RetrogeneDB ID: retro_fcat_1375

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C2:136510325..136511488(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000022091
• Aliases: None
• Description: None

Sequence

>retro_fcat_1375
TTCAGTGAGACAGGTGCTGGCAAGCATATGCCCAGGGCAGTGTTGGTAGACCTGGAATCCACAGTCATTGATGAAGTTCG
CACTGGCACCAATAGTCAGCTCTTCCACCCTGAGCAGCTCATCACAGGCAAGGAGAGATGCCACCAATAACTATGCCCAA
GGGCACCACAACACTGACGAGGAAATTACTGACCTTGTCTTGGACCGATTTCAGAAACTGGCCAACCAGGACACAGATCT
ACAAGGGCTTCTTGGTTTTTCCCAGCTATGGAGGGGGAACTAGTTCCTCTGCTGATGAATCATCTCTGTGGATTATGGCA
AGAAGTCCAAGCTAGAGTTCTCCAATTTTCCAGCCCCACAGATTTCCACAGTTGTAGCTGAGCCCTACAATTCCATCCTC
ACTATCCACAACAACCTGGAGCACTCTGATTGTACCTTCAGGGTAGACAGTGAGGCCATCTATGACATCTGTTGTAGGAG
CCTTGATATTGAACACCCAACCTACAGTAGCCTATATAGGTTAATAGATTAAATTGTGTCCTCCATCACTGCTTCCCTCA
GATTTGATGGAACCCTGAATGTCGGTCTGACAGAATTCCAGACGCATCTGGTGCCCTATCCCCACATCTACTTCTCTCTG
GCCACATATGCTCCTGTCATCTCTGCTGAGAAAGCCCACCACAAACAGCTTTCTATAGCAGAGATCACCAATGAATCCTT
TGAGCCAGCCAACCAGATGGTGAAATGTGACCTTCGCCATGGTAAACACATGGCTTATTGCCTGTTGTACCATGGCAACA
TGGTTCCCCAAAGATGCTAATGCTGCCATTGCCACCATCAAGACCAAGTGTACCACCCAGTTTGTGGACTGATGCCCCAT
TGGCCCCAATGTTGGCATTAATTACCAGTTTCCCACTGTGGTACCTGGTAGAGACCTGGCCAAAGTACAGCAGGATGTGT
GCATGCTGAGCAGCATTGCTGAGGCCTGGGTCTGCCTGAACCACACGTATGACCTGATGTATGACAAGTGTGCCTTTGTT
TACTGGTATGTGGATGAGGGTATGAAGGAAGGAGAGTTTCCTAAGGCCTGTGAGGACATGGCTGCCCTTGAGAAGGATTA
TGAGGTGGTTGGTATGGATTGTGTTGGAGGAGAGGTTGAAGAA

Alignment

ORF - retro_fcat_1375 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.28 %
• Parental protein coverage: 87.28 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FSETGAGKHVPRAVFVDLEPTVVDEVRTGTYRQLFHPEQLITGKE-DAANNYARGHYTIGREIVDLVLDR
          FSETGAGKH.PRAV.VDLE.TV.DEVRTGT..QLFHPEQLITGKE.DA.NNYA.GH.....EI.DLVLDR
Retrocopy FSETGAGKHMPRAVLVDLESTVIDEVRTGTNSQLFHPEQLITGKE>DATNNYAQGHHNTDEEITDLVLDR

Parental  IRKLADLCTGLQG-FLIFHSFGGTGSGFASLLMER-LSVDYGK-SKLEFAIYPAPQVSTAVVEPYNSILT
          ..KLA...T.LQG.FL.F.S....G.G..S...E...SVDYGK.SKLEF...PAPQ.ST.V.EPYNSILT
Retrocopy FQKLANQDTDLQG>FLVFPSY---GGGTSSSADES<ISVDYGKKSKLEFSNFPAPQISTVVAEPYNSILT

Parental  THTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLV
          .H..LEHSDC.F.VD.EAIYDIC.R.LDIE.PTY..L.RLI..IVSSITASLRFDG.LNV.LTEFQT.LV
Retrocopy IHNNLEHSDCTFRVDSEAIYDICCRSLDIEHPTYSSLYRLID*IVSSITASLRFDGTLNVGLTEFQTHLV

Parental  PYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPA-QMVKCDPRHGKYMACCMLYRGDVV-PKDVN
          PYP.I.F.LATYAPVISAEKA.H.QLS.AEITN..FEPA.QMVKCD.RHGK.MA.C.LY.G..V.PKD.N
Retrocopy PYPHIYFSLATYAPVISAEKAHHKQLSIAEITNESFEPANQMVKCDLRHGKHMAYCLLYHGNMV>PKDAN

Parental  AAIATIKTKRTIQFVDWCPTGFKVGINYQPPTVVPGGDLARVQRAVCMLSNTTAIAEAWARLDHKFDLMY
          AAIATIKTK.T.QFVD.CP.G..VGINYQ.PTVVPG.DLA.VQ..VCMLS....IAEAW..L.H..DLMY
Retrocopy AAIATIKTKCTTQFVD*CPIGPNVGINYQFPTVVPGRDLAKVQQDVCMLS---SIAEAWVCLNHTYDLMY

Parental  AKRAFVHWYVGEGMEEGEFSEAREDLAALEKDYEEVGVDSVEAEAEE
          .K.AFV.WYV.EGM.EGEF..A.ED.AALEKDYE.VG.D.V..E.EE
Retrocopy DKCAFVYWYVDEGMKEGEFPKACEDMAALEKDYEVVGMDCVGGEVEE

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.10 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1375 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1375 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011042	2 retrocopies	retro_amel_488, retro_amel_518,
Equus caballus	ENSECAG00000014403	1 retrocopy	retro_ecab_318,
Felis catus	ENSFCAG00000022091	2 retrocopies	retro_fcat_1375 , retro_fcat_647,
Felis catus	ENSFCAG00000024852	1 retrocopy	retro_fcat_361,
Felis catus	ENSFCAG00000027011	1 retrocopy	retro_fcat_588,
Felis catus	ENSFCAG00000027277	1 retrocopy	retro_fcat_596,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Mus musculus	ENSMUSG00000067338	1 retrocopy	retro_mmus_3356,