RetrogeneDB ID:

retro_mmus_2786

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:6:122644295..122644706(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Rps15
Ensembl ID:ENSMUSG00000063457
Aliases:Rps15, rig
Description:ribosomal protein S15 [Source:MGI Symbol;Acc:MGI:98117]


Retrocopy-Parental alignment summary:






>retro_mmus_2786
ATGGCCGAAGTGGAGCAGAAGAAGAAGCGGACCTTCTGCAAGTTCACCTACCGTGGCGTAGACCTCGACCAACTGCTCGA
CATGTCTTATGAGCAGCTGATGCAGCTGTACAGCGCCCGCCAGAGGCGGCGCCTGAACCATGGTCTTCGGAGGAAGCAGC
ACTCACTGCTCAAGCGCTTGAGAAAGGCCAAGAAGGAGGCGCCACCCATGGAGAAGCCCGAGGTGGTGAAGACGCACCTG
AGGGACATGATCATCCTGCCCGAGATGGTGGGTAGCATGGTGGGCGTGTACAACGGCAAGACCTTCAACCAGGTGGAGCT
CAAACCAGAGATGATCGGCCACTACCTGGGCGAGTTCTCTATCACCTACAAACCCGTGAAGCACGGCCGGCCAGCCCGGG
ATCGGTGCCAC

ORF - retro_mmus_2786 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.16 %
Parental protein coverage: 94.48 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAEVEQKKKRTFRKFTYRGVDLDQLLDMSYEQLMQLYSARQRRRLNRGLRRKQHSLLKRLRKAKKEAPPM
MAEVEQKKKRTF.KFTYRGVDLDQLLDMSYEQLMQLYSARQRRRLN.GLRRKQHSLLKRLRKAKKEAPPM
RetrocopyMAEVEQKKKRTFCKFTYRGVDLDQLLDMSYEQLMQLYSARQRRRLNHGLRRKQHSLLKRLRKAKKEAPPM
ParentalEKPEVVKTHLRDMIILPEMVGSMVGVYNGKTFNQVEIKPEMIGHYLGEFSITYKPVKHGRPGIGATH
EKPEVVKTHLRDMIILPEMVGSMVGVYNGKTFNQVE.KPEMIGHYLGEFSITYKPVKHGRP.....H
RetrocopyEKPEVVKTHLRDMIILPEMVGSMVGVYNGKTFNQVELKPEMIGHYLGEFSITYKPVKHGRPARDRCH

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain 0 .09 RPM 129 .06 RPM
SRP007412_cerebellum 0 .04 RPM 104 .25 RPM
SRP007412_heart 0 .19 RPM 177 .26 RPM
SRP007412_kidney 0 .12 RPM 132 .61 RPM
SRP007412_liver 0 .05 RPM 112 .76 RPM
SRP007412_testis 0 .00 RPM 82 .60 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_2786 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_2786 retrocopy.

TSS - click to see more details



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_11818054 libraries19 libraries339 libraries278 libraries382 libraries

The graphical summary, for retro_mmus_2786 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)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_mmus_2786 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2786 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 20 parental genes, and 69 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000197181 retrocopy
retro_btau_1856,
Callithrix jacchus ENSCJAG0000000563213 retrocopies
retro_cjac_143, retro_cjac_151, retro_cjac_1517, retro_cjac_1607, retro_cjac_1672, retro_cjac_1714, retro_cjac_2069, retro_cjac_2236, retro_cjac_2596, retro_cjac_2656, retro_cjac_48, retro_cjac_756, retro_cjac_86,
Cavia porcellus ENSCPOG000000039681 retrocopy
retro_cpor_495,
Dasypus novemcinctus ENSDNOG000000007062 retrocopies
retro_dnov_173, retro_dnov_85,
Echinops telfairi ENSETEG000000086451 retrocopy
retro_etel_2,
Felis catus ENSFCAG000000107691 retrocopy
retro_fcat_1570,
Homo sapiens ENSG000001152684 retrocopies
retro_hsap_1484, retro_hsap_2341, retro_hsap_2650, retro_hsap_530,
Gorilla gorilla ENSGGOG000000028184 retrocopies
retro_ggor_1136, retro_ggor_116, retro_ggor_141, retro_ggor_1851,
Macaca mulatta ENSMMUG000000030502 retrocopies
retro_mmul_2130, retro_mmul_838,
Monodelphis domestica ENSMODG000000051191 retrocopy
retro_mdom_1335,
Mus musculus ENSMUSG00000063457 8 retrocopies
retro_mmus_1270, retro_mmus_208, retro_mmus_2734, retro_mmus_2786 , retro_mmus_3166, retro_mmus_3642, retro_mmus_520, retro_mmus_917,
Nomascus leucogenys ENSNLEG000000016518 retrocopies
retro_nleu_105, retro_nleu_1858, retro_nleu_1922, retro_nleu_2390, retro_nleu_2465, retro_nleu_2559, retro_nleu_461, retro_nleu_544,
Otolemur garnettii ENSOGAG000000157764 retrocopies
retro_ogar_194, retro_ogar_210, retro_ogar_2237, retro_ogar_96,
Pongo abelii ENSPPYG000000093174 retrocopies
retro_pabe_1233, retro_pabe_2321, retro_pabe_67, retro_pabe_893,
Pan troglodytes ENSPTRG000000102001 retrocopy
retro_ptro_122,
Pteropus vampyrus ENSPVAG000000031682 retrocopies
retro_pvam_382, retro_pvam_926,
Rattus norvegicus ENSRNOG000000246038 retrocopies
retro_rnor_1384, retro_rnor_1711, retro_rnor_1712, retro_rnor_178, retro_rnor_2086, retro_rnor_2114, retro_rnor_2642, retro_rnor_700,
Sarcophilus harrisii ENSSHAG000000134241 retrocopy
retro_shar_632,
Sus scrofa ENSSSCG000000232481 retrocopy
retro_sscr_271,
Ictidomys tridecemlineatus ENSSTOG000000064232 retrocopies
retro_itri_722, retro_itri_939,




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