RetrogeneDB ID: retro_mmus_3254

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:25351016..25351661(+)
• 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_3254
GGACTAGGTGTGGTAAGGATGCTTGAAAATGCAGACATGAATGGTGAAAACCCTACCAAACTGTGTTATTGCAGAACATG
AAGAATTGAAAGAAGGTGATGACTGAGGAACAGTCCCCAAAGAGTGCTGTGGTGATAGTCATCCAGATTTCCCAGAGGGT
GCAGATATAGATTTAAAAGATGTAGGTGAAGTTTTGTTAATAGCTGAAGACTTACAAACATTGGAAACACTTTTTTTCAA
GTCTCAGGACTGGGGTAGCTATTAAAAAAATATGAGAAGGTTTTAAGGTATGTGGATAGTTCAAAGGCTGCTATTGAGAA
AGCAGATACATTCATACTGCAACCTATAGCCTTAAGTTGTGTGCTGAATGTCAGTGGTGGTAAATTGAAGATGAGAAATT
GGCAACAAGCAATTAACCATTATGTGGAGGCTCTTGAAATGGATATGCTATCAAATATCAGAGCACTATACTGGAAAGCA
CAAGGATGGCAAGGATTAAATGAATAAGATCAGGAATTGGCTGATCTGAAGAAGGTGCCAGAGATAGCCCCAGGAGCTAA
AGCTATCCAGGCAGAATGGCTTAAATTCAAACATGTTAAAGATGTGGAAAGAGAATGAGAAAGAGTGTATGCAAAAATGT
TTGCT

Alignment

ORF - retro_mmus_3254 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.36 %
• Parental protein coverage: 58.38 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GLGVARTLENVEVNGE-KPAKL-CVIAECGELKEGDDWGIFPKDGSGDSHPDFPEDADIDLKDVDKILLI
          GLGV.R.LEN...NGE.KP....CVIAE..ELKEGDD.G..PK...GDSHPDFPE.ADIDLKDV...LLI
Retrocopy GLGVVRMLENADMNGE<KPYQT<CVIAEHEELKEGDD*GTVPKECCGDSHPDFPEGADIDLKDVGEVLLI

Parental  SEDLKNIGNTFFKSQNWEM-AIKKYAKVLRYVDSSKAVIEKADRSRLQPIALSCVLNIGACKLKMSNWQG
          .EDL......FFKSQ.W.....KKY.KVLRYVDSSKA.IEKAD...LQPIALSCVLN....KLKM.NWQ.
Retrocopy AEDLQTLETLFFKSQDWGS<LLKKYEKVLRYVDSSKAAIEKADTFILQPIALSCVLNVSGGKLKMRNWQQ

Parental  AIDSCLEALEMDP-SNTKALYRKAQGWQGLKEYDQALADLKKAQEIAPGDKAIQAELLKVKQMIKAQKDK
          AI....EALEMD..SN..ALY.KAQGWQGL.E.DQ.LADLKK..EIAPG.KAIQAE.LK.K.........
Retrocopy AINHYVEALEMDMLSNIRALYWKAQGWQGLNE*DQELADLKKVPEIAPGAKAIQAEWLKFKHVKDVERE*

Parental  EKAVYAKMFA
          E..VYAKMFA
Retrocopy ER-VYAKMFA

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	0.04 RPM	41.21 RPM
SRP007412_heart	0.00 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_3254 was not detected

EST

No EST(s) were mapped for retro_mmus_3254 retrocopy.

TSS

No TSS is located nearby retro_mmus_3254 retrocopy 5' end.

Lab

retro_mmus_3254 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3254 has 0 orthologous retrocopies within eutheria group .

---

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,