RetrogeneDB ID: retro_fcat_1102

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:87792144..87793130(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_fcat_1102
ATGGTGGATGTGAAAATCCTGAATCCTGAGGCTGAGGTGGCCCAAGCTCAGGCAGTACTGACAGTCAACATCAGTGTGGT
CTAAGGGTCAGGATTTGCTGAGGACCAACTTGGAGACTAAGTGAGCCGTGGAGATGCTTATTTCTGGTACCAGAGACATT
ACATTTACTAAATATGGTAATGTGATGCTTCTTGAAATACAAATTCAACACCCAACAGCTGCCTTACAAGGCAAAGTAGC
AACAGCCCAGGATGACATAACTGGTGATGACACCACTTCCAATGACCTAATCATTGACAAGTTGCTGAAACAGGCCGTCT
GCATTTCTGAAGGTCTTTATCCCAGAATAACAGAAGGATTTGAAGCTGCAAAGGAAAGGCACTTCAGTTTTTAGAACAAG
CCAAAGTAAACAAAGAAATGGACAGGAAAACATTTATAGATGTGGCTAGAACATCTCCTCGTACTAAAGTGCATGTTGAC
CTTGCTAATGTCTTAACAGAGGCTGTAGTGGACTCCATTTTCACCATTAAAAAACAAGATGAACCAATTGATCTCTCTGT
TGTTGAGATCATGGAGATGAAACATAATTTTGAAACTGATACAAGCTTAATCAGAGGTCTTGTTTGAACCTTGGGGCATG
ACATCCTGATGTGAAAAAAAAAAAAAAAGATGCATATGTCCTTACATGCAATGTGTCATTAGAATATGAAAAAATGGAAG
TAAATTCTGGCTTTATTTTACAAGAGTGCACAAGAAAGAAAGAAACTTGTAAATACTGAAAGAAAACTCATTGAAGATAG
AGTTAAAAAATAATAGAACTGAAAAAGAAAGTCTGCAGTGATTCAGATAAAAGATTTGTTGTTAACCAAAAGGGAATTGA
CCTCATTTCCTTAGATGCTCTAACAAAAGAAGGCATAGTAGCTCTCTGTAGAGCTAAAAGAAGAAATATGGAAAGGCTGA
CCCTTGCTTGCAGTGGAATTCTTTTG

Alignment

ORF - retro_fcat_1102 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.15 %
• Parental protein coverage: 62.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MAAVKTLNPKAEVARAQAALAVNISA-ARGLQDVLRTNLGPKGTMKMLVSGAGDIKLTKDGNVLLHEMQI
          M..VK.LNP.AEVA.AQA.L.VNIS....G.QD.LRTNL..K....ML.SG..DI..TK.GNV.L.E.QI
Retrocopy MVDVKILNPEAEVAQAQAVLTVNISV>SKG-QDLLRTNLETK*AVEMLISGTRDITFTKYGNVMLLEIQI

Parental  QHPTASLIAKVATAQDDITGDGTTSNVLIIGELLKQADLYISEGLHPRIITEGFEAAKE-KALQFLEQVK
          QHPTA.L..KVATAQDDITGD.TTSN.LII..LLKQA...ISEGL.PRI.TEGFEAAKE.KALQFLEQ.K
Retrocopy QHPTAALQGKVATAQDDITGDDTTSNDLIIDKLLKQA-VCISEGLYPRI-TEGFEAAKE<KALQFLEQAK

Parental  VSKEMDRETLIDVARTSLRTKVHAELADVLTEAVVDSILAIKKQDEPIDLFMVEIMEMKHKSETDTSLIR
          V.KEMDR.T.IDVARTS.RTKVH..LA.VLTEAVVDSI..IKKQDEPIDL..VEIMEMKH..ETDTSLIR
Retrocopy VNKEMDRKTFIDVARTSPRTKVHVDLANVLTEAVVDSIFTIKKQDEPIDLSVVEIMEMKHNFETDTSLIR

Parental  GLV-LDHGARHPDMKKRVEDAYILTCNVSLEYEKTEVNSGF-FYKSAEEREKLVKAERKFIEDRVK-KII
          GLV.L..GA.HPD......DAY.LTCNVSLEYEK.EVNSGF.FYKSA.ER.KLV..ERK.IEDRVK.KII
Retrocopy GLV<LNLGA*HPDVXXXXXDAYVLTCNVSLEYEKMEVNSGF>FYKSAQERKKLVNTERKLIEDRVK<KII

Parental  ELKKKVCGDSDKGFVVINQKGIDPFSLDALAKEGIVALRRAKRRNMERLTLACGGVAL
          ELKKKVC.DSDK.FVV.NQKGID..SLDAL.KEGIVAL.RAKRRNMERLTLAC.G..L
Retrocopy ELKKKVCSDSDKRFVV-NQKGIDLISLDALTKEGIVALCRAKRRNMERLTLACSGILL

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	0.00 RPM	108.21 RPM
SRP017611_liver	0.00 RPM	71.27 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1102 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1102 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,