RetrogeneDB ID: retro_mmus_1888

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:15127604..15128593(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083860
• 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_1888
CCACGCATCCCCGGCAGCCAAGCCCTCCAACTCCAAGTCTTCTTTGACGGGGACATCGGTGGGGAGCGAGTTGGACTAAT
TGTTTTAGAATTGTTTGCAGATATTGTTCCCAAAACTGCAGAAAATTTTCATGCATTGTACAGGAGAAAAAGGAACTGGG
TCCACTACCGGAAAGCCTCTCCATTTTAAAGGATGCCCTTTCTACCGAATTATTAAGAACTTTGTGATTCAGGGTGGAGA
CTTCTCAAATCAGAATGGGACAGGTGGCAAAAGTATTTATGGTGAAAAATTTGAAGATGAAATTTTTCATTATAAGCATG
ATCGGGAGGGTTTGCTGAGCATGGCAAATGCAGGTCCCAAATACGAGTGGTTCTCAGCTCTTTAACACAACAGTTCCAAC
TCCTCATTTGGATGGGAAACATGTGGTATTTGGTGAAGTCATAAAAGGACTAGGTTGGCAAGGATGCTTGAAATGTAGAA
GTGAATGGTGAAAAACCTGCCAAACTCTGTGTTATTGCAGAATGTGAAGAATTGAAAGAAGGGGACGACTGGGGAATATT
TCCCAAAGATGGCTCTGGTGACAGTCATCCAGACTTCCTGAGGATGCAGATATAGATTTAAAAGATGTAGATAAAATTTT
ATTAATATCTGAGGACTTAAAAAACATTAGAAATACTCTTTTCAAATCTCAGAACTGGGAGATGTCTATTAAACAATATG
TGAAGATTTTAAGTTATGTGGATAGTTCAAAGGCTGTTATTGAGAAAGCAGATAGATCCAGACTGCAACCTATAGCCTTA
AGTTGTGTACTGAATATTGGTGCTTGTAAGCTGAAGATGTCAAATTGGCAGGGGGCAATTGACAGTTGCTTAGAGGCTCT
TGAAATGGACCCTTCAAATACTAAAGCACTGTACTGAAAAGCGCAAGGATGGCTAGGATTGAAAGAGTTTGATCAAGCAT
TGGCTGATCTTAAGAAGGCACAGGAGATA

Alignment

ORF - retro_mmus_1888 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.31 %
• Parental protein coverage: 89.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PAAKPSNSKNPRVFFDVDIGGERVGRIVLELFADIV-PKTAENFRALCTGEKGTGSTTGKPLHFKGCPFH
          P....S......VFFD.DIGGERVG.IVLELFADIV.PK....F...CTGEKGTGSTTGKPLHFKGCPF.
Retrocopy PRIPGSQALQLQVFFDGDIGGERVGLIVLELFADIV>PKLQKIFMH-CTGEKGTGSTTGKPLHFKGCPFY

Parental  RIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDREGLLSMANAGP-NTNGSQFFITTVPTPHLD
          RIIK.F.IQGGDFSNQNGTGG.SIYGEKFEDE.FHYKHDREGLLSMANAGP.NT.GSQ.F.TTVPTPHLD
Retrocopy RIIKNFVIQGGDFSNQNGTGGKSIYGEKFEDEIFHYKHDREGLLSMANAGP>NTSGSQLFNTTVPTPHLD

Parental  GKHVVFGQVIKGLG-VARTLE-NVEVNGEKPAKLCVIAECGELKEGDDWGIFPKDGSGDSHPDF-PEDAD
          GKHVVFG.VIKGLG..AR.LE.NVEVNGEKPAKLCVIAEC.ELKEGDDWGIFPKDGSGDSHPDF.PEDAD
Retrocopy GKHVVFGEVIKGLG<LARMLE<NVEVNGEKPAKLCVIAECEELKEGDDWGIFPKDGSGDSHPDF<PEDAD

Parental  IDLKDVDKILLISEDLKNIGNTFFKSQNWEMAIKKYAKVLRYVDSSKAVIEKADRSRLQPIALSCVLNIG
          IDLKDVDKILLISEDLKNI.NT.FKSQNWEM.IK.Y.K.L.YVDSSKAVIEKADRSRLQPIALSCVLNIG
Retrocopy IDLKDVDKILLISEDLKNIRNTLFKSQNWEMSIKQYVKILSYVDSSKAVIEKADRSRLQPIALSCVLNIG

Parental  ACKLKMSNWQGAIDSCLEALEMDPSNTKALYRKAQGWQGLKEYDQALADLKKAQEI
          ACKLKMSNWQGAIDSCLEALEMDPSNTKALY.KAQGW.GLKE.DQALADLKKAQEI
Retrocopy ACKLKMSNWQGAIDSCLEALEMDPSNTKALY*KAQGWLGLKEFDQALADLKKAQEI

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	0.00 RPM	28.61 RPM
SRP007412_kidney	0.02 RPM	30.09 RPM
SRP007412_liver	0.03 RPM	28.67 RPM
SRP007412_testis	0.05 RPM	29.59 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1888 was not detected

EST

No EST(s) were mapped for retro_mmus_1888 retrocopy.

TSS

No TSS is located nearby retro_mmus_1888 retrocopy 5' end.

Lab

retro_mmus_1888 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1888 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,