RetrogeneDB ID: retro_fcat_1772

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: F1:16496640..16497048(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000031337
• Aliases: None
• Description: None

Sequence

>retro_fcat_1772
CCTGCCAGGAGAGCAGCAGGGGTCTTATGGGGAGACCGCGTGGGTCCAGAGCATACCTTCCCTGGTGAGTCTGAGGAACG
GGGGCCACACCAGAGCCCTGCAGAAGGCGTGGGGATTAAAGCACAGAGGAGCCTCGGGAAGAACAGGGAGAAGTGGGAGC
AGGCCCAGCTGGCTATTCCTACCAGGCTCCGAACCAAGATGCTGAACAGAGGAGGCAGAGCCGGCACGATGGGGGACGGA
GGCAGAGCTGCTGACACGCAGAACTGGATCCAGGTCCTAGGGCTTCACAGGCCAGACTCTCAGTTAAGAGTCAGGATGAA
GATGGAAAGAGAGCCAACAGCACAGAGCAACCACAGCTCTGTTTCCATGCGCCCAGAACATGCTAAACTGGTGAGAAGGG
CAAAGGCT

Alignment

ORF - retro_fcat_1772 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.74 %
• Parental protein coverage: 74.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PARMAAVVLGRDTMGPERIFPNQTEELGPHQGPTEGTG-DWSSEEPEEEQEETGAGPAGYSYQPLNQDPE
          PAR.AA.VL..D..GPE..FP...EE.GPHQ.P.EG.G.D.S.EEP.EEQ.E.GAGPAGYSYQ..NQD.E
Retrocopy PARRAAGVLWGDRVGPEHTFPGESEERGPHQSPAEGVG<D*STEEPREEQGEVGAGPAGYSYQAPNQDAE

Parental  -PEEVELA-PVGDGEDVVADIQDRIQALGLHLPDPPLESEDEEEEGATGLSNHSSIPMDPEHVELVKRTM
          ..EE.E.A...GDG....AD.Q..IQ.LGLH.PD..L......E...T..SNHSS..M.PEH..LV.R..
Retrocopy <TEEAEPA<TMGDG-GRAADTQNWIQVLGLHRPDSQLRVRMKMEREPTAQSNHSSVSMRPEHAKLVRRAK

Parental  A
          A
Retrocopy A

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	47.97 RPM
SRP017611_kidney	0.00 RPM	39.57 RPM
SRP017611_liver	0.00 RPM	16.78 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1772 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1772 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012655	1 retrocopy	retro_amel_1620,
Bos taurus	ENSBTAG00000005536	1 retrocopy	retro_btau_240,
Canis familiaris	ENSCAFG00000001756	1 retrocopy	retro_cfam_1643,
Callithrix jacchus	ENSCJAG00000004894	2 retrocopies	retro_cjac_2054, retro_cjac_824,
Cavia porcellus	ENSCPOG00000022111	1 retrocopy	retro_cpor_1530,
Echinops telfairi	ENSETEG00000002439	1 retrocopy	retro_etel_236,
Felis catus	ENSFCAG00000031337	1 retrocopy	retro_fcat_1772 ,
Loxodonta africana	ENSLAFG00000013881	1 retrocopy	retro_lafr_60,
Myotis lucifugus	ENSMLUG00000012138	2 retrocopies	retro_mluc_1819, retro_mluc_851,
Monodelphis domestica	ENSMODG00000019002	1 retrocopy	retro_mdom_878,
Oryctolagus cuniculus	ENSOCUG00000001565	2 retrocopies	retro_ocun_1312, retro_ocun_1446,
Pelodiscus sinensis	ENSPSIG00000002330	1 retrocopy	retro_psin_56,
Pteropus vampyrus	ENSPVAG00000008711	1 retrocopy	retro_pvam_266,
Rattus norvegicus	ENSRNOG00000017144	2 retrocopies	retro_rnor_716, retro_rnor_961,
Tupaia belangeri	ENSTBEG00000012294	2 retrocopies	retro_tbel_1462, retro_tbel_3528,
Tursiops truncatus	ENSTTRG00000006996	1 retrocopy	retro_ttru_357,