RetrogeneDB ID: retro_fcat_1927

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:73632920..73633834(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000001874
• Aliases: None
• Description: None

Sequence

>retro_fcat_1927
ATTGTTAATAAGTCCCTTTATGATACATGTTCTGTCTTTGGAAACATTCTTTCTTGTAAAGTAGTAACTGATGAAAGTGG
ATCAAGGGGTTTTGGATTTGTGCATTTTGAGAAATCAGATGCCACTGAAAGGGCTGTTGCAAAGATTAATGGTATTCTGT
TGAAAGGTAGGCGAGTTTTTTTGGGCAGTTTAAACCTCGCAAAAAAAGGGAAGCAGAGCTCAGAGCTAAAGCAAATATAT
TTACCAGTGTTTACATCAAGAATTTTGGAGATGATGTAGATGATGAATGCCTTAGAGAAATTTTTGGTGAGTTTGGTTCT
GTATTAAGTATCAGAGTTATGACTTTTGAAAGTGGAAAATCCAAAGGGTTTGGATTTGTGAGTTTTGAAAATTGTGAAGA
TGCAAAGAAAGCCATTGAAGAAATGAATGGAAAAGTCCTTAATGGAAATCAAATTTATGTTGGTAGAGCCCAGAACAAAC
TGGAGAGACACTATGAACTAAAACACAAATTTGAACAAATAAAGCAGGGTAAACTCACCAAGGGCAAGGAGGCTAACCTC
TATGTGAAAAATCTTGAAGACGAAATTGATGACAAACAACTGAGAAGAGAATTCTCTCTCTATGGGACAATCTCTAGTGC
CAGGGTCATGATGGAGGCAAGCCACAGCAAAGGCTTTGGTTTTGTTTGGTATACAACTCCTGAGGAAGCTAATAAAGCTG
TCATGGAAATGAATGGGAAAATTGTGATCACCAAACCACTGTATGTGGCTATTGCGCAGAGTAAGGATGAGTGCCATGCT
TTCCTCACCAAGAACTATATGGAGAGAATCTCAGCTGTGAGAGATGAAGATAATCCTATAATCAACTATTGAAATACAAC
ATCATCAAATAACTTCATGTCGATTCTTCCTCAG

Alignment

ORF - retro_fcat_1927 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.5 %
• Parental protein coverage: 54.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVG-RFKSRKE
          I.NK.LYDT.S.FGNILSCKVV.DE.GS.G.GFVHFE...A.ERA..K.NG.LL..R.VF.G..FK.RK.
Retrocopy IVNKSLYDTCSVFGNILSCKVVTDESGSRGFGFVHFEKSDATERAVAKINGILLKGRRVFLG<QFKPRKK

Parental  REAELGARAKEFTNVYIKNFGEDMDDERLKDLFGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAV
          REAEL.A.A..FT.VYIKNFG.D.DDE.L...FG.FG..LS..VMT.ESGKSKGFGFVSFE..EDA.KA.
Retrocopy REAELRAKANIFTSVYIKNFGDDVDDECLREIFGEFGSVLSIRVMTFESGKSKGFGFVSFENCEDAKKAI

Parental  DEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFG
          .EMNGK.LNG.QIYVGRAQ.K.ER..ELK.KFEQ.KQ...T.....NLYVKNL.D.IDD..LR.EFS..G
Retrocopy EEMNGKVLNGNQIYVGRAQNKLERHYELKHKFEQIKQGKLTKGKEANLYVKNLEDEIDDKQLRREFSLYG

Parental  TITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMAS
          TI.SA.VMME...SKGFGFV....PEEA.KAV.EMNG.IV.TKPLYVA.AQ.K.E..A.LT..YM.R...
Retrocopy TISSARVMMEASHSKGFGFVWYTTPEEANKAVMEMNGKIVITKPLYVAIAQSKDECHAFLTKNYMERISA

Parental  VRAVPNPVINPYQPAPPSGYFMAAIPQ
          VR...NP.IN.Y.....S..FM...PQ
Retrocopy VRDEDNPIIN-Y*NTTSSNNFMSILPQ

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	118.79 RPM
SRP017611_kidney	0.00 RPM	393.17 RPM
SRP017611_liver	0.00 RPM	532.74 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1927 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1927 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 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000348	1 retrocopy	retro_amel_1650,
Choloepus hoffmanni	ENSCHOG00000008178	1 retrocopy	retro_chof_2531,
Callithrix jacchus	ENSCJAG00000015833	5 retrocopies	retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Cavia porcellus	ENSCPOG00000012917	1 retrocopy	retro_cpor_1324,
Dasypus novemcinctus	ENSDNOG00000008718	2 retrocopies	retro_dnov_1530, retro_dnov_2259,
Felis catus	ENSFCAG00000001874	1 retrocopy	retro_fcat_1927 ,
Felis catus	ENSFCAG00000015254	2 retrocopies	retro_fcat_116, retro_fcat_545,
Homo sapiens	ENSG00000070756	1 retrocopy	retro_hsap_88,
Gorilla gorilla	ENSGGOG00000006785	1 retrocopy	retro_ggor_1986,
Myotis lucifugus	ENSMLUG00000012245	1 retrocopy	retro_mluc_579,
Macaca mulatta	ENSMMUG00000017786	2 retrocopies	retro_mmul_1462, retro_mmul_895,
Monodelphis domestica	ENSMODG00000006222	4 retrocopies	retro_mdom_123, retro_mdom_1867, retro_mdom_216, retro_mdom_43,
Mus musculus	ENSMUSG00000022283	2 retrocopies	retro_mmus_102, retro_mmus_2164,
Oryctolagus cuniculus	ENSOCUG00000004354	1 retrocopy	retro_ocun_13,
Pongo abelii	ENSPPYG00000018790	3 retrocopies	retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Rattus norvegicus	ENSRNOG00000008639	3 retrocopies	retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Sarcophilus harrisii	ENSSHAG00000011267	1 retrocopy	retro_shar_24,
Tarsius syrichta	ENSTSYG00000004229	2 retrocopies	retro_tsyr_1743, retro_tsyr_273,