RetrogeneDB ID: retro_mmus_148

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:61259079..61259961(-)
• Located in intron of: ENSMUSG00000024575

Retrocopy information

• Ensembl ID: ENSMUSG00000091957
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Rps2
• Ensembl ID: ENSMUSG00000044533
• Aliases: Rps2, Llrep3, S4
• Description: ribosomal protein S2 [Source:MGI Symbol;Acc:MGI:105110]

Sequence

>retro_mmus_148
ATGGCGGATGACGCCGGTGCAGCGGGAGGGCCCGGAGGACCCGGGGGCCCAGGATTAGGAGGCCGCGGCGGCTTCCGCGG
AGGATTCGGCAGCGGTCTTAGGGGCCGTGGTCGTGGCCGAGGCCGTGGCCGTGGTCGAGGCCGCGGGGCTCGTGGAGGTA
AAGCTGAAGACAAGGAGTGGATCCCCGTCACCAAGCTGGGCCGCCTGGTTAAGGACATGAAGATCAAGTCCTTGGAGGAG
ATCTACCTGTTCTCCCTGCCCATTAAGGAGTCTGAGATCATTGATTTCTTCCTGGGTGCGTCCCTAAAGGATGAGGTTCT
GAAAATCATGCCAGTGCAGAAGCAGACTCGGGCTGGCCAGCGGACCAGGTTCAAGGCTTTCGTCGCTATTGGGGACTACA
ATGGTCACGTTGGTCTTGGTGTTAAGTGCTCCAAGGAGGTTGCTACTGCCATACGAGGGGCCATCATCTTGGCCAAGCTT
TCCATCGTCCCTGTGCGGAGAGGCTACTGGGGGAACAAGATTGGCAAGCCCCACACTGTTCCATGCAAGGTGACAGGCCG
CTGTGGCTCTGTGCTGGTGCGTCTCATCCCTGCCCCCAGAGGCACTGGCATTGTCTCTGCTCCTGTGCCCAAGAAGCTCC
TGATGATGGCCGGTATAGATGACTGCTACACTTCAGCCAGAGGCTGCACTGCCACCCTGGGCAACTTTGCTAAGGCCACC
TTTGATGCCATCTCCAAGACTTACAGCTACCTGACCCCCGACCTCTGGAAAGAGACTGTCTTCACCAAGTCTCCTTATCA
GGAATTCACGGATCATCTTGTGAAAACCCACACCAGAGTCTCTGTTCAGAGGACCCAGGCTCCAGCTGTGGCTACCACAT
AA

Alignment

ORF - retro_mmus_148 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MADDAGAAGGPGGPGGPGLGGRGGFRGGFGSGLRGRGRGRGRGRGRGRGARGGKAEDKEWIPVTKLGRLV
          MADDAGAAGGPGGPGGPGLGGRGGFRGGFGSGLRGRGRGRGRGRGRGRGARGGKAEDKEWIPVTKLGRLV
Retrocopy MADDAGAAGGPGGPGGPGLGGRGGFRGGFGSGLRGRGRGRGRGRGRGRGARGGKAEDKEWIPVTKLGRLV

Parental  KDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLG
          KDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLG
Retrocopy KDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGLG

Parental  VKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVP
          VKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVP
Retrocopy VKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGIVSAPVP

Parental  KKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRV
          KKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRV
Retrocopy KKLLMMAGIDDCYTSARGCTATLGNFAKATFDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRV

Parental  SVQRTQAPAVATT
          SVQRTQAPAVATT
Retrocopy SVQRTQAPAVATT

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	51.77 RPM
SRP007412_cerebellum	0.00 RPM	16.20 RPM
SRP007412_heart	0.00 RPM	160.82 RPM
SRP007412_kidney	0.04 RPM	85.85 RPM
SRP007412_liver	0.00 RPM	99.76 RPM
SRP007412_testis	0.00 RPM	25.11 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_148 was not detected

EST

No EST(s) were mapped for retro_mmus_148 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_60445	796 libraries	245 libraries	31 libraries	0 libraries	0 libraries

The graphical summary, for retro_mmus_148 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_148 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_148 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 123 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002549	1 retrocopy	retro_acar_57,
Bos taurus	ENSBTAG00000009535	7 retrocopies	retro_btau_1236, retro_btau_1420, retro_btau_1656, retro_btau_317, retro_btau_590, retro_btau_661, retro_btau_956,
Canis familiaris	ENSCAFG00000019472	19 retrocopies	retro_cfam_1028, retro_cfam_1252, retro_cfam_1321, retro_cfam_1460, retro_cfam_1560, retro_cfam_1592, retro_cfam_1842, retro_cfam_1848, retro_cfam_1932, retro_cfam_1983, retro_cfam_2007, retro_cfam_2012, retro_cfam_2046, retro_cfam_2053, retro_cfam_2110, retro_cfam_271, retro_cfam_323, retro_cfam_490, retro_cfam_629,
Cavia porcellus	ENSCPOG00000011651	11 retrocopies	retro_cpor_1030, retro_cpor_1238, retro_cpor_1376, retro_cpor_1469, retro_cpor_1527, retro_cpor_177, retro_cpor_19, retro_cpor_437, retro_cpor_718, retro_cpor_769, retro_cpor_808,
Dipodomys ordii	ENSDORG00000007375	18 retrocopies	retro_dord_163, retro_dord_206, retro_dord_215, retro_dord_284, retro_dord_392, retro_dord_445, retro_dord_465, retro_dord_499, retro_dord_500, retro_dord_505, retro_dord_568, retro_dord_571, retro_dord_572, retro_dord_683, retro_dord_703, retro_dord_711, retro_dord_723, retro_dord_89,
Equus caballus	ENSECAG00000009065	7 retrocopies	retro_ecab_1025, retro_ecab_1105, retro_ecab_509, retro_ecab_632, retro_ecab_876, retro_ecab_892, retro_ecab_949,
Loxodonta africana	ENSLAFG00000004696	11 retrocopies	retro_lafr_1072, retro_lafr_1092, retro_lafr_1103, retro_lafr_174, retro_lafr_284, retro_lafr_327, retro_lafr_376, retro_lafr_75, retro_lafr_801, retro_lafr_812, retro_lafr_917,
Macropus eugenii	ENSMEUG00000004508	2 retrocopies	retro_meug_156, retro_meug_2103,
Monodelphis domestica	ENSMODG00000016077	1 retrocopy	retro_mdom_536,
Mus musculus	ENSMUSG00000044533	1 retrocopy	retro_mmus_148 ,
Procavia capensis	ENSPCAG00000002090	2 retrocopies	retro_pcap_251, retro_pcap_433,
Pteropus vampyrus	ENSPVAG00000016704	8 retrocopies	retro_pvam_1395, retro_pvam_1486, retro_pvam_221, retro_pvam_240, retro_pvam_34, retro_pvam_459, retro_pvam_521, retro_pvam_595,
Rattus norvegicus	ENSRNOG00000014179	12 retrocopies	retro_rnor_1882, retro_rnor_2191, retro_rnor_2257, retro_rnor_2274, retro_rnor_2903, retro_rnor_438, retro_rnor_631, retro_rnor_681, retro_rnor_690, retro_rnor_809, retro_rnor_810, retro_rnor_878,
Sarcophilus harrisii	ENSSHAG00000015213	5 retrocopies	retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525, retro_shar_783,
Tursiops truncatus	ENSTTRG00000011393	12 retrocopies	retro_ttru_1341, retro_ttru_1346, retro_ttru_1414, retro_ttru_149, retro_ttru_1762, retro_ttru_1816, retro_ttru_37, retro_ttru_375, retro_ttru_419, retro_ttru_650, retro_ttru_719, retro_ttru_872,
Vicugna pacos	ENSVPAG00000006867	6 retrocopies	retro_vpac_114, retro_vpac_164, retro_vpac_220, retro_vpac_354, retro_vpac_379, retro_vpac_518,