RetrogeneDB ID: retro_mmus_2568

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:55624411..55625590(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083902
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Papd4
• Ensembl ID: ENSMUSG00000042167
• Aliases: Papd4, 8030446C20Rik, AI649009, GLD-2, Gld2
• Description: PAP associated domain containing 4 [Source:MGI Symbol;Acc:MGI:2140950]

Sequence

>retro_mmus_2568
GGAAAATGGCAGCATTTCCATTCACCACACCAAGAGCCAACTATAATCAACCAGCTAGTGCCTTTATCAGGTGACAGAAG
ATATTCCATGCCACCGTTGTTTCACACGCACTATATACCAGATATAGTCAGATGTGTTCCACCTCTTCGAGAAATTCCAC
TGTTAGAACCTCGAGAAATCACACTGCCTGAGGCCAAAGATAAGTTGAGTCAGCAGATACTAGAGTTGTTTGAAACTTGT
CAGCAGCAAGCAAGTGACTTGAAGAAGAAAGAACTCTGTAGAGCACAGCTGCAGAGAGAGATCCAGCTGCTCTTCCCACA
AAGCAGACTTTTTCTCCTTGGATCATCTTTGAATGGATTTGGTGCCCGAAGCAGTGATGGCGATTTATGCTTAGTTGTTA
AAGAAGAACCAGTAAATCAGAAGACTGAAGCATGACATATACTCACCTTAGTCCATAAGTACTTCTGTACTAGATTGTCT
GGCTATACTGAGAGACCTCAGCTGATTCGTGCAAAAGTGCCAATTGTGAAGTTCAGGGATAAAGTCAGTTGTGTGGAATT
CGACTTAAATGTAAACAATACCGTTGGAATTAGAAATACATTCCTTCTCAGAACCTATGCATACCTTGAAAATCGAGTTC
GTCCATTAGTGCTGGTGATTAAGAAGTGGGCAAGTCACCATGACATCAATGATGCCAGTCGTGGCACATTAAGCAGCTAT
AGTCTTGTATTGATGGTTTTGCACTATTTACAAACCCTACCTGAACCCATCCTTCCATCCCTCCAAAAAATTTACCCAGA
ATCTTTTAGTACTTCTGTCCAGCTGCACCTTGTTCATCATGCCCCATGTAATGTCCCTCCTTACCTCTCAAAGAATGAAT
CAAGTCGTGGGGACCTCTTACTGGGCTTTCTGAAATATTATGCTACAGAATTTGACTGGAACACTCAGGTGATTTCAGTT
CGTGAAGCCAACGCCATCCCAAGGCCTGAGGATATGGAATGGAGAAATAAATACATCTGTGTTGAAGAACCTTTTGATGG
AACTAATACCGCCAGAGCTGTGCATGAGAAGCAGAAGTTTGATATGATCAAGGATCAATTTTTAAAGTTATGGCAGAGAT
TGAAAAACAAGAGAGATCTGAACAGTGTGCTGCCTTTGAGAGCTGCTACCCTGAAAAGA

Alignment

ORF - retro_mmus_2568 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.22 %
• Parental protein coverage: 82.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GKRQRFHSPHQEPTIINQLVPLSGDRRYSMPPLFHTHYIPDIVRCVPPLREIPLLEPREITLPEAKDKLS
          GK.Q.FHSPHQEPTIINQLVPLSGDRRYSMPPLFHTHYIPDIVRCVPPLREIPLLEPREITLPEAKDKLS
Retrocopy GKWQHFHSPHQEPTIINQLVPLSGDRRYSMPPLFHTHYIPDIVRCVPPLREIPLLEPREITLPEAKDKLS

Parental  QQILELFETCQQQASDLKKKELCRAQLQREIQLLFPQSRLFLVGSSLNGFGARSSDGDLCLVVKEEPCFF
          QQILELFETCQQQASDLKKKELCRAQLQREIQLLFPQSRLFL.GSSLNGFGARSSDGDLCLVVKEEP...
Retrocopy QQILELFETCQQQASDLKKKELCRAQLQREIQLLFPQSRLFLLGSSLNGFGARSSDGDLCLVVKEEP---

Parental  QVNQKTEARHILTLVHKHFCTRLSGYIERPQLIRAKVPIVKFRDKVSCVEFDLNVNNTVGIRNTFLLRTY
          .VNQKTEA.HILTLVHK.FCTRLSGY.ERPQLIRAKVPIVKFRDKVSCVEFDLNVNNTVGIRNTFLLRTY
Retrocopy -VNQKTEA*HILTLVHKYFCTRLSGYTERPQLIRAKVPIVKFRDKVSCVEFDLNVNNTVGIRNTFLLRTY

Parental  AYLENRVRPLVLVIKKWASHHDINDASRGTLSSYSLVLMVLHYLQTLPEPILPSLQKIYPESFSTSVQLH
          AYLENRVRPLVLVIKKWASHHDINDASRGTLSSYSLVLMVLHYLQTLPEPILPSLQKIYPESFSTSVQLH
Retrocopy AYLENRVRPLVLVIKKWASHHDINDASRGTLSSYSLVLMVLHYLQTLPEPILPSLQKIYPESFSTSVQLH

Parental  LVHHAPCNVPPYLSKNESSLGDLLLGFLKYYATEFDWNTQMISVREAKAIPRPDDMEWRNKYICVEEPFD
          LVHHAPCNVPPYLSKNESS.GDLLLGFLKYYATEFDWNTQ.ISVREA.AIPRP.DMEWRNKYICVEEPFD
Retrocopy LVHHAPCNVPPYLSKNESSRGDLLLGFLKYYATEFDWNTQVISVREANAIPRPEDMEWRNKYICVEEPFD

Parental  GTNTARAVHEKQKFDMIKDQFLKSWQRLKNKRDLNSVLPLRAATLKR
          GTNTARAVHEKQKFDMIKDQFLK.WQRLKNKRDLNSVLPLRAATLKR
Retrocopy GTNTARAVHEKQKFDMIKDQFLKLWQRLKNKRDLNSVLPLRAATLKR

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	0.14 RPM	11.61 RPM
SRP007412_cerebellum	0.22 RPM	8.86 RPM
SRP007412_heart	0.09 RPM	6.44 RPM
SRP007412_kidney	0.25 RPM	8.35 RPM
SRP007412_liver	0.25 RPM	9.04 RPM
SRP007412_testis	0.09 RPM	7.36 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2568 was not detected

EST

1 EST(s) were mapped to retro_mmus_2568 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AI465931	55624529	55624743	100	214	0	214

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_114530	680 libraries	341 libraries	48 libraries	2 libraries	1 library

The graphical summary, for retro_mmus_2568 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_2568 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2568 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000042167	1 retrocopy	retro_mmus_2568 ,