RetrogeneDB ID: retro_mmus_639

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:43373486..43373918(-)
• Located in intron of: ENSMUSG00000038240

Retrocopy information

• Ensembl ID: ENSMUSG00000089839
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rps19
• Ensembl ID: ENSMUSG00000040952
• Aliases: Rps19, Dsk3
• Description: ribosomal protein S19 [Source:MGI Symbol;Acc:MGI:1333780]

Sequence

>retro_mmus_639
ATGCCTGGAGTTACTGTAAAAGACGTTAACCAGCAGGAGTTCGTCAAAGCTCTGGCAGCCTTCCTCAAAAAGTTCCGGAA
GCTGAAAGTCCCCAAATGGGGAGACACAGTCAAGCTGGCCAAACATAAAAGCTTGCCCCATATGATGAGCTCTGATCCTA
CACACCAGCTGCTTTCACAGCACGGCACCTGTACCTCCGTGGGGGTGCTGGGGTTGGTTCTATGACCAAGATCTATGGAG
GATGGTAGAGATATGGTGTCAGACCCAGCCACTTCAGCCAGAGGCTCTAAGAGTGTGGCCCGCCGGGACCTCCAAGCCCT
GGAGGGGCTGAAAATGGTGGAAAAGGACTAAGATGGGGCCACAAGCTATCACCTCAGGGACAGAGATCTGGACAGGATCA
CTGGACAGGTGGCAGCTGTCAACAAGAAGCAT

Alignment

ORF - retro_mmus_639 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.27 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPGVTVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHK-ELAPYDENWFYTRAASTARHLYLRGG
          MPGVTVKDVNQQEFV.ALAAFLKK..KLKVP.W.DTVKLAKHK..LAPYDE...YT.AA.TARHLYLRGG
Retrocopy MPGVTVKDVNQQEFVKALAAFLKKFRKLKVPKWGDTVKLAKHK<KLAPYDEL*SYTPAAFTARHLYLRGG

Parental  AGVGSMTKIYGGRQRNGVRPSHFS-RGSKSVARRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQV
          AGVGSMTKIYGG..R.GVRPSHFS.RGSKSVARR.LQALEGLKMVEKD.DG.........RDLDRI.GQV
Retrocopy AGVGSMTKIYGGW*RYGVRPSHFS>RGSKSVARRDLQALEGLKMVEKD*DGATSYHLR-DRDLDRITGQV

Parental  AAANKKH
          AA.NKKH
Retrocopy AAVNKKH

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	0.00 RPM	27.33 RPM
SRP007412_cerebellum	0.00 RPM	7.38 RPM
SRP007412_heart	0.00 RPM	33.18 RPM
SRP007412_kidney	0.04 RPM	20.48 RPM
SRP007412_liver	0.00 RPM	25.26 RPM
SRP007412_testis	0.00 RPM	11.30 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_639 was not detected

EST

No EST(s) were mapped for retro_mmus_639 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_3389	207 libraries	373 libraries	413 libraries	64 libraries	15 libraries

The graphical summary, for retro_mmus_639 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_639 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_639 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000028485	10 retrocopies	retro_cfam_1017, retro_cfam_1074, retro_cfam_1155, retro_cfam_1251, retro_cfam_1377, retro_cfam_149, retro_cfam_1998, retro_cfam_2212, retro_cfam_249, retro_cfam_499,
Callithrix jacchus	ENSCJAG00000020243	5 retrocopies	retro_cjac_1968, retro_cjac_2004, retro_cjac_2094, retro_cjac_2324, retro_cjac_3,
Dasypus novemcinctus	ENSDNOG00000002376	4 retrocopies	retro_dnov_1084, retro_dnov_1124, retro_dnov_1838, retro_dnov_2456,
Equus caballus	ENSECAG00000009738	2 retrocopies	retro_ecab_263, retro_ecab_815,
Macaca mulatta	ENSMMUG00000013429	8 retrocopies	retro_mmul_1201, retro_mmul_1358, retro_mmul_1807, retro_mmul_2007, retro_mmul_2443, retro_mmul_404, retro_mmul_607, retro_mmul_691,
Monodelphis domestica	ENSMODG00000010067	3 retrocopies	retro_mdom_1531, retro_mdom_1888, retro_mdom_883,
Mustela putorius furo	ENSMPUG00000007164	4 retrocopies	retro_mputfur_1071, retro_mputfur_1148, retro_mputfur_1470, retro_mputfur_1503,
Mus musculus	ENSMUSG00000040952	15 retrocopies	retro_mmus_1206, retro_mmus_1207, retro_mmus_1528, retro_mmus_1711, retro_mmus_1713, retro_mmus_2095, retro_mmus_2295, retro_mmus_2535, retro_mmus_2850, retro_mmus_3337, retro_mmus_3499, retro_mmus_639 , retro_mmus_643, retro_mmus_684, retro_mmus_899,
Otolemur garnettii	ENSOGAG00000026255	3 retrocopies	retro_ogar_1315, retro_ogar_1663, retro_ogar_2305,
Rattus norvegicus	ENSRNOG00000048199	3 retrocopies	retro_rnor_221, retro_rnor_299, retro_rnor_51,
Sus scrofa	ENSSSCG00000003042	3 retrocopies	retro_sscr_1064, retro_sscr_308, retro_sscr_58,
Ictidomys tridecemlineatus	ENSSTOG00000003502	3 retrocopies	retro_itri_256, retro_itri_751, retro_itri_872,