RetrogeneDB ID: retro_btau_1856

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:129382028..129382406(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000034266
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS15
• Ensembl ID: ENSBTAG00000019718
• Aliases: None
• Description: 40S ribosomal protein S15 [Source:UniProtKB/Swiss-Prot;Acc:Q56K10]

Sequence

>retro_btau_1856
GTGGCAGAAGTGAAGCAAAAGAAGCAGACCTTCCCCAAGTCCACCTACTTCAGGTGTGGACCTTGACCAGCTGCTGGACA
AGTCCTACAAGCCACTGATGCAAATGTAAAGCACCTGGCAGCAACCATGGCTGAATTGGGCCTGCAGAGGAAGCAACATC
TCATGGCTGAAGTGCCTGCACAAGGCCAGAATGAGGCACCGCCCACAGAGAAGCCTAAGGTTGTGATGACATACCTGTGG
GACATGATCATCCTATCCAAGATGGCAGGTGGCTACAACAGCAAGACATTCACCCAGGTGGAAATCAAGCCTGGCATGAT
TAGACACTGTGCAGGCAGGTTCTCAATGACCTACCAGCCTGTGAAGCCTGAAGCCCCT

Alignment

ORF - retro_btau_1856 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.39 %
• Parental protein coverage: 90.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEVEQKKKRTFRKFTY-RGVDLDQLLDMSYEQLMQLYSARQRRRLN-RGLRRKQHSLLKRLRKAKKDAP
          .AEV.QKK..TF.K.TY..GVDLDQLLD.SY..LMQ..S..Q...LN..GL.RKQH............AP
Retrocopy VAEVKQKKQ-TFPKSTY>SGVDLDQLLDKSYKPLMQM*STWQQPWLN<LGLQRKQHLMAEVPAQGQNEAP

Parental  PMEKPEVVKTHLRDMIILPEMVGSMVGVYNGKTFNQVEIKPEMIGHYLGEFSITYKPVKHGRP
          P.EKP.VV.T.L.DMIIL......M.G.YN.KTF.QVEIKP.MI.H..G.FS.TY.PVK...P
Retrocopy PTEKPKVVMTYLWDMIILSK----MAGGYNSKTFTQVEIKPGMIRHCAGRFSMTYQPVKPEAP

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
ERP005899_liver	0.00 RPM	46.29 RPM
ERP005899_muscle	0.00 RPM	984.31 RPM
SRP017611_brain	0.00 RPM	56.96 RPM
SRP017611_kidney	0.00 RPM	122.81 RPM
SRP017611_liver	0.00 RPM	80.49 RPM
SRP030211_testis	0.00 RPM	63.11 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1856 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1856 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1856 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019718	1 retrocopy	retro_btau_1856 ,
Callithrix jacchus	ENSCJAG00000005632	13 retrocopies	retro_cjac_143, retro_cjac_151, retro_cjac_1517, retro_cjac_1607, retro_cjac_1672, retro_cjac_1714, retro_cjac_2069, retro_cjac_2236, retro_cjac_2596, retro_cjac_2656, retro_cjac_48, retro_cjac_756, retro_cjac_86,
Cavia porcellus	ENSCPOG00000003968	1 retrocopy	retro_cpor_495,
Echinops telfairi	ENSETEG00000008645	1 retrocopy	retro_etel_2,
Felis catus	ENSFCAG00000010769	1 retrocopy	retro_fcat_1570,
Homo sapiens	ENSG00000115268	4 retrocopies	retro_hsap_1484, retro_hsap_2341, retro_hsap_2650, retro_hsap_530,
Gorilla gorilla	ENSGGOG00000002818	4 retrocopies	retro_ggor_1136, retro_ggor_116, retro_ggor_141, retro_ggor_1851,
Monodelphis domestica	ENSMODG00000005119	1 retrocopy	retro_mdom_1335,
Mus musculus	ENSMUSG00000063457	8 retrocopies	retro_mmus_1270, retro_mmus_208, retro_mmus_2734, retro_mmus_2786, retro_mmus_3166, retro_mmus_3642, retro_mmus_520, retro_mmus_917,
Nomascus leucogenys	ENSNLEG00000001651	8 retrocopies	retro_nleu_105, retro_nleu_1858, retro_nleu_1922, retro_nleu_2390, retro_nleu_2465, retro_nleu_2559, retro_nleu_461, retro_nleu_544,
Otolemur garnettii	ENSOGAG00000015776	4 retrocopies	retro_ogar_194, retro_ogar_210, retro_ogar_2237, retro_ogar_96,
Pongo abelii	ENSPPYG00000009317	4 retrocopies	retro_pabe_1233, retro_pabe_2321, retro_pabe_67, retro_pabe_893,
Pan troglodytes	ENSPTRG00000010200	1 retrocopy	retro_ptro_122,
Pteropus vampyrus	ENSPVAG00000003168	2 retrocopies	retro_pvam_382, retro_pvam_926,
Rattus norvegicus	ENSRNOG00000024603	8 retrocopies	retro_rnor_1384, retro_rnor_1711, retro_rnor_1712, retro_rnor_178, retro_rnor_2086, retro_rnor_2114, retro_rnor_2642, retro_rnor_700,
Ictidomys tridecemlineatus	ENSSTOG00000006423	2 retrocopies	retro_itri_722, retro_itri_939,