RetrogeneDB ID: retro_mmus_2228

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:19708414..19709150(-)
• Located in intron of: None

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_2228
ACTGAATCCAGAACTGGGAAACCTCTCCATTTTAAATGACCTGTCTATCAAATTATTAAGAAATTTATGATTCAGGGTGG
AAACATCTCAAATCAGAATGGGACAGATGGAGAAAGTATTTATGGTGAGACAGTTGAAGATCAAAATTTTCATTATAAGC
CTGATCAGGAGGGTTGGCTGAGCATGGCAAATGCTGACCCCGATGAAAATGGTTCTCAGTTCTTTATCACGACAGTTCTG
ACTCCTCATTCGGATGGGAAACATGTTGTGTTTGGTCAAGTAATTAAAGGACTGGGTGTGGCAAGGGTGCTAGAAAATGT
AGAAGTGAGGGTTGACAACCTGTCAAACTGTGTGTTATTACAGAATGTGGAGGACGGAAAGAAGGGGATGACCCACAAAG
ATGGCTCTGATGATAGTCATACAGATTTCACTGAGAATGCAGATACAGATTAAAATATGGAGATAAATTTTATTAATATC
TGAAGACTTAGAAAACATTGGAAATTCAAGTCTCAGAACTGGGATGTGGCTATTAAAAAAGGTTTTAAGGTGCTTGGATA
GTTCAAAGGTTGTTATTGAGAAAGCAGATTCATCCAGACTGCAGCCTGTAGCCTTAGGCTGTGTGCTGTGTGCCTGTAAA
TTGAAGGTGTCAGATTGGCATGGGGCAACTGACAGTTGTTTGGAGGTTCCTGAAATGCACCTGTCAAACACCAAAGCAGT
ATACCAAAAATCAAGG

Alignment

ORF - retro_mmus_2228 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.62 %
• Parental protein coverage: 69.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TGSTTGKPLHFKGCPFHRIIKKFMIQGGDFSNQNGTGGESIYGEKFEDENFHYKHDREGLLSMANAGPNT
          T.S.TGKPLHFK..P...IIKKFMIQGG..SNQNGT.GESIYGE..ED.NFHYK.D.EG.LSMANA.P..
Retrocopy TESRTGKPLHFK*-PVYQIIKKFMIQGGNISNQNGTDGESIYGETVEDQNFHYKPDQEGWLSMANADPDE

Parental  NGSQFFITTVPTPHLDGKHVVFGQVIKGLGVARTLENVEVNGEKPAKLCVIAECGELKEGDDWGIFPKDG
          NGSQFFITTV.TPH.DGKHVVFGQVIKGLGVAR.LENVEV........CV.........G...G...KDG
Retrocopy NGSQFFITTVLTPHSDGKHVVFGQVIKGLGVARVLENVEVRVDNLSN-CVLLQ--NVEDGKK-GMTHKDG

Parental  SGDSHPDFPEDADID-LKDVDK-ILLISEDLKNIGNTFFKSQNWEMAIKKYAKVLRYVDSSKAVIEKADR
          S.DSH.DF.E.AD.D.LK..DK.ILLISEDL.NIGN.......W....KK....L...DSSK.VIEKAD.
Retrocopy SDDSHTDFTENADTD<LKYGDK<ILLISEDLENIGNSSLRTGMW--LLKKVLRCL---DSSKVVIEKADS

Parental  SRLQPIALSCVLNIGACKLKMSNWQGAIDSCLEALEMDPSNTKALYRKAQ
          SRLQP.AL.CVL...ACKLK.S.W.GA.DSCLE..EM..SNTKA.Y.K..
Retrocopy SRLQPVALGCVL--CACKLKVSDWHGATDSCLEVPEMHLSNTKAVYQKSR

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	0.09 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 actvity near the 5' end of retro_mmus_2228 was not detected

EST

No EST(s) were mapped for retro_mmus_2228 retrocopy.

TSS

No TSS is located nearby retro_mmus_2228 retrocopy 5' end.

Lab

retro_mmus_2228 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2228 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,