RetrogeneDB ID: retro_mmus_2274

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:90722550..90723293(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

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_2274
CTGTTTGAATTCGGTGCCTTCCCTCCAGAGAGCAAGTATTTGTTTCTCGGAGACTATGTGGATGGAGAAAACAGTCACTG
GAGATGATCTGCCTCTTGCTGGCCTACAAATCAAGTGTCTGGAGAACTTCTTTCTTCTCAGAGGGAACCATGAGTGTCAC
AGCATCAATAGAACCTATGGATTTTATGATGAATGTAAAAGAAGATACATTAAGCTGTGGAAAATGTTTACAGACTGTTT
TAACTGCTTACCAATAACAACCATAGTGGACAAGAAGATATTCTGCTGTCAGGGAGGATTATCACCAGATCTTCAATCTA
TGGAGCAGATTTGGCAAATTATGAGACCAACTGATGTACCAGATCAAGGTCTTCTTTGTTATCTTTTGTGGCCTGACCCT
AATAAAGATATCTTCGACTGAGATGAAAATGACAGAGGAGTGTCCTTCACATTTGGTGCAGAACTGGTTGCAAAATTTCT
CAATAAGCATGATTTGGCTCTTATATGTAGAGCCTATCAAGTGGTTGAAGATAGGTATGAGTTTTTTTGCAAAGACGCAG
TTAGTCGCTCTGTTTTCTGCACCCAACTACTGTGGTGAGTTTGACAATGCAGGTGCCATGATGAGTGTGGATGGAACACT
CATGTGTTCCTTCCAGATTTGAAAGACTTCAGAGAAAAAGAAACTCAATGCCACAAGACCTGTCACACCACCACAGGGTA
TGATCACAAAGCAAGCAAAGAAA

Alignment

ORF - retro_mmus_2274 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 77.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LFEYGGFPPESNYLFLGDYVDRG-KQSLETICLLLAYK-IKYPENFFLLRGNHECASINRIYGFYDECKR
          LFE.G.FPPES.YLFLGDYVD...KQSLE.ICLLLAYK.IK..ENFFLLRGNHEC.SINR.YGFYDECKR
Retrocopy LFEFGAFPPESKYLFLGDYVDGE<KQSLEMICLLLAYK<IKCLENFFLLRGNHECHSINRTYGFYDECKR

Parental  RYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKD
          RY.IKLWK.FTDCFNCLPI..IVD.KIFCC.GGLSPDLQSMEQI..IMRPTDVPDQGLLC.LLW.DP.KD
Retrocopy RY-IKLWKMFTDCFNCLPITTIVDKKIFCCQGGLSPDLQSMEQIWQIMRPTDVPDQGLLCYLLWPDPNKD

Parental  VLGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYE-FFAKRQLVTLFSAPNYCGEFDNAGA
          .....ENDRGVSFTFGAE.VAKFL.KHDL.LICRA.QVVED.YE.FFAK.QLV.LFSAPNYCGEFDNAGA
Retrocopy IFD*DENDRGVSFTFGAELVAKFLNKHDLALICRAYQVVEDRYE>FFAKTQLVALFSAPNYCGEFDNAGA

Parental  MMSVDETLMCSFQILKPAEKKKPNATRPVTPPRGMITKQAKK
          MMSVD.TLMCSFQI.K..EKKK.NATRPVTPP.GMITKQAKK
Retrocopy MMSVDGTLMCSFQI*KTSEKKKLNATRPVTPPQGMITKQAKK

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

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2274 was not detected

EST

No EST(s) were mapped for retro_mmus_2274 retrocopy.

TSS

No TSS is located nearby retro_mmus_2274 retrocopy 5' end.

Lab

retro_mmus_2274 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2274 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,