RetrogeneDB ID: retro_mmus_1086

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:25582273..25583386(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000080840
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1086
ATGTCCCACCCATCCCGGGCAGCCACGCCCTCCAACTCCAAGAACCCGCAAGTCTTCTTTGATGTGGACGTTGGCGGGGA
GCGAGTTGGACAAATTGTTTTAGAATTGTTTGCAGATACTGTTCCCAAAACTGCAGAAAATTTTCGTGCATTGTGTACAG
GAGAAAAAGGAACTGGGTCCGCGACCGGGAAGCCTCTCCATTTTAAAGAATGCCCTTTCCACCGAATTATTAAGAAATTT
ATGATTCAGGGTGGAGACTTCTCAAATCAGAATGGGACAGGTGGCGAAAGTATTTATGGTGAAAAATTTGAAGATGAAAA
TTTTCATTATAAGCATGATCGGGAGGGTTTGCTGAGCATGGCAAATGCAGGCCCCAAATACGAGTGGTTCTCAGCTCTTT
ATCACAACAGTTCCGACTCCTCATTTGGATGGGAAACATGTGGTATTTGGTCAAGTCATAAAACGACTAGGTGTGGCAAG
GACGCTTGAAAATGTAGAAGTGAATGGTGAAAAACCTGCTAAACTCTGTGTTATTGCAGACTGTGGAGAATTGAAAGAAG
GGGATGACTGGGGAATATTCCCCAAAGATGGCGATGGTGACAGTCATCCAGACTTCCCCGAGGATGCAGATATAGATTTA
AAAGATGTAGATAAAATTTTATTAATATCTGAAGACTTAAAAAAACATTGGAAATACTTTTTTTCAAGTCTCAGAACTGG
AAGATGGCTATTAAAAAATATGCGAAGGTTTTAAAGGTATGTGGATAGTTCAAAGGCTGTTATTGAGAAAGCAGATAGAT
CCAGACTGCAACCTATAGCCTTAAGTCGTGTGCTGAATATTGGTGCTTGTAAGCTGAAGATGTCAAATTGGCAAGGGGTA
ATTGACAGTTGCTTAGAGGCTCTTGAAATGGACCCTTCAAATACTAAAGCACTGTAATGAAAAGCGCAAGGATGGCAAAG
ATTGAAGGAATATGATGAAACATTGGCTGATCTGAAGAAGGCACAGGAGATAGCCCCAGGAGATAAAGCTATCCAGGCAG
AATGCTTAAAGTCAAACAAATAATAAAGGCACAGAAAGATAAAGAGAAGGCCATGTATGCAAAAATGTTTGCT

Alignment

ORF - retro_mmus_1086 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MSHASPAAKPSNSKNPRVFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGTGSTTGKPLHFKG
          MSH.S.AA.PSNSKNP.VFFDVD.GGERVG.IVLELFAD.VPKTAENFRALCTGEKGTGS.TGKPLHFK.
Retrocopy MSHPSRAATPSNSKNPQVFFDVDVGGERVGQIVLELFADTVPKTAENFRALCTGEKGTGSATGKPLHFKE

Parental  CPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDREGLLSMANAGP-NTNGSQFFITTVPT
          CPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDREGLLSMANAGP.NT.GSQ.FITTVPT
Retrocopy CPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDREGLLSMANAGP>NTSGSQLFITTVPT

Parental  PHLDGKHVVFGQVIKGLGVARTLENVEVNGEKPAKLCVIAECGELKEGDDWGIFPKDGSGDSHPDFPEDA
          PHLDGKHVVFGQVIK.LGVARTLENVEVNGEKPAKLCVIA.CGELKEGDDWGIFPKDG.GDSHPDFPEDA
Retrocopy PHLDGKHVVFGQVIKRLGVARTLENVEVNGEKPAKLCVIADCGELKEGDDWGIFPKDGDGDSHPDFPEDA

Parental  DIDLKDVDKILLISEDL-KNIGNT-FFKSQNWEMAIKKYAKVL-RYVDSSKAVIEKADRSRLQPIALSCV
          DIDLKDVDKILLISEDL.KNIGNT.FFKSQNW.MAIKKYAKVL.RYVDSSKAVIEKADRSRLQPIALS.V
Retrocopy DIDLKDVDKILLISEDL>KNIGNT>FFKSQNWKMAIKKYAKVL>RYVDSSKAVIEKADRSRLQPIALSRV

Parental  LNIGACKLKMSNWQGAIDSCLEALEMDPSNTKALYRKAQGWQGLKEYDQALADLKKAQEIAPGDKAIQAE
          LNIGACKLKMSNWQG.IDSCLEALEMDPSNTKAL..KAQGWQ.LKEYD..LADLKKAQEIAPGDKAIQAE
Retrocopy LNIGACKLKMSNWQGVIDSCLEALEMDPSNTKAL**KAQGWQRLKEYDETLADLKKAQEIAPGDKAIQAE

Parental  -LLKVKQMIKAQKDKEKAVYAKMFA
          ..LKVKQ.IKAQKDKEKA.YAKMFA
Retrocopy <MLKVKQIIKAQKDKEKAMYAKMFA

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	49.39 RPM
SRP007412_cerebellum	0.00 RPM	41.21 RPM
SRP007412_heart	0.09 RPM	28.61 RPM
SRP007412_kidney	0.02 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 actvity near the 5' end of retro_mmus_1086 was not detected

EST

No EST(s) were mapped for retro_mmus_1086 retrocopy.

TSS

No TSS is located nearby retro_mmus_1086 retrocopy 5' end.

Lab

retro_mmus_1086 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1086 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,