RetrogeneDB ID: retro_fcat_320

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A2:43004052..43005642(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000023308
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000027654
• Aliases: None
• Description: None

Sequence

>retro_fcat_320
ATGGCGGCTGTGAAGACCCTGAACCCTAAGGCCGAGGTAGCCAGAGCCCAGGCGGCACTGGCGGTCAACATCAGCGTGGC
CCGGGGACTGCAGGACGTGCTGAGGACCAACTTGGGGCCTAAAGACACCATGAAGATGCTTGTTTCTGGTGCTGGAGACA
TCAAGCTTACTAAAGATGGCAATGTGCTGCTTCATGAAATGCAAATTCAACACCCAACAGCCTCCTTAATAGCCAAACTA
GCAATAGCCCAGGATGACATAACTGGTGATGGTACCACTTCCAATGTCCTAATCATTGGAGAACTACTGAAACAGGTGGA
TCTCTACATTTCTGAAGGTCTTCATCCCAGAATAATAACAGAAGGATTTGAAGCTGCAAAGGAAAAGGTACTTCAGTTTT
TGGAACAAGTCAAAGTAAGCAAAGAAATGGACAGAGAAACACTTATAGATGTGGCCAGAACATCTCTACGTACTAAAGTG
CATGCTGAACTTGCTGATGTCTTAACAGAGGCTGTGGTGGATTTCATTTTGGTTATCAAAAAACAAGATGAACCTATTGA
CCTCTTCATGGTTGAGATTATTGAGATGAAACATAAATCTGAAACTGATACAAGCTTAATCAGAGGTCTTGTTTTAGACC
ATGGGGCGCAGCATCCTGATATGAAAAAAAGAGCAGAAGATGCATACATCCTCACATGCAATGTGTCATTAGAATATGAA
AAAACAAGTGAATTCTGGCTTTTTTTACAAGAGTGCAGAAGAGAGAGAGAAGCTTGTAAAAGCTGAAAGAAAATTCATTG
ATGATAGAGTTAAAAAAATAATAGAACTGAAAAAGAAAGTCTGTGGTGATTCAGATAAAGGATTTGTGGTTATTAATCAA
AAGGGAATTGACCCCTTTTCCTTAGATGCTCTTGCAAAAGAAGGCATAGTAGCTCTGCGGAGGGCTAAAAGGAGAAATAT
GGAAAGGCTGACTCTTGCTTGTGGTGGAGTAGCTCTAAATTCTTTTGATGACCTAAATCCTGATTGTTTGGGACATGCAG
GACTTGTCTATGAATATACATTGGGAGAAGAGAAATTCACCTTTATTGAGAAATGTAACAACCCTCACTCTGTCACATTA
TTGGTCAAAGGACCAAATAAGCACACACTCACTCAAATCAAGATGCAATAAGAGATGGCTTGAGGGCTGTTAAAAATGCT
ATTGATGATGGCTGTGTAGTTCCAGGTGCTGGTGCAGTGGAAGTGGCAATGGCAGAAGCCTTGATTAAATATAAGCCCAG
TGTAAAGGGCAGGGCCCAGCTTGGAGTGCAAGCATTTGCTGATGCATTGCTCATTATTCCCAAGGTTCTTGCTCAGAATT
CTGGTTTTGACCTTCAAGAAACACTAGTTAAGGTTCAAGCAGAACATTCAGAATCAGGTCAACTTGTAGGTGTGGACTTG
AACACAGGTGAGCCAATGGTAGCTGCTGAAGTAGGCATATGGGATAACTATTGTGTAAAGAAACAGCTTCTTCATTCCTG
CACTGTGATTGCCACCAACATTCTCCTGGTTGATGAGATCATGCGAGCTGGAATGTCTTCTCTAAAAGGT

Alignment

ORF - retro_fcat_320 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.12 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAVKTLNPKAEVARAQAALAVNISAARGLQDVLRTNLGPKGTMKMLVSGAGDIKLTKDGNVLLHEMQIQ
          MAAVKTLNPKAEVARAQAALAVNIS.ARGLQDVLRTNLGPK.TMKMLVSGAGDIKLTKDGNVLLHEMQIQ
Retrocopy MAAVKTLNPKAEVARAQAALAVNISVARGLQDVLRTNLGPKDTMKMLVSGAGDIKLTKDGNVLLHEMQIQ

Parental  HPTASLIAKVATAQDDITGDGTTSNVLIIGELLKQADLYISEGLHPRIITEGFEAAKEKALQFLEQVKVS
          HPTASLIAK.A.AQDDITGDGTTSNVLIIGELLKQ.DLYISEGLHPRIITEGFEAAKEK.LQFLEQVKVS
Retrocopy HPTASLIAKLAIAQDDITGDGTTSNVLIIGELLKQVDLYISEGLHPRIITEGFEAAKEKVLQFLEQVKVS

Parental  KEMDRETLIDVARTSLRTKVHAELADVLTEAVVDSILAIKKQDEPIDLFMVEIMEMKHKSETDTSLIRGL
          KEMDRETLIDVARTSLRTKVHAELADVLTEAVVD.IL.IKKQDEPIDLFMVEI.EMKHKSETDTSLIRGL
Retrocopy KEMDRETLIDVARTSLRTKVHAELADVLTEAVVDFILVIKKQDEPIDLFMVEIIEMKHKSETDTSLIRGL

Parental  VLDHGARHPDMKKRVEDAYILTCNVSLEYEKTEV-NSGFFYKSAEEREKLVKAERKFIEDRVKKIIELKK
          VLDHGA.HPDMKKR.EDAYILTCNVSLEYEKT......F.....E.REKLVKAERKFI.DRVKKIIELKK
Retrocopy VLDHGAQHPDMKKRAEDAYILTCNVSLEYEKTSE>SGFFYKSAEE-REKLVKAERKFIDDRVKKIIELKK

Parental  KVCGDSDKGFVVINQKGIDPFSLDALAKEGIVALRRAKRRNMERLTLACGGVALNSFDDLNPDCLGHAGL
          KVCGDSDKGFVVINQKGIDPFSLDALAKEGIVALRRAKRRNMERLTLACGGVALNSFDDLNPDCLGHAGL
Retrocopy KVCGDSDKGFVVINQKGIDPFSLDALAKEGIVALRRAKRRNMERLTLACGGVALNSFDDLNPDCLGHAGL

Parental  VYEYTLGEEKFTFIEKCNNPRSVTLLVKGPNKHTLTQIK-DAIRDGLRAVKNAIDDGCVVPGAGAVEVAM
          VYEYTLGEEKFTFIEKCNNP.SVTLLVKGPNKHTLTQIK.DAIRDGLRAVKNAIDDGCVVPGAGAVEVAM
Retrocopy VYEYTLGEEKFTFIEKCNNPHSVTLLVKGPNKHTLTQIK<DAIRDGLRAVKNAIDDGCVVPGAGAVEVAM

Parental  AEALIKYKPSVKGRAQLGVQAFADALLIIPKVLAQNSGFDLQETLVKVQAEHSESGQLVGVDLNTGEPMV
          AEALIKYKPSVKGRAQLGVQAFADALLIIPKVLAQNSGFDLQETLVKVQAEHSESGQLVGVDLNTGEPMV
Retrocopy AEALIKYKPSVKGRAQLGVQAFADALLIIPKVLAQNSGFDLQETLVKVQAEHSESGQLVGVDLNTGEPMV

Parental  AAEVGIWDNYCVKKQLLHSCTVIATNILLVDEIMRAGMSSLKG
          AAEVGIWDNYCVKKQLLHSCTVIATNILLVDEIMRAGMSSLKG
Retrocopy AAEVGIWDNYCVKKQLLHSCTVIATNILLVDEIMRAGMSSLKG

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	0.11 RPM	106.97 RPM
SRP017611_kidney	0.72 RPM	108.21 RPM
SRP017611_liver	0.20 RPM	71.27 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_320 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_320 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 18 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016077	1 retrocopy	retro_amel_855,
Canis familiaris	ENSCAFG00000010149	1 retrocopy	retro_cfam_431,
Choloepus hoffmanni	ENSCHOG00000000654	3 retrocopies	retro_chof_1183, retro_chof_1193, retro_chof_150,
Callithrix jacchus	ENSCJAG00000021279	2 retrocopies	retro_cjac_1320, retro_cjac_580,
Dipodomys ordii	ENSDORG00000001249	1 retrocopy	retro_dord_617,
Felis catus	ENSFCAG00000027654	2 retrocopies	retro_fcat_1102, retro_fcat_320 ,
Homo sapiens	ENSG00000146731	2 retrocopies	retro_hsap_2741, retro_hsap_3290,
Gorilla gorilla	ENSGGOG00000011439	1 retrocopy	retro_ggor_133,
Loxodonta africana	ENSLAFG00000012791	1 retrocopy	retro_lafr_808,
Macaca mulatta	ENSMMUG00000015272	1 retrocopy	retro_mmul_2582,
Monodelphis domestica	ENSMODG00000006565	1 retrocopy	retro_mdom_1330,
Nomascus leucogenys	ENSNLEG00000015664	1 retrocopy	retro_nleu_1355,
Oryctolagus cuniculus	ENSOCUG00000017674	1 retrocopy	retro_ocun_468,
Procavia capensis	ENSPCAG00000015532	1 retrocopy	retro_pcap_263,
Pongo abelii	ENSPPYG00000025820	1 retrocopy	retro_pabe_2719,
Pan troglodytes	ENSPTRG00000019206	2 retrocopies	retro_ptro_1854, retro_ptro_2225,
Pteropus vampyrus	ENSPVAG00000001421	1 retrocopy	retro_pvam_663,
Rattus norvegicus	ENSRNOG00000000923	1 retrocopy	retro_rnor_2226,