RetrogeneDB ID: retro_mmus_260

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:4689401..4689926(-)
• Located in intron of: ENSMUSG00000020640

Retrocopy information

• Ensembl ID: ENSMUSG00000091732
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Rpl18a
• Ensembl ID: ENSMUSG00000045128
• Aliases: Rpl18a, 2510019J09Rik
• Description: ribosomal protein L18A [Source:MGI Symbol;Acc:MGI:1924058]

Sequence

>retro_mmus_260
GCGCGCAGGCTTCGGGAGTACAAGGTGGTGGGGTGCTGCTTGCCAACCCCAAAATGCCACACACCACCACTGTACCGTAT
GCGAATCTTTGCACCCAACCATGTGGTGGCCAAGTCCCACTTCTGGTACTTTGTGTTGCAGCTGAAGAGGATGAAGAAGT
CACCCGGGGAGATTGTGTACTGCGGGCAGGTGTTTGAGAAGTCACCCCTGCGCGTGAAGAACTTTGGCATCTGGCCACGC
TGTGACTCCCGCAGTGGCACACACAACATGTACCGGGAGTACGGGGACCTGACCACTGCTGGTGCAGTCTCACAGTGCTA
CCGAGACATGGGTACCCGACACCGTGCCCGTGCCCACTCCATCCAGATCATGAAGGTGGAAGAGATTGAAGCTGGCAAGT
GCCGCCGGCCAGCTGTCAAGCAGTTCCATGACTCCAAGATCAAATTCCCACTGCCCCACCGCGTGTTGTTGCAGCACCAG
CACAAGCCACACTTTACCACCAAGAGGCCCAACACCTTCTTCTAG

Alignment

ORF - retro_mmus_260 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.23 %
• Parental protein coverage: 96.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LREYKVVGRCLPTPKCHTPPLYRMRIFAPNHVVAKSRFWYFVSQLKKMKKSSGEIVYCGQVFEKSPLRVK
          LREYKVVG.CLPTPKCHTPPLYRMRIFAPNHVVAKS.FWYFV.QLK.MKKS.GEIVYCGQVFEKSPLRVK
Retrocopy LREYKVVGCCLPTPKCHTPPLYRMRIFAPNHVVAKSHFWYFVLQLKRMKKSPGEIVYCGQVFEKSPLRVK

Parental  NFGIWLRYDSRSGTHNMYREYRDLTTAGAVTQCYRDMGARHRARAHSIQIMKVEEIAAGKCRRPAVKQFH
          NFGIW.R.DSRSGTHNMYREY.DLTTAGAV.QCYRDMG.RHRARAHSIQIMKVEEI.AGKCRRPAVKQFH
Retrocopy NFGIWPRCDSRSGTHNMYREYGDLTTAGAVSQCYRDMGTRHRARAHSIQIMKVEEIEAGKCRRPAVKQFH

Parental  DSKIKFPLPHRV-LRRQHKPRFTTKRPNTFF
          DSKIKFPLPHRV.L..QHKP.FTTKRPNTFF
Retrocopy DSKIKFPLPHRVLLQHQHKPHFTTKRPNTFF

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	38.62 RPM
SRP007412_cerebellum	0.04 RPM	40.86 RPM
SRP007412_heart	0.03 RPM	83.68 RPM
SRP007412_kidney	0.13 RPM	75.27 RPM
SRP007412_liver	0.11 RPM	65.79 RPM
SRP007412_testis	0.05 RPM	43.31 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_260 was not detected

EST

No EST(s) were mapped for retro_mmus_260 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_23369	394 libraries	499 libraries	179 libraries	0 libraries	0 libraries

The graphical summary, for retro_mmus_260 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_260 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_260 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 99 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003125	1 retrocopy	retro_acar_86,
Bos taurus	ENSBTAG00000015831	5 retrocopies	retro_btau_145, retro_btau_1586, retro_btau_842, retro_btau_917, retro_btau_922,
Canis familiaris	ENSCAFG00000015122	1 retrocopy	retro_cfam_231,
Callithrix jacchus	ENSCJAG00000014006	7 retrocopies	retro_cjac_1628, retro_cjac_2814, retro_cjac_3192, retro_cjac_3906, retro_cjac_4134, retro_cjac_441, retro_cjac_642,
Cavia porcellus	ENSCPOG00000015205	1 retrocopy	retro_cpor_1478,
Equus caballus	ENSECAG00000015258	1 retrocopy	retro_ecab_745,
Homo sapiens	ENSG00000105640	11 retrocopies	retro_hsap_1053, retro_hsap_128, retro_hsap_135, retro_hsap_1610, retro_hsap_1961, retro_hsap_2254, retro_hsap_2676, retro_hsap_2776, retro_hsap_4129, retro_hsap_4734, retro_hsap_4776,
Gorilla gorilla	ENSGGOG00000002870	8 retrocopies	retro_ggor_1215, retro_ggor_1680, retro_ggor_1868, retro_ggor_1933, retro_ggor_195, retro_ggor_227, retro_ggor_2775, retro_ggor_2940,
Macropus eugenii	ENSMEUG00000003228	2 retrocopies	retro_meug_36, retro_meug_49,
Myotis lucifugus	ENSMLUG00000006701	4 retrocopies	retro_mluc_1671, retro_mluc_1893, retro_mluc_1978, retro_mluc_2191,
Macaca mulatta	ENSMMUG00000028844	6 retrocopies	retro_mmul_1416, retro_mmul_1591, retro_mmul_2233, retro_mmul_2547, retro_mmul_292, retro_mmul_364,
Monodelphis domestica	ENSMODG00000019167	2 retrocopies	retro_mdom_349, retro_mdom_680,
Mustela putorius furo	ENSMPUG00000015786	4 retrocopies	retro_mputfur_1007, retro_mputfur_1189, retro_mputfur_1574, retro_mputfur_457,
Mus musculus	ENSMUSG00000045128	8 retrocopies	retro_mmus_1606, retro_mmus_260 , retro_mmus_2910, retro_mmus_2924, retro_mmus_326, retro_mmus_346, retro_mmus_937, retro_mmus_951,
Nomascus leucogenys	ENSNLEG00000005889	7 retrocopies	retro_nleu_1087, retro_nleu_1180, retro_nleu_1940, retro_nleu_2261, retro_nleu_2605, retro_nleu_2672, retro_nleu_680,
Otolemur garnettii	ENSOGAG00000031828	4 retrocopies	retro_ogar_1016, retro_ogar_1891, retro_ogar_2226, retro_ogar_2564,
Pongo abelii	ENSPPYG00000009725	10 retrocopies	retro_pabe_1200, retro_pabe_1319, retro_pabe_1620, retro_pabe_2239, retro_pabe_2302, retro_pabe_3680, retro_pabe_3717, retro_pabe_3802, retro_pabe_482, retro_pabe_487,
Pan troglodytes	ENSPTRG00000010686	3 retrocopies	retro_ptro_1078, retro_ptro_1803, retro_ptro_27,
Rattus norvegicus	ENSRNOG00000018795	6 retrocopies	retro_rnor_108, retro_rnor_1655, retro_rnor_2279, retro_rnor_2362, retro_rnor_2821, retro_rnor_888,
Sarcophilus harrisii	ENSSHAG00000000406	3 retrocopies	retro_shar_435, retro_shar_474, retro_shar_706,
Ictidomys tridecemlineatus	ENSSTOG00000007788	1 retrocopy	retro_itri_694,
Tupaia belangeri	ENSTBEG00000010488	4 retrocopies	retro_tbel_2865, retro_tbel_2925, retro_tbel_635, retro_tbel_919,