RetrogeneDB ID: retro_mmus_616

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:5848463..5849565(-)
• Located in intron of: ENSMUSG00000019775

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ppid
• Ensembl ID: ENSMUSG00000027804
• Aliases: Ppid, 4930564J03Rik, CYP-40, Ppidl, Ppif
• Description: peptidylprolyl isomerase D (cyclophilin D) [Source:MGI Symbol;Acc:MGI:1914988]

Sequence

>retro_mmus_616
ATGTCCCACCCATCCCCAGCAGCCAAGCCCTCCAACTCCAAGAACCCATGAGGCTTCTTTGACATGGACATCGGCGGGGA
GCAAGTTGGATGAATTGTTTTAGAATTGTTTACAGATATTGTTCCCAAAGCTGCAGACAATTTTCATGCATTGTGTACAG
GAGAAAAAGGAACTGGATCCGTGACCGGGAAGCCTCACCATTTTAAATGATGCCCTTTTCACTGAATTTTTAAGAAATTT
ATGATTCACGGTGGAGACTTCTCAAATCAGAATGGGACAGGCGGAGAAAGTATTTATGGTGAAAAATTTGAAGATGAAAA
TTTTCATTATAAGCATGAATGGGGAGGGTTTGCTGAGCATGGCAAATGCAGGTCCCAATATGAGTGGTTCTCAGATCTTT
ATCACAACAGTTCCGACTCCTCATTTGGATGGGAAACATGTGGTATTTGGTCAGGTCATAAAAGGACTAGGTGTGGCAAG
GACGCTTGAAAATGTAGACGTGAATGGTGAAAAACCTGCCAAACTCTGTGTTATTGGAGAATGTGGAGAATTGAAAGAAG
GGGACGACTGAGGAATATTCCCCAAAGATGGCTCTGGTGATAGTCATCCAGACTTCCCCGAGGCTGCAGATATAGATTAA
AAGGATGTAAATAAAATTTTATTAATATCTGAAGACGTAAAAAAACATTGGAAATACTTTTTTCAAGTCTCAAAACTGGG
AGATGGCTATTAAAAATATGCGAAGGTTTTAAGGTACATGGCTAGTTCAAAGGCTGCTATTGAGAAAGCAGATACATCCA
GACTGCAACCTATAGCCTTAAGTTGTGTGCTGAATGTAGGTGTTTGTAAGCTGAAGATGTCAGATTGGCAGGAGGCAATT
GACAGTTGCTTGGAGGCTCTTGAAATAGACCCTTCAAATACTAAAGCACTATACCGAAAAGCGCAAGGATGGCTAGGATT
GAAGGAATATGATCAAGCATTGGCTGATCTTAAGAATGCACAGGAGATAGCCCCAGGAGATAAAGCTATCCAGGCAGAAT
TGCTTAAAGTCAAACAAATGATAAAGGCACAGAAAGATAAAGAGAAGGCTGAGTATGCAAAA

Alignment

ORF - retro_mmus_616 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.38 %
• Parental protein coverage: 99.19 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSHASPAAKPSNSKNPRVFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGTGSTTGKPLHFKG
          MSH.SPAAKPSNSKNP..FFD.DIGGE.VG.IVLELF.DIVPK.A.NF.ALCTGEKGTGS.TGKP.HFK.
Retrocopy MSHPSPAAKPSNSKNP*GFFDMDIGGEQVG*IVLELFTDIVPKAADNFHALCTGEKGTGSVTGKPHHFK*

Parental  CPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHD-REGLLSMANAGPNTNGSQFFITTVPT
          CPFH.I.KKFMI.GGDFSNQNGTGGESIYGEKFEDENFHYKH...EGLLSMANAGPN..GSQ.FITTVPT
Retrocopy CPFH*IFKKFMIHGGDFSNQNGTGGESIYGEKFEDENFHYKHE>GEGLLSMANAGPNMSGSQIFITTVPT

Parental  PHLDGKHVVFGQVIKGLGVARTLENVEVNGEKPAKLCVIAECGELKEGDDWGIFPKDGSGDSHPDFPEDA
          PHLDGKHVVFGQVIKGLGVARTLENV.VNGEKPAKLCVI.ECGELKEGDD.GIFPKDGSGDSHPDFPE.A
Retrocopy PHLDGKHVVFGQVIKGLGVARTLENVDVNGEKPAKLCVIGECGELKEGDD*GIFPKDGSGDSHPDFPEAA

Parental  DIDLKDVDKILLISEDL-KNIGNTFFKSQNWEMAIK-KYAKVLRYVDSSKAVIEKADRSRLQPIALSCVL
          DID.KDV.KILLISED..KNIGNTFFKSQNWEMAIK.KYAKVLRY..SSKA.IEKAD.SRLQPIALSCVL
Retrocopy DID*KDVNKILLISEDV>KNIGNTFFKSQNWEMAIK<KYAKVLRYMASSKAAIEKADTSRLQPIALSCVL

Parental  NIGACKLKMSNWQGAIDSCLEALEMDPSNTKALYRKAQGWQGLKEYDQALADLKKAQEIAPGDKAIQAEL
          N.G.CKLKMS.WQ.AIDSCLEALE.DPSNTKALYRKAQGW.GLKEYDQALADLK.AQEIAPGDKAIQAEL
Retrocopy NVGVCKLKMSDWQEAIDSCLEALEIDPSNTKALYRKAQGWLGLKEYDQALADLKNAQEIAPGDKAIQAEL

Parental  LKVKQMIKAQKDKEKAVYAK
          LKVKQMIKAQKDKEKA.YAK
Retrocopy LKVKQMIKAQKDKEKAEYAK

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	0.16 RPM	49.39 RPM
SRP007412_cerebellum	0.00 RPM	41.21 RPM
SRP007412_heart	0.03 RPM	28.61 RPM
SRP007412_kidney	0.00 RPM	30.09 RPM
SRP007412_liver	0.00 RPM	28.67 RPM
SRP007412_testis	0.00 RPM	29.59 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_616 was not detected

EST

No EST(s) were mapped for retro_mmus_616 retrocopy.

TSS

No TSS is located nearby retro_mmus_616 retrocopy 5' end.

Lab

retro_mmus_616 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_616 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000012655	2 retrocopies	retro_etel_10, retro_etel_633,
Macaca mulatta	ENSMMUG00000017768	2 retrocopies	retro_mmul_281, retro_mmul_348,
Mus musculus	ENSMUSG00000027804	6 retrocopies	retro_mmus_1086, retro_mmus_1888, retro_mmus_2228, retro_mmus_2555, retro_mmus_3254, retro_mmus_616 ,
Rattus norvegicus	ENSRNOG00000027408	1 retrocopy	retro_rnor_188,