RetrogeneDB ID: retro_mmus_304

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:31615303..31616659(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000070960
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Paox
• Ensembl ID: ENSMUSG00000025464
• Aliases: Paox, 2410012F02Rik, AI118225, Pao
• Description: polyamine oxidase (exo-N4-amino) [Source:MGI Symbol;Acc:MGI:1916983]

Sequence

>retro_mmus_304
GGTGGTGTAGTGGAGCTGGGTGCACACTGGATCCATGGGCCCTCCCAGGACAATCCTGTCTTCCAGCTGGCTGCAGAATT
CGGGCTCCTGGGGGAGAAAGAATTATCGGAAGAGAACCAGCTTGTGGATACAGGAGGGCACGTGGCCCTGCCCTCCATGA
TCTGGTCCAGCTCTGGAACAAGTGTGAGCCTGGAGCTGATGACAGAGATGGCCCGTCTGTTCTATGGACTGATAGAGCGG
ACCCGAGAATTCCTGAATGAATCTGAAACCCCAATGGCCAGTGTTGGAGAGTTCCTGAAGAAGGAGATAAGTCAGCAGGT
GGCTAGCTGGACCGAGGATGATGAGGACACCAGAAAGCGCAAGCTGGCTATCCTGAATACTTTCTTCAACATAGAGTGTT
GTGTGAGCGGCACCCACAGCATGGACCTGGTGGCTCTTGCACCGTTCGGGGAGTATACAGTGCTGCCTGGGCTGGATTGC
ATCTTGGCTGGTGGCTACCAAGGACTTACCGACCGCATACTGGCTTCCTTGCCCAAGGATACGGTCGCTTTTGACAAGCC
GGTGAAGACCATTCACTGGAATGGGTCCTTCCAGGAAGCTGCTTTTCCAGGGGAGACCTTCCCCGTATTGGTGGAGTGTG
AAGATGGTGCCCGCCTGCCTGCACATCATGTCATTGTCACAGTGCCATTAGGTTTTCTTAAAGAACACCAAGATACCTTT
TTTGAGCCACCACTGCCTGCCAAAAAAGCAGAAGCCATCAAAAAACTAGGCTTTGGTACCAACAACAAAATCTTCTTGGA
GTTTGAAGAGCCCTTCTGGGAGCCCGACTGCCAGTTCATCCAGGTGGTGTGGGAAGATACATCGCCCTTACAGGACACAG
CTCTCTCACTCCAAGACACCTGGTTCAAGAAGCTCATTGGATTTTTGGTCCAGCCTTCTTTTGAGTCTTCACATGTGCTC
TGTGGGTTTATTGCTGGGCTGGAGTCGGAGTTTATGGAGACTCTGTCAGATGAAGAAGTGCTTCTGTCTCTAACCCAAGT
ACTCCGGAGAGTGACAGGAAACCCACAATTGCCAGCAGCCAAGAGCGTACGAAGGTCTCAGTGGCACAGTGCCCCGTACA
CCCGAGGTTCCTACAGCTATGTGGCTGTGGGCAGCACTGGCGATGACCTAGATCTGATGGCTCAGCCCCTCCCTGAAGAT
GGAACTGGCACCCAGCTCCAGGTACTCTTTGCTGGGGAAGCCACACATCGGACATTTTATTCTACCACACATGGGGCCCT
CCTGTCTGGCTGGAGAGAAGCTGATCGCCTCGTTAGTCTGTGGGACTCACAGGTGGAGCAGTCGCGGCCCAGGCTG

Alignment

ORF - retro_mmus_304 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 89.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGVVELGAHWIHGPSQDNPVFQLAAEFGLLGEKELSEENQLVDTGGHVALPSMIWSSSGTSVSLELMTEM
          GGVVELGAHWIHGPSQDNPVFQLAAEFGLLGEKELSEENQLVDTGGHVALPSMIWSSSGTSVSLELMTEM
Retrocopy GGVVELGAHWIHGPSQDNPVFQLAAEFGLLGEKELSEENQLVDTGGHVALPSMIWSSSGTSVSLELMTEM

Parental  ARLFYGLIERTREFLNESETPMASVGEFLKKEISQQVASWTEDDEDTRKRKLAILNTFFNIECCVSGTHS
          ARLFYGLIERTREFLNESETPMASVGEFLKKEISQQVASWTEDDEDTRKRKLAILNTFFNIECCVSGTHS
Retrocopy ARLFYGLIERTREFLNESETPMASVGEFLKKEISQQVASWTEDDEDTRKRKLAILNTFFNIECCVSGTHS

Parental  MDLVALAPFGEYTVLPGLDCILAGGYQGLTDRILASLPKDTVAFDKPVKTIHWNGSFQEAAFPGETFPVL
          MDLVALAPFGEYTVLPGLDCILAGGYQGLTDRILASLPKDTVAFDKPVKTIHWNGSFQEAAFPGETFPVL
Retrocopy MDLVALAPFGEYTVLPGLDCILAGGYQGLTDRILASLPKDTVAFDKPVKTIHWNGSFQEAAFPGETFPVL

Parental  VECEDGARLPAHHVIVTVPLGFLKEHQDTFFEPPLPAKKAEAIKKLGFGTNNKIFLEFEEPFWEPDCQFI
          VECEDGARLPAHHVIVTVPLGFLKEHQDTFFEPPLPAKKAEAIKKLGFGTNNKIFLEFEEPFWEPDCQFI
Retrocopy VECEDGARLPAHHVIVTVPLGFLKEHQDTFFEPPLPAKKAEAIKKLGFGTNNKIFLEFEEPFWEPDCQFI

Parental  QVVWEDTSPLQDTALSLQDTWFKKLIGFLVQPSFESSHVLCGFIAGLESEFMETLSDEEVLLSLTQVLRR
          QVVWEDTSPLQDTALSLQDTWFKKLIGFLVQPSFESSHVLCGFIAGLESEFMETLSDEEVLLSLTQVLRR
Retrocopy QVVWEDTSPLQDTALSLQDTWFKKLIGFLVQPSFESSHVLCGFIAGLESEFMETLSDEEVLLSLTQVLRR

Parental  VTGNPQLPAAKSVRRSQWHSAPYTRGSYSYVAVGSTGDDLDLMAQPLPEDGTGTQLQVLFAGEATHRTFY
          VTGNPQLPAAKSVRRSQWHSAPYTRGSYSYVAVGSTGDDLDLMAQPLPEDGTGTQLQVLFAGEATHRTFY
Retrocopy VTGNPQLPAAKSVRRSQWHSAPYTRGSYSYVAVGSTGDDLDLMAQPLPEDGTGTQLQVLFAGEATHRTFY

Parental  STTHGALLSGWREADRLVSLWDSQVEQSRPRL
          STTHGALLSGWREADRLVSLWDSQVEQSRPRL
Retrocopy STTHGALLSGWREADRLVSLWDSQVEQSRPRL

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	0.89 RPM
SRP007412_cerebellum	0.04 RPM	0.78 RPM
SRP007412_heart	0.00 RPM	1.15 RPM
SRP007412_kidney	0.23 RPM	1.75 RPM
SRP007412_liver	1.28 RPM	12.23 RPM
SRP007412_testis	0.27 RPM	0.78 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_304 was not detected

EST

3 EST(s) were mapped to retro_mmus_304 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA239911	31615585	31616078	99.2	488	4	484
AI466958	31615585	31616073	99.2	484	3	479
BF011657	31615630	31616140	100	510	0	510

TSS

No TSS is located nearby retro_mmus_304 retrocopy 5' end.

Lab

retro_mmus_304 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_304 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	ENSMUSG00000025464	1 retrocopy	retro_mmus_304 ,