RetrogeneDB ID: retro_fcat_456

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A3:127274607..127275200(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000029051
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS8
• Ensembl ID: ENSFCAG00000022996
• Aliases: None
• Description: ribosomal protein S8 [Source:HGNC Symbol;Acc:10441]

Sequence

>retro_fcat_456
ATGGGCATCTCTTGGGACAACTGGCACAGGAGTTCCAAGACCGGGGGCAGGAGAAAGCTCTACCACAGGAAGCACGAGCT
GGGACGCCCCATTGCCAACACTAAGATTGGCCCCCACCGCATACACGCAGTTCAAGTTCCGGGAGGCAGTAAGTACTGTG
CCTTGAGGCTGGACCTGGGAAACTTTTCCTGGGGCTCCAAGTGTTGTATGCACAAAACAAGGATTGCTGAAGTTGTCCAC
ATGCATCCAACAACCGACTGGTCCACACCAAGCCCCTGGTGGAGGACTGGATCGTGTTCACTGACAGCACCTGGTACCCA
CAGTGGTACGGGTCCCCCTGTGCACTGCTCCCGGGCCACAAGAAGGGGACCAAGCTGGTTCCCGAGGAGGAAGGGATTTT
AACCAAAAAACATTCAAAGAAAATTCAGGAGAAATATGATGAAAGGAAAAAGAATGCCAAAATCAGCAGTCTTCTGGAGG
AGCCGTTCCAGCAGGGCGAGTTCCTTGCACGCATGGCTTCAAGACCAGGCCAGTGTGGCCCAGCAGATGGCTGTGTGCTA
GAAGGCAAGGAGCTCGAGCTCCATCTTAGGAAA

Alignment

ORF - retro_fcat_456 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.87 %
• Parental protein coverage: 99.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRLDVGNFSWGSE
          MGIS.DNWH...KTGG.RK.YH..RK.ELGRP.ANTKIGP.RIH.V.V.GG.K.Y.ALRLD.GNFSWGS.
Retrocopy MGISWDNWHRSSKTGGRRKLYH--RKHELGRPIANTKIGPHRIHAVQVPGGSK-YCALRLDLGNFSWGSK

Parental  CCTRKTRIIDVVY-NASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPLGRKKGAKLTPEEEEILNK
          CC..KTRI..VV...ASNN.LV.TK.LV...IV..DST.Y.QWY.S..AL..G.KKG.KL.PEEE.IL..
Retrocopy CCMHKTRIAEVVH<HASNNRLVHTKPLVEDWIVFTDSTWYPQWYGSPCALLPGHKKGTKLVPEEEGILTX

Parental  KRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPGQCGRADGYVLEGKELEFYLRK
          ...................SSLLEE.FQQG..LA..ASRPGQCG.ADG.VLEGKELE..LRK
Retrocopy XXXXXXXXXXXXXXXXXXXSSLLEEPFQQGEFLARMASRPGQCGPADGCVLEGKELELHLRK

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	88.26 RPM
SRP017611_kidney	0.00 RPM	417.90 RPM
SRP017611_liver	0.00 RPM	208.75 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_456 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_456 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 30 parental genes, and 203 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015697	1 retrocopy	retro_acar_124,
Ailuropoda melanoleuca	ENSAMEG00000014147	3 retrocopies	retro_amel_1883, retro_amel_373, retro_amel_972,
Bos taurus	ENSBTAG00000015285	2 retrocopies	retro_btau_1388, retro_btau_1593,
Canis familiaris	ENSCAFG00000004745	8 retrocopies	retro_cfam_1336, retro_cfam_1662, retro_cfam_1730, retro_cfam_2139, retro_cfam_2177, retro_cfam_261, retro_cfam_589, retro_cfam_791,
Choloepus hoffmanni	ENSCHOG00000008785	10 retrocopies	retro_chof_1197, retro_chof_1258, retro_chof_1466, retro_chof_1638, retro_chof_2066, retro_chof_2617, retro_chof_2633, retro_chof_274, retro_chof_331, retro_chof_951,
Callithrix jacchus	ENSCJAG00000004197	5 retrocopies	retro_cjac_1068, retro_cjac_181, retro_cjac_3138, retro_cjac_6, retro_cjac_951,
Cavia porcellus	ENSCPOG00000000723	3 retrocopies	retro_cpor_1099, retro_cpor_335, retro_cpor_621,
Dasypus novemcinctus	ENSDNOG00000025236	3 retrocopies	retro_dnov_1717, retro_dnov_802, retro_dnov_908,
Dipodomys ordii	ENSDORG00000009287	1 retrocopy	retro_dord_429,
Echinops telfairi	ENSETEG00000004002	13 retrocopies	retro_etel_1000, retro_etel_1063, retro_etel_1201, retro_etel_147, retro_etel_1495, retro_etel_1733, retro_etel_1864, retro_etel_1941, retro_etel_2050, retro_etel_2060, retro_etel_302, retro_etel_368, retro_etel_395,
Felis catus	ENSFCAG00000022996	4 retrocopies	retro_fcat_1222, retro_fcat_200, retro_fcat_456 , retro_fcat_962,
Gorilla gorilla	ENSGGOG00000005645	5 retrocopies	retro_ggor_1127, retro_ggor_1170, retro_ggor_1357, retro_ggor_1465, retro_ggor_556,
Loxodonta africana	ENSLAFG00000027596	3 retrocopies	retro_lafr_531, retro_lafr_647, retro_lafr_904,
Macropus eugenii	ENSMEUG00000001388	1 retrocopy	retro_meug_119,
Microcebus murinus	ENSMICG00000008024	4 retrocopies	retro_mmur_1180, retro_mmur_1434, retro_mmur_1501, retro_mmur_380,
Myotis lucifugus	ENSMLUG00000001559	30 retrocopies	retro_mluc_1114, retro_mluc_1132, retro_mluc_1165, retro_mluc_1277, retro_mluc_1288, retro_mluc_1418, retro_mluc_1467, retro_mluc_1476, retro_mluc_1486, retro_mluc_1634, retro_mluc_1656, retro_mluc_1689, retro_mluc_1808, retro_mluc_1911, retro_mluc_1938, retro_mluc_2043, retro_mluc_2055, retro_mluc_2085, retro_mluc_2111, retro_mluc_2153, retro_mluc_2182, retro_mluc_2209, retro_mluc_2414, retro_mluc_460, retro_mluc_662, retro_mluc_730, retro_mluc_773, retro_mluc_820, retro_mluc_821, retro_mluc_906,
Macaca mulatta	ENSMMUG00000015270	2 retrocopies	retro_mmul_275, retro_mmul_70,
Monodelphis domestica	ENSMODG00000028389	1 retrocopy	retro_mdom_998,
Mustela putorius furo	ENSMPUG00000013485	6 retrocopies	retro_mputfur_334, retro_mputfur_337, retro_mputfur_493, retro_mputfur_780, retro_mputfur_908, retro_mputfur_986,
Mus musculus	ENSMUSG00000047675	33 retrocopies	retro_mmus_1003, retro_mmus_1067, retro_mmus_1184, retro_mmus_1694, retro_mmus_1755, retro_mmus_1796, retro_mmus_2001, retro_mmus_2002, retro_mmus_2003, retro_mmus_2031, retro_mmus_2132, retro_mmus_2173, retro_mmus_2264, retro_mmus_2732, retro_mmus_2772, retro_mmus_2847, retro_mmus_2861, retro_mmus_293, retro_mmus_2956, retro_mmus_2998, retro_mmus_3018, retro_mmus_3052, retro_mmus_3057, retro_mmus_3279, retro_mmus_3307, retro_mmus_3521, retro_mmus_364, retro_mmus_392, retro_mmus_548, retro_mmus_559, retro_mmus_596, retro_mmus_646, retro_mmus_876,
Nomascus leucogenys	ENSNLEG00000014147	1 retrocopy	retro_nleu_34,
Oryctolagus cuniculus	ENSOCUG00000012476	1 retrocopy	retro_ocun_168,
Otolemur garnettii	ENSOGAG00000006922	16 retrocopies	retro_ogar_1156, retro_ogar_1746, retro_ogar_1895, retro_ogar_2501, retro_ogar_2529, retro_ogar_2556, retro_ogar_2699, retro_ogar_2723, retro_ogar_2947, retro_ogar_308, retro_ogar_3291, retro_ogar_3436, retro_ogar_394, retro_ogar_521, retro_ogar_730, retro_ogar_805,
Pongo abelii	ENSPPYG00000001426	1 retrocopy	retro_pabe_147,
Pteropus vampyrus	ENSPVAG00000009859	10 retrocopies	retro_pvam_1285, retro_pvam_1315, retro_pvam_1345, retro_pvam_403, retro_pvam_419, retro_pvam_463, retro_pvam_514, retro_pvam_578, retro_pvam_685, retro_pvam_991,
Rattus norvegicus	ENSRNOG00000018768	2 retrocopies	retro_rnor_222, retro_rnor_235,
Sarcophilus harrisii	ENSSHAG00000000111	5 retrocopies	retro_shar_408, retro_shar_472, retro_shar_480, retro_shar_636, retro_shar_667,
Sus scrofa	ENSSSCG00000003930	4 retrocopies	retro_sscr_353, retro_sscr_550, retro_sscr_607, retro_sscr_919,
Tupaia belangeri	ENSTBEG00000000418	20 retrocopies	retro_tbel_1066, retro_tbel_1537, retro_tbel_1538, retro_tbel_163, retro_tbel_1699, retro_tbel_2356, retro_tbel_244, retro_tbel_2580, retro_tbel_3058, retro_tbel_3230, retro_tbel_3478, retro_tbel_3905, retro_tbel_3950, retro_tbel_4241, retro_tbel_4250, retro_tbel_4530, retro_tbel_552, retro_tbel_803, retro_tbel_827, retro_tbel_934,
Tarsius syrichta	ENSTSYG00000005525	5 retrocopies	retro_tsyr_1412, retro_tsyr_1507, retro_tsyr_2176, retro_tsyr_552, retro_tsyr_734,