RetrogeneDB ID: retro_fcat_519

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:28058794..28060016(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EWSR1
• Ensembl ID: ENSFCAG00000004243
• Aliases: None
• Description: EWS RNA-binding protein 1 [Source:HGNC Symbol;Acc:3508]

Sequence

>retro_fcat_519
CCCAGCAGGGCCAGTACTTATGCTACCCAGCCCACTCAAGAATATGCACAGACCATACAGGCATATGGGCAGCAAAATTG
TGGAACCTATGGACAGCCCACTGATGTCAGCTCTACCCAGCCTCAGACGACTGCGACCTATGGGCAGATTATCTGTGCAA
CTTCTTATGGGCAGCCTACTGTTGGTTATAATACTCCAAGATTTGATCTTGGAAGCATCAGTGGAGGTGGGCGGGAAGGA
GTCTGTGGTGGAATGGGTGCTAGAGAGCAAGGTGGCTTCAGTAAGCCTGGTGGACTCATGGACAAAGGACCAGATCTTGA
TCTAGGCCCAATTGTAGATCCAGATAAAGACTCTGACAGCATTGCAATTTATATGCAAGGCTTAAACGACAGCGTGACCC
TAGGTAATCTGGCAGACTTCTTAAACAGTGTAGAGTTGTTAAGATGAAGAAGATAATCAGACAACCCATGATCCCTATCT
TCTTAGACAAGGAAACAGGGAAGCCCAAAGGCAGTGCTGCAGTGCCCTACGAAGACCTGCCAACTATCAAGGCTGCCTTG
GAGTGGTTTGTTGGGAAAAAGTTTTAAGGGAACAAACTTGAGGTTCCGCTTGCTCTGAGGAAGCTTCTGGTGAATAGCAT
GCGGGGTGGTATGACTCCCTGTGAGGGTAGATGGATGCCACCACCACTCCCTGGAGGTCCAGAAGGCCCCAGAGGTTGCA
TAGACCATGGAGGAGATAGAGATGGATTCCTCAGAAGAGGGTCCCAAGATTCCCAAGGGAATCCATCTGGAGGAGGACAC
ATCCACCACCAAGCTAGACCCTGGCAGTGCCCCAATCTGGGGTGTGAAAACCAGAACTTCACCCAGAGAACAGAATACAA
CCAGTGTAAGGCCTCAAAGCCCAAAGGCTTCCTTCCACCATCCTTTCCACCCCTGGGTATTGACCTTGGCAGGGGTGGCC
CCAGTGGCATGTGGGAAAGAAGAGGTGTCCGCATGGACCACCGTGGTCCTGGTGGAATGTTCAGAGGTGGCCCTGGTGAA
GACAGAGGTGGCTTTCATTGTGGTTGGGGCCTGGACTGAGGTGGCTTTGGTGGAGGAAAATTAGGTGGCCCTAGTGACCC
CCTGGACCTTTGATAGCACAGATGGGAGGCAGAAGAAGTGGATATGGAGGATGTGGAAAAATGGATAAAGGCAAGCACTG
TTGAGCATGCAGAGACTGGCCC

Alignment

ORF - retro_fcat_519 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.75 %
• Parental protein coverage: 63.11 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PPQTGSYSQAPSQ-YSQQSSSYGQQSSFRQDHPSSMGVYGQESGGFSGPGENRSMSGPDNRGRGRGGFDR
          P.....Y...P.Q.Y.Q....YGQQ.......P..............G........G....G.....FD.
Retrocopy PSRASTYATQPTQEYAQTIQAYGQQNCGTYGQPTDVSSTQPQTTATYGQIICATSYGQPTVGYNTPRFDL

Parental  GGMSRGGRGGGRGGMGAGERGGFNKPGGPMDEGPDLDLGPPVDPDEDSDNSAIYVQGLNDNVTLDDLADF
          G..S.GGR.G..GGMGA.E.GGF.KPGG.MD.GPDLDLGP.VDPD.DSD..AIY.QGLND.VTL..LADF
Retrocopy GSISGGGREGVCGGMGAREQGGFSKPGGLMDKGPDLDLGPIVDPDKDSDSIAIYMQGLNDSVTLGNLADF

Parental  F-KQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP
          ..KQC.VVKM.K...QPMI.I.LDKETGKPKG.A.V.YED.PT.KAA.EWF.GK.F.G.KL.V.LA..K.
Retrocopy L<KQCRVVKMKKIIRQPMIPIFLDKETGKPKGSAAVPYEDLPTIKAALEWFVGKKF*GNKLEVPLALRKL

Parental  PMNSMRGGMPPREGRGMPPPLRGGPGGPGGPGGPMGRMGGRGGDRGGFPPRGPRGSRGNPSGGGNVQHRA
          ..NSMRGGM.P.EGR.MPPPL...PGGP.GP.G.....G.R.G....F..RG...S.GNPSGGG...H.A
Retrocopy LVNSMRGGMTPCEGRWMPPPL---PGGPEGPRGCIDHGGDRDG----FLRRGSQDSQGNPSGGGHIHHQA

Parental  GDWQCPNPGCGNQNFAWRTECNQCKAPKPEGFLPPPFPPPGGDRGRGGPGGMRGGRGGLMDRGGPGGMFR
          ..WQCPN.GC.NQNF..RTE.NQCKA.KP.GFLPP.FPP.G.D.GRGGP.GM...RG..MD..GPGGMFR
Retrocopy RPWQCPNLGCENQNFTQRTEYNQCKASKPKGFLPPSFPPLGIDLGRGGPSGMWERRGVRMDHRGPGGMFR

Parental  GGRGGDRGGFRGGRGMDRGGFGGGRRGGPGG-PPGPLMEQMGGRRGGRGGPGKMDKGEHRQERRDRP
          GG.G.DRGGF..G.G.D.GGFGGG..GGP...PPGPL..QMGGRR.G.GG.GKMDKG.H....RD.P
Retrocopy GGPGEDRGGFHCGWGLD*GGFGGGKLGGPSD<PPGPLIAQMGGRRSGYGGCGKMDKGKHC*ACRDWP

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	105.02 RPM
SRP017611_kidney	0.00 RPM	142.12 RPM
SRP017611_liver	0.10 RPM	71.47 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_519 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_519 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 10 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012160	8 retrocopies	retro_cfam_1142, retro_cfam_1183, retro_cfam_1225, retro_cfam_133, retro_cfam_1397, retro_cfam_1736, retro_cfam_1889, retro_cfam_560,
Callithrix jacchus	ENSCJAG00000019987	4 retrocopies	retro_cjac_1716, retro_cjac_2022, retro_cjac_2813, retro_cjac_2911,
Cavia porcellus	ENSCPOG00000009502	1 retrocopy	retro_cpor_1353,
Felis catus	ENSFCAG00000004243	1 retrocopy	retro_fcat_519 ,
Macropus eugenii	ENSMEUG00000008703	1 retrocopy	retro_meug_1424,
Myotis lucifugus	ENSMLUG00000012058	1 retrocopy	retro_mluc_328,
Monodelphis domestica	ENSMODG00000008679	1 retrocopy	retro_mdom_279,
Mustela putorius furo	ENSMPUG00000013432	2 retrocopies	retro_mputfur_56, retro_mputfur_572,
Oryctolagus cuniculus	ENSOCUG00000004432	2 retrocopies	retro_ocun_1346, retro_ocun_242,
Ictidomys tridecemlineatus	ENSSTOG00000023177	1 retrocopy	retro_itri_1892,