RetrogeneDB ID: retro_fcat_1919

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:53863029..53863658(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_fcat_1919
GAAAACCTTCTTAATTTGGTCCAGCATAACGTGAACATTTTAAATTAATCATTCTTAATATCGTAAAATACAGCCTAAAC
TGCAAGTTGTTTGTTGTTTCCAATCCAGTGGGTATCTTGACCTATGTGGCTTGGAAGATAAGTGGCTTTCCCAAAAACCG
TGTTACTGGAAGTGGTTGTAATCTGGGTTCATTCTGGTTCCATTACTTAATTGGGGAAAGGCTGGGAGTTCACCCATTAA
GCTGGCATAGGTGGGTCCCTGGGGAGCATGGAGATTCTAGTGTGCCTCTATGCAGTGGAGTAAATGTTGCTGGTGTCTTC
CTTAAGAATCTTCACCCTGACTTAGGCACTGATGCAGATAAGGAACAATGGAAAGAGGTTCACAAATAGGTGGTTGACAG
TGCCTATGAGGTGATCAAACTGAAAAGGCTACACTTCCTGGGCCATTGGGCTATTTGTGGAAGATTTGGAGAAAGTATAA
TGAAGAATCATCGGCAGGTGCATCCAATTTCCATCATGACTAAGGGTCTCTATGGAATAAAAGATGCTGTTTACCTTAGT
GTTCTTTGCATCTTGGGACAGAATGGAATCTCAGATGTTGTGAAGGTGACTCTGACTCCTGAGGAAGAG

Alignment

ORF - retro_fcat_1919 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.63 %
• Parental protein coverage: 58.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ESRLNLVQRNVNI-FKFIIPNVVKYSPNCKLLVVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRY
          E..LNLVQ.NVNI.FK.II.N.VKYS.NCKL.VVSNPV.ILTYVAWKISGFPKNRV.GSGCNL.S..F.Y
Retrocopy ENLLNLVQHNVNI<FKLIILNIVKYSLNCKLFVVSNPVGILTYVAWKISGFPKNRVTGSGCNLGSFWFHY

Parental  LMGERLGVHALSCHGWVLGEHGDSSVPVWSGVNVAGVSLKNLHPDLGTDADKEKWKEVHKQVVDSAYEVI
          L.GERLGVH.LS.H.WV.GEHGDSSVP..SGVNVAGV.LKNLHPDLGTDADKE.WKEVHK.VVDSAYEVI
Retrocopy LIGERLGVHPLSWHRWVPGEHGDSSVPLCSGVNVAGVFLKNLHPDLGTDADKEQWKEVHK*VVDSAYEVI

Parental  KLK-GYTSWAIGLSVADL-AESIMKNLRRVHPISTMIKGLYGIKDDVFLSVPCILGQNGISDVVKVTLTP
          KLK.GYTSWAIGL.V.DL..ESIMKN.R.VHPIS.M.KGLYGIKD.V.LSV.CILGQNGISDVVKVTLTP
Retrocopy KLK>GYTSWAIGLFVEDL<GESIMKNHRQVHPISIMTKGLYGIKDAVYLSVLCILGQNGISDVVKVTLTP

Parental  EEE
          EEE
Retrocopy EEE

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_1919 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1919 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,