RetrogeneDB ID: retro_mmus_57

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:97760129..97760588(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000069117
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Rps18
• Ensembl ID: ENSMUSG00000008668
• Aliases: Rps18, H-2Ke3, H2-Ke3, Ke-3, ke3
• Description: ribosomal protein S18 [Source:MGI Symbol;Acc:MGI:98146]

Sequence

>retro_mmus_57
ATGTCTCTAGTGATCCCTGAGAAGTTCCAGCACATTTTGCGAGTACTCAACACCAACATCGATGGGCGGCGGAAAATAGC
CTTCGCCATCACTGCCATTAAGGGCGTGGGGCGGAGATATGCTCATGTGGTGTTGAGGAAAGCAGACATCGACCTCACCA
AGAGGGCTGGAGAACTCACGGAGGACGAGGTGGAGCGAGTGATCACCATCATGCAGAACCCACGACAGTACAAGATCCCA
GACTGGTTCCTGAACAGACAGAAGGATGTGAAGGATGGGAAGTACAGCCAGGTTCTGGCCAACGGTCTAGACAACAAGCT
GCGTGAGGACCTGGAGCGGCTGAAGAAAATTCGAGCCCATAGAGGGCTGCACCACTTTTGGGGCCTTCGTGTCCGCGGTC
AGCACACCAAGACCACTGGCCGCAGGGGCCAAACTGTGGGTGTATCCAAGAAGAAATGA

Alignment

ORF - retro_mmus_57 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITI
          MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITI
Retrocopy MSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITI

Parental  MQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLRHFWGLRVRGQHTKTTG
          MQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGL.HFWGLRVRGQHTKTTG
Retrocopy MQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLHHFWGLRVRGQHTKTTG

Parental  RRGRTVGVSKKK
          RRG.TVGVSKKK
Retrocopy RRGQTVGVSKKK

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	4.95 RPM	27.31 RPM
SRP007412_cerebellum	24.19 RPM	14.59 RPM
SRP007412_heart	0.09 RPM	70.88 RPM
SRP007412_kidney	45.18 RPM	48.64 RPM
SRP007412_liver	37.00 RPM	69.75 RPM
SRP007412_testis	45.19 RPM	28.22 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_57 in 2 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	13:97760378..97760593
ENCFF001YKA	POLR2A	13:97760207..97760588

EST

No EST(s) were mapped for retro_mmus_57 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_31913	641 libraries	390 libraries	39 libraries	2 libraries	0 libraries

The graphical summary, for retro_mmus_57 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_57 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_57 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000950	7 retrocopies	retro_cfam_1311, retro_cfam_1607, retro_cfam_2132, retro_cfam_414, retro_cfam_522, retro_cfam_789, retro_cfam_856,
Dipodomys ordii	ENSDORG00000013825	6 retrocopies	retro_dord_185, retro_dord_326, retro_dord_426, retro_dord_481, retro_dord_50, retro_dord_772,
Gorilla gorilla	ENSGGOG00000006571	5 retrocopies	retro_ggor_1496, retro_ggor_2310, retro_ggor_344, retro_ggor_77, retro_ggor_93,
Loxodonta africana	ENSLAFG00000032173	1 retrocopy	retro_lafr_1171,
Macaca mulatta	ENSMMUG00000003867	1 retrocopy	retro_mmul_2198,
Monodelphis domestica	ENSMODG00000014210	4 retrocopies	retro_mdom_1041, retro_mdom_1286, retro_mdom_1514, retro_mdom_642,
Mus musculus	ENSMUSG00000008668	2 retrocopies	retro_mmus_57 , retro_mmus_66,
Nomascus leucogenys	ENSNLEG00000006840	10 retrocopies	retro_nleu_1074, retro_nleu_1161, retro_nleu_1176, retro_nleu_1466, retro_nleu_219, retro_nleu_2572, retro_nleu_2616, retro_nleu_525, retro_nleu_60, retro_nleu_737,
Oryctolagus cuniculus	ENSOCUG00000010546	1 retrocopy	retro_ocun_31,
Procavia capensis	ENSPCAG00000005854	2 retrocopies	retro_pcap_235, retro_pcap_319,
Pongo abelii	ENSPPYG00000025953	14 retrocopies	retro_pabe_1138, retro_pabe_128, retro_pabe_1481, retro_pabe_1482, retro_pabe_1813, retro_pabe_1881, retro_pabe_2303, retro_pabe_2407, retro_pabe_2663, retro_pabe_2833, retro_pabe_2967, retro_pabe_3013, retro_pabe_3070, retro_pabe_368,
Pan troglodytes	ENSPTRG00000018039	1 retrocopy	retro_ptro_121,
Rattus norvegicus	ENSRNOG00000028505	4 retrocopies	retro_rnor_102, retro_rnor_234, retro_rnor_29, retro_rnor_70,
Sarcophilus harrisii	ENSSHAG00000006857	2 retrocopies	retro_shar_265, retro_shar_563,
Sarcophilus harrisii	ENSSHAG00000008658	1 retrocopy	retro_shar_618,