RetrogeneDB ID: retro_mmus_392

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:177786856..177787468(+)
• Located in intron of: ENSMUSG00000015961

Retrocopy information

• Ensembl ID: ENSMUSG00000089657
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rps8
• Ensembl ID: ENSMUSG00000047675
• Aliases: None
• Description: ribosomal protein S8 [Source:MGI Symbol;Acc:MGI:98166]

Sequence

>retro_mmus_392
GGCATCTCTCAGTACAACTGGCACAAGTGCCGCAAGACCGGCGGTAAGCAAAAACCCTACCACAAGAAGCGGAAGTATGA
GCTGGGACCCTGCTGCCAACACGAAGATTGGCCCTCGCCGCATATACATAGTCCGAGTTCGAGGACAAATAAGAAGTACC
GTGCCCTGAGATTGGATGTGGGGAACTTTTCCTGGGGCTCTGAGTGTTGTACTCGCACAAGGATCATTGATGCTGTCTAC
AATGCATCCAACAACGAGCTTGTCCGCACCAAGACCCTGGTGAAGAACTACATCGTGCTTATTGACAGCACGCCTTACGG
ACAGTGGTACGAGTCCCACTATGCACTGCCCCTGGGCTGCAAGAAGGGGGCCAAGCTGACTCCTGAGGAGGAAGAGATTT
TAAACAAAAAATGATCAAAGAAAATTCAAAAGAAATACGACGAAAGGAAAAAGAATGCCAAAATCAGCAGTCTCCTGGAG
CAGTTCCAGCAGGGCAAGCTTCTAGCCTGTATTGCCTCAAGACCAGGCCAGTGTGGCAGAGCAGACCGCTATGTGCTCGA
AGGCAAGGAGCTGGAGTTCTATCTGCGGAAGATCAAAGCCCGGAAAGGCAAA

Alignment

ORF - retro_mmus_392 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.9 %
• Parental protein coverage: 99.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGP-RRIHTVRVRG-GNKKYRALRLDVGNFSWGS
          GIS..NWHK.RKTGGK.KPYHKKRKYELG.P.......P.RRI..VRVRG..NKKYRALRLDVGNFSWGS
Retrocopy GISQYNWHKCRKTGGKQKPYHKKRKYELG-PCCQHEDWP>RRIYIVRVRG<TNKKYRALRLDVGNFSWGS

Parental  ECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPLGRKKGAKLTPEEEEILNK
          ECCTR.TRIID.VYNASNNELVRTKTLVKN.IVLIDSTPY.QWYESHYALPLG.KKGAKLTPEEEEI...
Retrocopy ECCTR-TRIIDAVYNASNNELVRTKTLVKNYIVLIDSTPYGQWYESHYALPLGCKKGAKLTPEEEEIXXX

Parental  KRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPGQCGRADGYVLEGKELEFYLRKIKARKGK
          ...............NAKISSLL.EQFQQGKLLACIASRPGQCGRAD.YVLEGKELEFYLRKIKARKGK
Retrocopy XXXXXXXXXXXXXXXNAKISSLL-EQFQQGKLLACIASRPGQCGRADRYVLEGKELEFYLRKIKARKGK

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
SRP007412_brain	0.05 RPM	63.94 RPM
SRP007412_cerebellum	0.17 RPM	45.81 RPM
SRP007412_heart	0.03 RPM	115.74 RPM
SRP007412_kidney	0.12 RPM	96.29 RPM
SRP007412_liver	0.05 RPM	88.04 RPM
SRP007412_testis	0.05 RPM	46.29 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_392 was not detected

EST

No EST(s) were mapped for retro_mmus_392 retrocopy.

TSS

No TSS is located nearby retro_mmus_392 retrocopy 5' end.

Lab

retro_mmus_392 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_392 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 116 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015697	1 retrocopy	retro_acar_124,
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,
Dipodomys ordii	ENSDORG00000009287	1 retrocopy	retro_dord_429,
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,
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,
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,
Rattus norvegicus	ENSRNOG00000018768	2 retrocopies	retro_rnor_222, retro_rnor_235,