RetrogeneDB ID:

retro_mmus_3580

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:X:15110861..15111380(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000045217
Aliases:Ppp1r2-ps9, 4930403L05Rik
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Ppp1r2
Ensembl ID:ENSMUSG00000047714
Aliases:Ppp1r2, 0610025N14Rik, 2310007G06Rik, 4930440J04Rik, 5430408E15Rik, D16Ertd248e, IPP-2
Description:protein phosphatase 1, regulatory (inhibitor) subunit 2 [Source:MGI Symbol;Acc:MGI:1914099]


Retrocopy-Parental alignment summary:






>retro_mmus_3580
ATGGCAGCCTCCTCCACCTCACACAGACCCATCAAGGGGATACTCAAAAACAAAAGTTCATCATCTTCAATGGAGGATTC
TTCCGAGTCATCTGGAAGACCAGGCACCCAGGAGTTGCAACGGAAGAAATCGCAGAAGTGGGATGAATCCAACATACTAG
CAACCCACTATCCATCCTACAAAGACTATGATCTGAGGAAGAAGAATGAGCCCGGCAATCCCTTTGGCAGCGTGCCACAT
GATGGAGAAGACACCTTAAGTGAAATTCAAGGAAAAGACGCCATGACCTCTGACACCTTAGCGAAGAAACTCGCAGCCCC
TGACACTTTGGGAACCAGTTATCAGGGTGAGGAGCAAGAAAGCAGCGGTGCGCATAGCAGCAAATTCTTCCTGGACAAAC
AAGAAAGGCAACGGCAATTTGAGTTGAAAAGGAAGTTACACTACAACGAAGGATTAAACATCAAATTGGCCAGACAACTG
ATATCGGAGGAGCTACAATCTGAAGTAGAGGAAGATGAA

ORF - retro_mmus_3580 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 54.02 %
Parental protein coverage: 84.47 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAASTASHRPIKGILKNKTSAASPPVVPSAEQPRPIVEEELSKKSQKWDEMNILATYHPADKDYGLMKID
MAAS..SHRPIKGILKNK.S..S.....S....RP...E...KKSQKWDE.NILAT..P..KDY.L.K..
RetrocopyMAASSTSHRPIKGILKNKSSSSSMED-SSESSGRPGTQELQRKKSQKWDESNILATHYPSYKDYDLRKKN
ParentalEPNTPYHNMIGDDEDAYSDSEGNEVMTPDILAKKLAAAEGSEPKYRTREQESSGEEDNDLSPEEREKKRQ
EP..P......D.ED..S...G...MT.D.LAKKLAA.......Y...EQESSG...........E..RQ
RetrocopyEPGNPFGSVPHDGEDTLSEIQGKDAMTSDTLAKKLAAPDTLGTSYQGEEQESSGAHSSKFFLDKQERQRQ
ParentalFEMKRKLHYNEGLNIKLARQLISKDLHDDDEDEE
FE.KRKLHYNEGLNIKLARQLIS..L....E..E
RetrocopyFELKRKLHYNEGLNIKLARQLISEELQSEVEEDE

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 .00 RPM 62 .17 RPM
SRP007412_cerebellum 0 .00 RPM 36 .00 RPM
SRP007412_heart 0 .00 RPM 40 .53 RPM
SRP007412_kidney 0 .00 RPM 35 .73 RPM
SRP007412_liver 0 .00 RPM 15 .87 RPM
SRP007412_testis 14 .77 RPM 41 .62 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_3580 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_3580 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_1557771066 libraries2 libraries1 library0 libraries3 libraries

The graphical summary, for retro_mmus_3580 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_3580 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_3580 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 23 parental genes, and 58 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000094102 retrocopies
retro_amel_1164, retro_amel_53,
Canis familiaris ENSCAFG000000326481 retrocopy
retro_cfam_44,
Choloepus hoffmanni ENSCHOG000000132102 retrocopies
retro_chof_1353, retro_chof_2148,
Callithrix jacchus ENSCJAG000000138762 retrocopies
retro_cjac_1252, retro_cjac_2429,
Cavia porcellus ENSCPOG000000220062 retrocopies
retro_cpor_1144, retro_cpor_82,
Dasypus novemcinctus ENSDNOG000000236191 retrocopy
retro_dnov_1698,
Equus caballus ENSECAG000000180501 retrocopy
retro_ecab_3,
Felis catus ENSFCAG000000247491 retrocopy
retro_fcat_55,
Homo sapiens ENSG000001842037 retrocopies
retro_hsap_1262, retro_hsap_1271, retro_hsap_2303, retro_hsap_2505, retro_hsap_3258, retro_hsap_3576, retro_hsap_3800,
Gorilla gorilla ENSGGOG000000259085 retrocopies
retro_ggor_1563, retro_ggor_1705, retro_ggor_2412, retro_ggor_2554, retro_ggor_992,
Loxodonta africana ENSLAFG000000120101 retrocopy
retro_lafr_85,
Macaca mulatta ENSMMUG000000193962 retrocopies
retro_mmul_1314, retro_mmul_1666,
Mustela putorius furoENSMPUG000000037532 retrocopies
retro_mputfur_1269, retro_mputfur_172,
Mus musculus ENSMUSG00000047714 8 retrocopies
retro_mmus_1540, retro_mmus_1610, retro_mmus_1611, retro_mmus_1868, retro_mmus_2760, retro_mmus_3350, retro_mmus_3428, retro_mmus_3580 ,
Nomascus leucogenys ENSNLEG000000083716 retrocopies
retro_nleu_123, retro_nleu_1435, retro_nleu_1943, retro_nleu_2147, retro_nleu_2315, retro_nleu_2740,
Oryctolagus cuniculus ENSOCUG000000141232 retrocopies
retro_ocun_188, retro_ocun_942,
Otolemur garnettii ENSOGAG000000025971 retrocopy
retro_ogar_10,
Procavia capensis ENSPCAG000000136141 retrocopy
retro_pcap_397,
Pongo abelii ENSPPYG000000144296 retrocopies
retro_pabe_105, retro_pabe_1056, retro_pabe_1979, retro_pabe_3025, retro_pabe_3105, retro_pabe_96,
Pteropus vampyrus ENSPVAG000000116381 retrocopy
retro_pvam_18,
Rattus norvegicus ENSRNOG000000017332 retrocopies
retro_rnor_245, retro_rnor_2860,
Sus scrofa ENSSSCG000000118301 retrocopy
retro_sscr_1191,
Sus scrofa ENSSSCG000000304551 retrocopy
retro_sscr_1161,


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