RetrogeneDB ID: retro_mmus_3418

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:10011953..10012746(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081898
• 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_3418
AAGATATGTGGTGACATCCACAGGCAATACTATAGTTTGCTCCTTCTGTTTGAGCATGGTGACTTCCTCCAGAAAACAAC
TATTTGTTTCTCAGGGACTATGTGGAGAGGGGCAAATAGTCACTAGAGATGATCTGCCTCTTGCTGGCCTACAAAATCAA
GTGTCTGGAGAACATTTTTCTTCTCAGAGAGAACCACGAGTGTGCCAGCATCAATAGGATCTACGAATTTTATGATGAGT
GTAAAAGAAGATATAACATTAAGCTATGGAAAACATTCACAGACTGTTTTAATTGCTTACTGATAGCAGCCATCGTGGAC
AAGAAGATAGTCTGCTGTCATGGAGGTTTATCACCAGATCTTCAATCTATGGAGCAGAGTCTGCGAATTATGAGACCAAC
TGATGTACCAGATCAAGGTCTTCTTTGTGATATTTTGTGATCTGACCCTGATAAAGATGTCTTAGGCTGGGGTGAAAAAT
GAAAGAGGAGTGTCCTTCACATTTGGTGCAGAAGTGGTTGCAAAATTTCTCCATAAGCATGATTTGGCTCTTATACGTAG
AGCCCAAGAAGTGGTTGAAGATGGGTATGAGGTTTTTTGCAAAGAGGCAGTTAGTCACTCTGTTTTCTGCACCCAACTAC
TGTGGTGAGTTTGACAATGCAGGCTCCATCATGAGTGTGGATGAAACCCTCATATGTTCCTTCCAGAATTTAAAGACAGC
AGAGAAAAAGAAGCCCAATGCCACGAGACCTGTCATACTGCCACAGGGCATGATCGATCATAAAGCAAGCAAA

Alignment

ORF - retro_mmus_3418 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.27 %
• Parental protein coverage: 81.73 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KICGDIHGQYYDLLRLFEYGGF-PPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECA
          KICGDIH.QYY.LL.LFE.G.F.PPE.NYLFL.DYV.RGK.SLE.ICLLLAYKIK..EN.FLLR.NHECA
Retrocopy KICGDIHRQYYSLLLLFEHGDF<PPENNYLFLRDYVERGK*SLEMICLLLAYKIKCLENIFLLRENHECA

Parental  SINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQ
          SINRIY.FYDECKRRYNIKLWKTFTDCFNCL.IAAIVD.KI.CCHGGLSPDLQSMEQ..RIMRPTDVPDQ
Retrocopy SINRIYEFYDECKRRYNIKLWKTFTDCFNCLLIAAIVDKKIVCCHGGLSPDLQSMEQSLRIMRPTDVPDQ

Parental  GLLCDLLWSDPDKDVLGWGE-NDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYE-FFAKRQLVTL
          GLLCD.L.SDPDKDVLGWGE.N.RGVSFTFGAEVVAKFLHKHDL.LI.RA..VVEDGYE.FFAKRQLVTL
Retrocopy GLLCDIL*SDPDKDVLGWGE>NERGVSFTFGAEVVAKFLHKHDLALIRRAQEVVEDGYE>FFAKRQLVTL

Parental  FSAPNYCGEFDNAGAMMSVDETLMCSFQILKPAEKKKPNATRPVTPPRGMITKQAKK
          FSAPNYCGEFDNAG..MSVDETL.CSFQ.LK.AEKKKPNATRPV..P.GMI...A.K
Retrocopy FSAPNYCGEFDNAGSIMSVDETLICSFQNLKTAEKKKPNATRPVILPQGMIDHKASK

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	28.99 RPM
SRP007412_cerebellum	0.00 RPM	40.08 RPM
SRP007412_heart	0.06 RPM	17.50 RPM
SRP007412_kidney	0.00 RPM	24.10 RPM
SRP007412_liver	0.03 RPM	11.96 RPM
SRP007412_testis	0.00 RPM	147.23 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3418 was not detected

EST

No EST(s) were mapped for retro_mmus_3418 retrocopy.

TSS

No TSS is located nearby retro_mmus_3418 retrocopy 5' end.

Lab

retro_mmus_3418 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3418 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,