RetrogeneDB ID: retro_mmus_3428

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:22461728..22462337(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000052025
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• 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]

Sequence

>retro_mmus_3428
ATGGCGGCCTGGATGGCCTCTCAACGACCAATCAAGGGAATCCTGAAGAACAAGACCTCAGCGTCTTCCCCGGTAGTGGC
CTCAGCTGAACAGCCCAGCCTGACCTTCAAAAAGCTGAATAAGAAGTCCCAGACCTGGGATGAAGCTAACATCTTATCAA
CTTATCATCCACCTGAGGAAGACTACGGACTGATGAAAACAAGTGCGCCAAACACACTATACCACAATTCGATGGCTTAT
GATAAAGATGCTGCTAATGCTTCAGAATGCCATGAAATGTTGAATCCAGATTGCTTAGAGAAGAAACTCACTGTTGATGA
AGATTCTGGGCCAAGCGATATGGAACTTGAAGAAGAAGGTGGTAGAGAGGAAGAAAATTACCTCTCCCCTCAAGAAAAGA
AGCGGCAGTTTGAAATGAAAAGGAAGCTTCACAGCAACGAAGGACTAAATATTAAATTAGCCAGACTGCTAATTTCAAAA
GACCTACATGATGATGATGACGAAGATGAAGAAATGTCAGAGGCTACAGACTTTGACAGCATCAATATTGACTAGTCGAA
TCAAGGATCTACCGAAAGTGACCATCTGCAACTGAAATCACAAAGTTCA

Alignment

ORF - retro_mmus_3428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAASTASHRPIKGILKNKTSAASPPVVPSAEQPRPIVEEELSKKSQKWDEMNILATYHPADKDYGLMKID
          MAA..AS.RPIKGILKNKTSA.SP.VV.SAEQP.......L.KKSQ.WDE.NIL.TYHP...DYGLMK..
Retrocopy MAAWMASQRPIKGILKNKTSASSP-VVASAEQPS-LTFKKLNKKSQTWDEANILSTYHPPEEDYGLMKTS

Parental  EPNTPYHNMIGDDEDAYSDSEGNEVMTPDILAKKLAAAEGSEPKYRTREQESSGEEDNDLSPEEREKKRQ
          .PNT.YHN....D.DA...SE..E...PD.L.KKL...E.S.P.....E.E...EE.N.LSP...EKKRQ
Retrocopy APNTLYHNSMAYDKDAANASECHEMLNPDCLEKKLTVDEDSGPSDMELEEEGGREEENYLSPQ--EKKRQ

Parental  FEMKRKLHYNEGLNIKLARQLISKDLH-DDDEDEEMAETADGDSMNVEESSQGSTTSDHLQHKSQSS
          FEMKRKLH.NEGLNIKLAR.LISKDLH.DDDEDEEM.E..D.DS.N...S.QGST.SDHLQ.KSQSS
Retrocopy FEMKRKLHSNEGLNIKLARLLISKDLHDDDDEDEEMSEATDFDSINID*SNQGSTESDHLQLKSQSS

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	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	25.02 RPM	41.62 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3428 was not detected

EST

No EST(s) were mapped for retro_mmus_3428 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_156731	1061 libraries	6 libraries	0 libraries	2 libraries	3 libraries
TSS #2	TSS_156732	1067 libraries	2 libraries	2 libraries	0 libraries	1 library

The graphical summary, for retro_mmus_3428 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_3428 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3428 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009410	2 retrocopies	retro_amel_1164, retro_amel_53,
Canis familiaris	ENSCAFG00000032648	1 retrocopy	retro_cfam_44,
Choloepus hoffmanni	ENSCHOG00000013210	2 retrocopies	retro_chof_1353, retro_chof_2148,
Callithrix jacchus	ENSCJAG00000013876	2 retrocopies	retro_cjac_1252, retro_cjac_2429,
Cavia porcellus	ENSCPOG00000022006	2 retrocopies	retro_cpor_1144, retro_cpor_82,
Dasypus novemcinctus	ENSDNOG00000023619	1 retrocopy	retro_dnov_1698,
Equus caballus	ENSECAG00000018050	1 retrocopy	retro_ecab_3,
Felis catus	ENSFCAG00000024749	1 retrocopy	retro_fcat_55,
Homo sapiens	ENSG00000184203	7 retrocopies	retro_hsap_1262, retro_hsap_1271, retro_hsap_2303, retro_hsap_2505, retro_hsap_3258, retro_hsap_3576, retro_hsap_3800,
Gorilla gorilla	ENSGGOG00000025908	5 retrocopies	retro_ggor_1563, retro_ggor_1705, retro_ggor_2412, retro_ggor_2554, retro_ggor_992,
Loxodonta africana	ENSLAFG00000012010	1 retrocopy	retro_lafr_85,
Macaca mulatta	ENSMMUG00000019396	2 retrocopies	retro_mmul_1314, retro_mmul_1666,
Mustela putorius furo	ENSMPUG00000003753	2 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	ENSNLEG00000008371	6 retrocopies	retro_nleu_123, retro_nleu_1435, retro_nleu_1943, retro_nleu_2147, retro_nleu_2315, retro_nleu_2740,
Oryctolagus cuniculus	ENSOCUG00000014123	2 retrocopies	retro_ocun_188, retro_ocun_942,
Otolemur garnettii	ENSOGAG00000002597	1 retrocopy	retro_ogar_10,
Procavia capensis	ENSPCAG00000013614	1 retrocopy	retro_pcap_397,
Pongo abelii	ENSPPYG00000014429	6 retrocopies	retro_pabe_105, retro_pabe_1056, retro_pabe_1979, retro_pabe_3025, retro_pabe_3105, retro_pabe_96,
Pteropus vampyrus	ENSPVAG00000011638	1 retrocopy	retro_pvam_18,
Rattus norvegicus	ENSRNOG00000001733	2 retrocopies	retro_rnor_245, retro_rnor_2860,
Sus scrofa	ENSSSCG00000011830	1 retrocopy	retro_sscr_1191,
Sus scrofa	ENSSSCG00000030455	1 retrocopy	retro_sscr_1161,