RetrogeneDB ID: retro_fcat_1829

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: F2:81758504..81758885(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARF1
• Ensembl ID: ENSFCAG00000029374
• Aliases: None
• Description: ADP-ribosylation factor 1 [Source:HGNC Symbol;Acc:652]

Sequence

>retro_fcat_1829
ATGGGAAGTATCTTCACAAACCTCTTCAAGGGCCTTTTTGGCAAAAAGAGAGACGTGCATTCTCACGGTGGGCTTGGACG
CTGCAGGGAAGACCACCATCCTGTACAAACTGAAGCTGGGTGAGATGGGGACCACCATTCCCACCACAGGCTTCCACGTG
GAGACCGTGGAGTAGGAGAACATCAGCTTCACCGTGCGCGACGTGGGCGGCCAGGACAAGATCGGCCCCTGTGGCGCCAC
TTCCGGAATACACAAGGCCTCATCCTCCTGGTGGACAGCAAGGTCAGAGAGGGCGTGAAGGAGGCCCGTGAGGAGCTCGT
GACGATGCTGGCGGGGGACGAGCTCAGGGATGCCGTCCGGCTGGTGTTCGCCAGCAAGCAG

Alignment

ORF - retro_fcat_1829 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.23 %
• Parental protein coverage: 64. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGNIFANLFKGLFGKK-EMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVG
          MG.IF.NLFKGLFGKK.E..IL.VGLDAAGKTTILYKLKLGE..TTIPT.GF.VETVE..NISFTV.DVG
Retrocopy MGSIFTNLFKGLFGKK>ETCILTVGLDAAGKTTILYKLKLGEMGTTIPTTGFHVETVE*ENISFTVRDVG

Parental  GQDKI-RPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQ
          GQDKI.RPLWRH.F.NTQGLI..VDS..RE.V.EAREEL..MLA.DELRDAV.LVFA.KQ
Retrocopy GQDKI<RPLWRH-FRNTQGLILLVDSKVREGVKEAREELVTMLAGDELRDAVRLVFASKQ

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	86.54 RPM
SRP017611_kidney	0.00 RPM	119.65 RPM
SRP017611_liver	0.00 RPM	47.01 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1829 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1829 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 16 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016671	10 retrocopies	retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Cavia porcellus	ENSCPOG00000021174	1 retrocopy	retro_cpor_1310,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Felis catus	ENSFCAG00000000088	2 retrocopies	retro_fcat_2, retro_fcat_59,
Felis catus	ENSFCAG00000029374	1 retrocopy	retro_fcat_1829 ,
Homo sapiens	ENSG00000143761	3 retrocopies	retro_hsap_1008, retro_hsap_1160, retro_hsap_3763,
Gallus gallus	ENSGALG00000005393	1 retrocopy	retro_ggal_7,
Gorilla gorilla	ENSGGOG00000011263	5 retrocopies	retro_ggor_161, retro_ggor_2531, retro_ggor_3071, retro_ggor_801, retro_ggor_906,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Myotis lucifugus	ENSMLUG00000007020	6 retrocopies	retro_mluc_1631, retro_mluc_242, retro_mluc_2605, retro_mluc_428, retro_mluc_511, retro_mluc_876,
Mus musculus	ENSMUSG00000048076	1 retrocopy	retro_mmus_1718,
Oryctolagus cuniculus	ENSOCUG00000023645	2 retrocopies	retro_ocun_1137, retro_ocun_247,
Pan troglodytes	ENSPTRG00000002066	2 retrocopies	retro_ptro_112, retro_ptro_5,
Tupaia belangeri	ENSTBEG00000009218	9 retrocopies	retro_tbel_1943, retro_tbel_2224, retro_tbel_2310, retro_tbel_2358, retro_tbel_2662, retro_tbel_2770, retro_tbel_3103, retro_tbel_4217, retro_tbel_4624,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,
Tursiops truncatus	ENSTTRG00000014186	2 retrocopies	retro_ttru_1679, retro_ttru_347,