RetrogeneDB ID: retro_mmus_2968

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:119740127..119741096(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000044341
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ppp1cc
• Ensembl ID: ENSMUSG00000004455
• Aliases: Ppp1cc, PP-1G, PP1, dis2m1
• Description: protein phosphatase 1, catalytic subunit, gamma isoform [Source:MGI Symbol;Acc:MGI:104872]

Sequence

>retro_mmus_2968
ATGGCGGATATCGACAAACTCAACATCGACAGCATCATCCAACGGCTGCTGGAAGTGAGAGGGTCCAAGCCAGGCAAGAA
TGTCCAGCTCCAGGAGAACGAGATCCGAGGACTCTGCCTGAAGTCTCGGGAGATCTTCCTCAGTCAGCCTATCCTTTTAG
AACTTGAAGCACCACTCAAGATATGTGGTGACATCCACGGGCAGTACTATGATTTGCTCCGTCTGTTTGAATACGGTGGC
TTTCCTCCAGAGAGCAACTATTTGTTTCTCGGGGACTATGTGGACAGGGGCAAGCAGTCCCTGGAGACAATCTGCCTCTT
GCTGGCCTACAAAATCAAGTATCCGGAGAACTTCTTTCTTCTCAGAGGGAACCACGAGTGCGCCAGCATCAATAGGATCT
ACGGATTTTATGATGAGTGTAAAAGAAGATACAACATTAAGCTGTGGAAAACGTTCACAGACTGTTTTAACTGCTTGCCG
ATAGCAGCCATCGTGGACGAGAAGATATTCTGCTGTCATGGAGGTTTATCACCAGATCTTCAATCTATGGAGCAGATTCG
GCGAATTATGAGACCAACTGATGTACCAGATCAAGGTCTTCTTTGTGATCTTTTGTGGTCTGACCCCGATAAAGATGTCT
TAGGCTGGGGTGAAAATGACAGAGGAGTGTCCTTCACATTTGGTGCAGAAGTGGTTGCAAAATTTCTCCATAAGCATGAT
TTGGATCTTATATGTAGAGCCCATCAGGTGGTTGAAGATGGCTATGAGTTTTTTGCAAAGAGGCAGTTAGTCACTCTGTT
TTCTGCACCCAACTACTGTGGCGAGTTTGACAATGCAGGCGCCATGATGAGTGTGGATGAGACCCTCATGTGTTCCTTCC
AGATTTTAAAGCCTGCAGAGAAAAAGAAGCCCAACGCCACGAGACCTGTCACACCACCACGGGGTATGATCACAAAGCAA
GCAAAGAAA

Alignment

ORF - retro_mmus_2968 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  MADIDKLNIDSIIQRLLEVRGSKPGKNVQLQENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYY
          MADIDKLNIDSIIQRLLEVRGSKPGKNVQLQENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYY
Retrocopy MADIDKLNIDSIIQRLLEVRGSKPGKNVQLQENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYY

Parental  DLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDEC
          DLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDEC
Retrocopy DLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDEC

Parental  KRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPD
          KRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPD
Retrocopy KRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPD

Parental  KDVLGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAG
          KDVLGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAG
Retrocopy KDVLGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAG

Parental  AMMSVDETLMCSFQILKPAEKKKPNATRPVTPPRGMITKQAKK
          AMMSVDETLMCSFQILKPAEKKKPNATRPVTPPRGMITKQAKK
Retrocopy AMMSVDETLMCSFQILKPAEKKKPNATRPVTPPRGMITKQAKK

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	0.54 RPM	28.99 RPM
SRP007412_cerebellum	1.09 RPM	40.08 RPM
SRP007412_heart	0.75 RPM	17.50 RPM
SRP007412_kidney	1.23 RPM	24.10 RPM
SRP007412_liver	0.27 RPM	11.96 RPM
SRP007412_testis	7.41 RPM	147.23 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2968 was not detected

EST

16 EST(s) were mapped to retro_mmus_2968 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AL034693	119740470	119740753	100	282	0	281
AV578978	119740657	119740879	100	222	0	222
AW209791	119740111	119740571	99.8	458	0	455
AW682422	119740330	119740714	100	384	0	384
BG142781	119740186	119740571	100	385	0	385
CA538375	119740622	119740820	100	198	0	198
CD560144	119740047	119740570	100	523	0	523
CF104161	119740104	119740571	99.2	463	4	459
CF982022	119740505	119740740	100	235	0	235
CJ047883	119740184	119740592	100	408	0	408
CJ055725	119740340	119740723	99.5	381	2	379
CJ137565	119740187	119740633	100	445	0	445
CN707525	119740165	119740649	100	484	0	484
CX233436	119740381	119740654	99.3	271	2	269
CX234471	119740526	119740735	100	209	0	209
DT911769	119740115	119740594	99.8	477	1	475

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_128187	222 libraries	586 libraries	259 libraries	2 libraries	3 libraries

The graphical summary, for retro_mmus_2968 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_2968 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2968 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013861	1 retrocopy	retro_amel_1721,
Bos taurus	ENSBTAG00000011198	2 retrocopies	retro_btau_6, retro_btau_960,
Ciona intestinalis	ENSCING00000004542	1 retrocopy	retro_cint_3,
Callithrix jacchus	ENSCJAG00000009147	7 retrocopies	retro_cjac_1062, retro_cjac_1165, retro_cjac_1408, retro_cjac_2304, retro_cjac_2535, retro_cjac_3288, retro_cjac_822,
Equus caballus	ENSECAG00000017228	1 retrocopy	retro_ecab_853,
Echinops telfairi	ENSETEG00000015721	1 retrocopy	retro_etel_2065,
Myotis lucifugus	ENSMLUG00000010661	2 retrocopies	retro_mluc_15, retro_mluc_2217,
Mus musculus	ENSMUSG00000004455	5 retrocopies	retro_mmus_2274, retro_mmus_2968 , retro_mmus_3418, retro_mmus_851, retro_mmus_925,
Sorex araneus	ENSSARG00000000571	1 retrocopy	retro_sara_700,
Drosophila melanogaster	FBgn0003134	5 retrocopies	retro_dmel_21, retro_dmel_37, retro_dmel_42, retro_dmel_48, retro_dmel_81,