RetrogeneDB ID: retro_fcat_1510

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D2:56022115..56022973(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000024894
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: STIP1
• Ensembl ID: ENSFCAG00000005937
• Aliases: None
• Description: stress-induced-phosphoprotein 1 [Source:HGNC Symbol;Acc:11387]

Sequence

>retro_fcat_1510
CAGAAGGCTTATGAGGATGGTTATAAAACCATTGACTTAAAGCTTGATGGAGGCAAGGGCTATTCACGAAAAGCAGCAGC
TCTTGAGTTCTTAAACCGATTTGAAGAAGCCAAGTGAACCTACAAAGAAGGTTGATAACATGAAGCAAATAATCTCAGCT
GAAAGAGGGCTTACAGAATATGGAGGCCCAGGTGGCAGAGAGGAGGTTCCATGAACCCTTTCAACATATCCAATCTGTAT
CAGAAGTTGGAGAGTGATCCCAGGACAAAGACAATGCTCACTGATCCTACCTACCAGGAAATGATAGAGCAGCTGTGAAA
CAAGCCATCTGACTTGGGCATGAAACTGCAAGATCCCCAGGTCATGAAGACTCTCAGTGTCCTCCTGGGAGTCGATCGGG
ACAGTATGGATGAGGAGGAGGAAGGTGCAATACCTCCACCATTACCTCCTCCCAAAAAGGATACCAAGCCAGAGCCAATG
GAAGAAGATCTTCCAGAGAATAAGAAGCAGGCACTGAAAGATAAGGAGTTGGGGAATGAATCCTACAAGAAGAAAGACTT
TGATACAGCCTTGAAGCACTACGACAGAGCCAGGGACCTGGACCCCACCAACAGGACTTACATGACCAATCAAGCATCTG
TGTACTCCGAGAAGGGCGACTACAGTAAATGCCTAGAGCTTTGTGAGAAGGCCATCAAAGTGGAATGAGAAAATCAAGAA
GAATATCGACAGATTGCCAAAGCTTATGCTCGAGTTGGCAACGCCTACTTCAAAGAAGAAAAGTACAAGGATGCCACCCA
TTTCTATAACAAGTCTTTGGCAGAGCACTGAACCCCAGATGTGCTCAAGAAATGCCAA

Alignment

ORF - retro_fcat_1510 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.99 %
• Parental protein coverage: 52.87 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QKAYEDGCKTVDLKPDWGKGYSRKAAALEFLNRFEEAKRTYEEGLKHEANN-PQLKEGLQNMEARLAERK
          QKAYEDG.KT.DLK.D.GKGYSRKAAALEFLNRFEEAK.TY.EG..HEANN..QLKEGLQNMEA..AER.
Retrocopy QKAYEDGYKTIDLKLDGGKGYSRKAAALEFLNRFEEAK*TYKEG**HEANN<SQLKEGLQNMEAQVAERR

Parental  F-MNPFNMPNLYQKLESDPRTRTLLADPTYRELIEQLRSKPSDLGTKLQDPRIMTTLSVLLGVDLGSMDE
          F.MNPFN..NLYQKLESDPRT.T.L.DPTY.E.IEQL..KPSDLG.KLQDP..M.TLSVLLGVD..SMDE
Retrocopy F>MNPFNISNLYQKLESDPRTKTMLTDPTYQEMIEQL*NKPSDLGMKLQDPQVMKTLSVLLGVDRDSMDE

Parental  DEEVAAPPPPPPPKKDTKPEPMEEDLPENKKQALKEKELGNEAYKKKDFDTALKHYDRAKDLDPTNMTYM
          .EE.A.PPP.PPPKKDTKPEPMEEDLPENKKQALK.KELGNE.YKKKDFDTALKHYDRA.DLDPTN.TYM
Retrocopy EEEGAIPPPLPPPKKDTKPEPMEEDLPENKKQALKDKELGNESYKKKDFDTALKHYDRARDLDPTNRTYM

Parental  TNQAAVYFEKGDYSKCRELCEKAIEVGRENREDYRQIAKAYARIGNSYFKEEKYKDAIHFYNKSLAEHRT
          TNQA.VY.EKGDYSKC.ELCEKAI.V..EN.E.YRQIAKAYAR.GN.YFKEEKYKDA.HFYNKSLAEH.T
Retrocopy TNQASVYSEKGDYSKCLELCEKAIKVE*ENQEEYRQIAKAYARVGNAYFKEEKYKDATHFYNKSLAEH*T

Parental  PDVLKKCQ
          PDVLKKCQ
Retrocopy PDVLKKCQ

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	102.61 RPM
SRP017611_kidney	0.00 RPM	71.01 RPM
SRP017611_liver	0.00 RPM	39.12 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1510 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1510 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 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015663	2 retrocopies	retro_btau_836, retro_btau_913,
Canis familiaris	ENSCAFG00000014672	6 retrocopies	retro_cfam_1077, retro_cfam_1172, retro_cfam_1722, retro_cfam_1982, retro_cfam_474, retro_cfam_497,
Callithrix jacchus	ENSCJAG00000018209	2 retrocopies	retro_cjac_1043, retro_cjac_2222,
Cavia porcellus	ENSCPOG00000002914	1 retrocopy	retro_cpor_1443,
Felis catus	ENSFCAG00000005937	1 retrocopy	retro_fcat_1510 ,
Homo sapiens	ENSG00000168439	1 retrocopy	retro_hsap_4867,
Gorilla gorilla	ENSGGOG00000012132	1 retrocopy	retro_ggor_3040,
Microcebus murinus	ENSMICG00000016933	1 retrocopy	retro_mmur_1045,
Macaca mulatta	ENSMMUG00000012953	1 retrocopy	retro_mmul_2607,
Nomascus leucogenys	ENSNLEG00000004777	1 retrocopy	retro_nleu_2000,
Pan troglodytes	ENSPTRG00000003820	1 retrocopy	retro_ptro_3242,
Rattus norvegicus	ENSRNOG00000021164	2 retrocopies	retro_rnor_2862, retro_rnor_468,
Ictidomys tridecemlineatus	ENSSTOG00000014262	1 retrocopy	retro_itri_1578,
Tursiops truncatus	ENSTTRG00000010235	1 retrocopy	retro_ttru_1900,