: None

Sequence

>retro_fcat_464
CCCTAGCAGTTTACAGCTGTCAAATTGTCTGATTCCAGAATTGCCCTGAAATCTGGCTATGGAAAATACCTTGGTATTAA
TTCAGATGGACTTGTTGTGGGGCATTCAGATGCAATTGGACAAAGAGAACAGTGGGAACCAGTCTTTCAAGATGGGAAAA
TGGCCCTATTGGCCTCAAATAGCTGTTTTGTTAGATGCAACGAAGCAGGCAATATAGAATCAAAAAGTAAAACAGCAGGA
GAAGAAAAAATGATAAAGATTAGATCCTGTGCTGAAAGAGAAACTAAGAAAAAAGATGATATGCCAGAAGAAGACAAAGG
AAATGTTAAACAGTGTGAAATCAATTATGTAGAGAAATTTCAGAGCTTCCAAGACCACAAACTTAAAATAAGAAGACAGT
AAAATTCTCAAAAAGGCCAGGAAGGATGGATTTTTGCATGAAACACTTCTGGACAGGAGAGCCAAATTGAAGGCTGATAG
ATACTGCAAA

Alignment

ORF - retro_fcat_464 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.35 %
• Parental protein coverage: 63.95 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PEQFTAVKLSDSRIALKSGYGKYLGINSDGLVVGRSDAIGPREQWEPVFQDGKMALLASNSCFIRCNEAG
          P.QFTAVKLSDSRIALKSGYGKYLGINSDGLVVG.SDAIG.REQWEPVFQDGKMALLASNSCF.RCNEAG
Retrocopy P*QFTAVKLSDSRIALKSGYGKYLGINSDGLVVGHSDAIGQREQWEPVFQDGKMALLASNSCFVRCNEAG

Parental  DIEAKSKTAGEEEMIKIRSCAERETKKKDDIPEEDKGNVKQCEINYV-KKFQSFQDHKLKISKEDSKILK
          .IE.KSKTAGEE.MIKIRSCAERETKKKDD.PEEDKGNVKQCEINYV...F.......LK...EDSKILK
Retrocopy NIESKSKTAGEEKMIKIRSCAERETKKKDDMPEEDKGNVKQCEINYV>RNFRASKTTNLK*--EDSKILK

Parental  KARKDGFLHETLLDRRAKLKADRYCK
          KARKDGFLHETLLDRRAKLKADRYCK
Retrocopy KARKDGFLHETLLDRRAKLKADRYCK

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	0.11 RPM	7.12 RPM
SRP017611_kidney	0.10 RPM	16.39 RPM
SRP017611_liver	0.00 RPM	8.29 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_464 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_464 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 11 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013503	1 retrocopy	retro_amel_1609,
Canis familiaris	ENSCAFG00000007135	1 retrocopy	retro_cfam_718,
Cavia porcellus	ENSCPOG00000022277	7 retrocopies	retro_cpor_1349, retro_cpor_1350, retro_cpor_1359, retro_cpor_1361, retro_cpor_1362, retro_cpor_1363, retro_cpor_864,
Felis catus	ENSFCAG00000025737	1 retrocopy	retro_fcat_464 ,
Myotis lucifugus	ENSMLUG00000023179	2 retrocopies	retro_mluc_1185, retro_mluc_1490,
Otolemur garnettii	ENSOGAG00000005749	2 retrocopies	retro_ogar_1523, retro_ogar_2535,
Pan troglodytes	ENSPTRG00000016671	1 retrocopy	retro_ptro_2930,
Rattus norvegicus	ENSRNOG00000009846	1 retrocopy	retro_rnor_88,
Sorex araneus	ENSSARG00000002471	1 retrocopy	retro_sara_368,
Tupaia belangeri	ENSTBEG00000014491	2 retrocopies	retro_tbel_1202, retro_tbel_3435,
Tarsius syrichta	ENSTSYG00000010985	2 retrocopies	retro_tsyr_1347, retro_tsyr_1778,