RetrogeneDB ID: retro_fcat_1116

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:118367815..118368838(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000008734
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TMEM185A
• Ensembl ID: ENSFCAG00000024483
• Aliases: LOC101093254, TMEM185A
• Description: transmembrane protein 185A [Source:HGNC Symbol;Acc:17125]

Sequence

>retro_fcat_1116
TTCAACCCGAGTAAGTTCCTCATCTACGCCTGCCTGCTGCTCTTCTCCGTGCTGCTGCCCCTCCGCCTGGACGGCGTCAT
CCAGTGGAGCTACTGGGCGGTCTTCGCCCCCATATGGCTGTGGAAGCTCCTGGTCATCGCCGGCGCCTCAGTGGGCGCAG
GCGTTTGGGCCCGCAACCCTCGATACCGCACGGAGGGGGAGGCCTGCGTGGAGTTCAAAGCCATGTTGATCGCCGTGGCT
ATCCACCTGCTGCTGCTCATGTTCGAAGTCCTGGTCTGCGACAGGGTGGAGAGGGGGACCCACTTCTGGCTGCTGGTCTT
CATGCCACTTTTTTTCGTATCCCCAGTGTCCGTGGCCGCCTGCGTCTGGGGCTTCCGACACGATAGGTCCCTAGAGCTGG
AGATCTTGTGCTCTGTCAACATCCTGCAGTTCATCTTCATCGCCCTAAGGCTGGACAGGATTATCCACTGGCCGTGGCTG
GTGGTGTTCGTGCCCCTGTGGATTCTCATGTCGTTCCTCTGCCTAGTCGTCCTCTATTACATCGTCTGGTCCCTCCTGTT
CCTTCGATCCTTGGATGTCGTTGCGGAACAGCGAAGGACACATGTGACCATGGCCATCAGCTGGATAACGATTGTCGTGC
CCCTGCTCACTTTTGAGGTTCTGCTCGTTCACAGATTGGACGGCCACAATACATTCTCTTACATCTCCATATTTGTCCCC
CTTTGGCTTTCATTAATAACTTTAATGGCCACGACGTTTAGGCGGAAGGGAGGCAACCATTGGTGGTTTGGGATTCGCAG
AGATTTCTGTCAGTTTCTGCTTGAAATTTTCCCATTTCTAAGAGAATATGGGAACATTTCCTATGATCTACATCATGAAG
ATAGTGAAGAAGCTGAAGAAACATCAGTCCCAGATGCTCCTAAAATTGCTCCGATGTTTGGAAAGAAGGCCAGGGTAGTT
ATAACCCAGAGTCCTGGAAAGTATGTTCCCCCGCCTCCCAAGTTAAATATTGATATGCCAGAT

Alignment

ORF - retro_fcat_1116 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.15 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FSPSKFLIYACLLLFSVLLALRLDGIIQWSYWAVFAPIWLWKLMVIVGASVGTGVWARNPQYRAEGETCV
          F.PSKFLIYACLLLFSVLL.LRLDG.IQWSYWAVFAPIWLWKL.VI.GASVG.GVWARNP.YR.EGE.CV
Retrocopy FNPSKFLIYACLLLFSVLLPLRLDGVIQWSYWAVFAPIWLWKLLVIAGASVGAGVWARNPRYRTEGEACV

Parental  EFKAMLIAVGIHLLLLMFEVLVCDRIERGSHFWLLVFMPLFFVSPVSVAACVWGFRHDRSLELEILCSVN
          EFKAMLIAV.IHLLLLMFEVLVCDR.ERG.HFWLLVFMPLFFVSPVSVAACVWGFRHDRSLELEILCSVN
Retrocopy EFKAMLIAVAIHLLLLMFEVLVCDRVERGTHFWLLVFMPLFFVSPVSVAACVWGFRHDRSLELEILCSVN

Parental  ILQFIFIALRLDKIIHWPWLVVCVPLWILMSFLCLVVLYYIVWSVLFLRSMDVIAEQRRTHITMALSWMT
          ILQFIFIALRLD.IIHWPWLVV.VPLWILMSFLCLVVLYYIVWS.LFLRS.DV.AEQRRTH.TMA.SW.T
Retrocopy ILQFIFIALRLDRIIHWPWLVVFVPLWILMSFLCLVVLYYIVWSLLFLRSLDVVAEQRRTHVTMAISWIT

Parental  IVVPLLTFEILLVHKLDGHNAFSCIPIFVPLWLSLITLMATTFGQKGGNHWWFGIRKDFCQFLLEIFPFL
          IVVPLLTFE.LLVH.LDGHN.FS.I.IFVPLWLSLITLMATTF..KGGNHWWFGIR.DFCQFLLEIFPFL
Retrocopy IVVPLLTFEVLLVHRLDGHNTFSYISIFVPLWLSLITLMATTFRRKGGNHWWFGIRRDFCQFLLEIFPFL

Parental  REYGNISYDLHHEDTEETEETPVPEPPKIAPMFRKKTRVVITQSPGKYVLPPPKLNIEMPD
          REYGNISYDLHHED.EE.EET.VP..PKIAPMF.KK.RVVITQSPGKYV.PPPKLNI.MPD
Retrocopy REYGNISYDLHHEDSEEAEETSVPDAPKIAPMFGKKARVVITQSPGKYVPPPPKLNIDMPD

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	3.56 RPM	58.30 RPM
SRP017611_kidney	3.71 RPM	17.62 RPM
SRP017611_liver	4.04 RPM	9.20 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1116 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1116 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 22 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008637	1 retrocopy	retro_acar_65,
Ailuropoda melanoleuca	ENSAMEG00000009351	1 retrocopy	retro_amel_8,
Bos taurus	ENSBTAG00000006818	1 retrocopy	retro_btau_1,
Canis familiaris	ENSCAFG00000019103	1 retrocopy	retro_cfam_159,
Dasypus novemcinctus	ENSDNOG00000011864	1 retrocopy	retro_dnov_2451,
Dipodomys ordii	ENSDORG00000015027	1 retrocopy	retro_dord_67,
Equus caballus	ENSECAG00000009399	1 retrocopy	retro_ecab_426,
Felis catus	ENSFCAG00000024483	1 retrocopy	retro_fcat_1116 ,
Homo sapiens	ENSG00000155984	1 retrocopy	retro_hsap_104,
Gorilla gorilla	ENSGGOG00000024268	1 retrocopy	retro_ggor_189,
Loxodonta africana	ENSLAFG00000003044	1 retrocopy	retro_lafr_898,
Microcebus murinus	ENSMICG00000004639	1 retrocopy	retro_mmur_106,
Macaca mulatta	ENSMMUG00000002888	1 retrocopy	retro_mmul_310,
Mustela putorius furo	ENSMPUG00000011896	1 retrocopy	retro_mputfur_46,
Mus musculus	ENSMUSG00000073139	1 retrocopy	retro_mmus_358,
Nomascus leucogenys	ENSNLEG00000013487	1 retrocopy	retro_nleu_2723,
Otolemur garnettii	ENSOGAG00000016414	1 retrocopy	retro_ogar_88,
Procavia capensis	ENSPCAG00000009160	1 retrocopy	retro_pcap_260,
Pongo abelii	ENSPPYG00000020809	1 retrocopy	retro_pabe_118,
Pteropus vampyrus	ENSPVAG00000013822	1 retrocopy	retro_pvam_30,
Rattus norvegicus	ENSRNOG00000011047	1 retrocopy	retro_rnor_6,
Tursiops truncatus	ENSTTRG00000000643	1 retrocopy	retro_ttru_868,