RetrogeneDB ID: retro_fcat_295

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A1:212343788..212344812(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000031860
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000015735
• Aliases: None
• Description: None

Sequence

>retro_fcat_295
ATTCCTCTTGGCTCTAAATCCAATATGGCAACTCTCAAGGATCAGCTGATTCAGAAACTTCTTAAGGAAGATCATAACCC
CCAGAATAAGATTACCATTGTTGGGGTTCATGCTGTTGGCACGGCTTGTGCCATCAGTGTCTTAATGAAGGACTTGGCAG
GTTGAACTTGCTCTTGTTGATGTCATGGAAGACAAACTGAAGGGAGAGATGATGGATCTCCAGCATGGCAACCTATTCCC
TAGAACACCAAAAATTGTCTCCAGCAAAAACTATCATGTGACTGCAAACTCCAAGCTGGTTATTATCACAGCTGGGGCAC
GTCAGCAAGAGGGAGAAAGCCATCTTAATTTGGTCCAGCATAATGTGAACATCTTTAAGTTCATCATTTCTAATATGGGT
TGTAAAATACAACCTAAACTGCAAATTGCTTATTGTTTCCAATCCAGTGGATATCTTGACCTAGGAGGCTTGGAAGATAA
GTGGCTTTCCCAAAAGCCATGTTATTAGAAGTGGTTGCAATCTGGATTCAGTCTGGTTCCGTTACCTAATGGGGGAAAGG
CTGGGACTTCACCCATTAAGCTGTCATGGGTACGTCTTGGGGAGCATGGAGACTCTAGTGTGCCTGTATGGAGTGGAATA
AATGTTGCTGGTGCCTTCCTGAAGAATCTGCACCCTGACTTAGGCACAGATGCAGATAAGGAACAGTGGAAAGAGGTTCA
CAAACAGGTGGCTGACAGTGCCTATGAGGTGATCAAACCGAAAGCCTATACTTCCTGGGCCATTGGACTGTCTGTGGCAG
ATTTGGCAGAAAGTATAATGAAGAATCTTAGGTGGGTGCCTCCAATTTCCACCATGATTAATGGTCCCTATGGAATAAAA
GATGATGTCTTCCTTAGTGTTCCTTGCATCTTGGGACAGAATGGAATCTCACATGTTGTGACGGCGACTCTGACTCCTGA
GGAAGAGGCCCATTTGAGGAAGAGTACAGATACACTTTGGGGGATCCAAAAAGAGCCGCAGTTT

Alignment

ORF - retro_fcat_295 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.3 %
• Parental protein coverage: 94.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IPFASKSNMATLKDQLIQNLLKEDHTPQNKITVVGVGAVGMACAISILMKDLAD-ELALVDVMEDKLKGE
          IP..SKSNMATLKDQLIQ.LLKEDH.PQNKIT.VGV.AVG.ACAIS.LMKDLA..ELALVDVMEDKLKGE
Retrocopy IPLGSKSNMATLKDQLIQKLLKEDHNPQNKITIVGVHAVGTACAISVLMKDLAG>ELALVDVMEDKLKGE

Parental  MMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNV-VKYSP-
          MMDLQHG.LF.RTPKIVS.K.Y.VTANSKLVIITAGARQQEGES.LNLVQ.NVNIFKFII.N...K..P.
Retrocopy MMDLQHGNLFPRTPKIVSSKNYHVTANSKLVIITAGARQQEGESHLNLVQHNVNIFKFIISNMGCKIQP>

Parental  NCKLLVVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHALSCHGWV-LGEHGDSSV
          NCKLL.VSNPVDILT..AWKISGFPK..VI.SGCNLDS..FRYLMGERLG.H.LSCHG.V.LGEHGDSSV
Retrocopy NCKLLIVSNPVDILT*EAWKISGFPKSHVIRSGCNLDSVWFRYLMGERLGLHPLSCHGYV<LGEHGDSSV

Parental  PVWSGVNVAGVSLKNLHPDLGTDADKEKWKEVHKQVVDSAYEVIKLKGYTSWAIGLSVADLAESIMKNLR
          PVWSG.NVAG..LKNLHPDLGTDADKE.WKEVHKQV.DSAYEVIK.K.YTSWAIGLSVADLAESIMKNLR
Retrocopy PVWSGINVAGAFLKNLHPDLGTDADKEQWKEVHKQVADSAYEVIKPKAYTSWAIGLSVADLAESIMKNLR

Parental  RVHPISTMIKGLYGIKDDVFLSVPCILGQNGISDVVKVTLTPEEEARLKKSADTLWGIQKELQF
          .V.PISTMI.G.YGIKDDVFLSVPCILGQNGIS.VV..TLTPEEEA.L.KS.DTLWGIQKE.QF
Retrocopy WVPPISTMINGPYGIKDDVFLSVPCILGQNGISHVVTATLTPEEEAHLRKSTDTLWGIQKEPQF

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	109.03 RPM
SRP017611_kidney	0.00 RPM	163.24 RPM
SRP017611_liver	0.00 RPM	655.67 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_295 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_295 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 7 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009211	8 retrocopies	retro_cfam_1061, retro_cfam_1149, retro_cfam_1182, retro_cfam_1317, retro_cfam_1617, retro_cfam_1946, retro_cfam_2006, retro_cfam_309,
Dipodomys ordii	ENSDORG00000003524	2 retrocopies	retro_dord_439, retro_dord_449,
Felis catus	ENSFCAG00000012639	1 retrocopy	retro_fcat_462,
Felis catus	ENSFCAG00000015735	4 retrocopies	retro_fcat_102, retro_fcat_1839, retro_fcat_1919, retro_fcat_295 ,
Myotis lucifugus	ENSMLUG00000016343	4 retrocopies	retro_mluc_1716, retro_mluc_2031, retro_mluc_2440, retro_mluc_365,
Ictidomys tridecemlineatus	ENSSTOG00000000014	3 retrocopies	retro_itri_1396, retro_itri_1526, retro_itri_535,
Tarsius syrichta	ENSTSYG00000008062	4 retrocopies	retro_tsyr_1811, retro_tsyr_2064, retro_tsyr_2071, retro_tsyr_731,