RetrogeneDB ID: retro_mmus_3604

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:44466661..44467233(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082775
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Itpa
• Ensembl ID: ENSMUSG00000074797
• Aliases: Itpa, 2010016I08Rik, AU020102, Itp
• Description: inosine triphosphatase (nucleoside triphosphate pyrophosphatase) [Source:MGI Symbol;Acc:MGI:96622]

Sequence

>retro_mmus_3604
TCTTTGGTGGGGAAGAGGACAGTGTTTGTGATGGGCAATGCAAAGAAGCTGGAGGAGGTCATTAAGATTCTAGGAGATAA
GTTTTCATGTACTTTGGTGGCAAAGAAAATTGACCTGCTTAACTATCAGGAAGAACTGGATGATATTTCCATACAGAAGT
ATCAGGAGACAGCTCACCAGGTGCGGGGCCCTGTACTTGTGAAGAATATCTGTCTGTGCTTTAATGCACTTAGGGGACTT
CCCAGTCCCTACATAAAATAGTTCCTGTAGAAGCTAAAGTCTGTAGGTCTCCACCAGCTCCTGGCTGGCTTTGAAGATAA
ATCGGCCTATGCACTCTGCAGATTGGCTCTCAGCCCTAGGGACCCAAGCCAGCCAGTACTCCTGTTCAGAGGCTAGAACT
TGGGAAAGACTGTGATCCCACCAGGATGCTGGGACTTTGCCTTTCAGCCTGATGGATATGAGCAAACATGTGTAGAGATG
CCAGACTAAGAAGAACACCATTTTCTCATCTGTTCCAGGCCCTACTTAAGCTACAAGAATACTTTAGTGTGACTGCTGGG
GCTGGTGACCAC

Alignment

ORF - retro_mmus_3604 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.9 %
• Parental protein coverage: 98.48 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLVGKKIVFVTGNAKKLEEVIQILGDNFPCTLEAQKIDLPEYQGEPDEISIQKCREAARQVQGPVLVEDT
          SLVGK..VFV.GNAKKLEEVI.ILGD.F.CTL.A.KIDL..YQ.E.D.ISIQK..E.A.QV.GPVLV...
Retrocopy SLVGKRTVFVMGNAKKLEEVIKILGDKFSCTLVAKKIDLLNYQEELDDISIQKYQETAHQVRGPVLVKNI

Parental  CLCFNALGGLPGPYIKWFLQKLKPEGLHQLLAGFEDKSAYALCTFALSTGDPSQPVLLFRGQTSGQIVMP
          CLCFNAL.GLP.PYIK.FL.KLK..GLHQLLAGFEDKSAYALC..ALS..DPSQPVLLFRG...G..V.P
Retrocopy CLCFNALRGLPSPYIK*FL*KLKSVGLHQLLAGFEDKSAYALCRLALSPRDPSQPVLLFRG*NLGKTVIP

Parental  RGSRDFGWDPCFQPDGYEQTYAEMP-KSEKNTISHRFRALHKLQEYFSVAAGAGDH
          .G.....WD..FQPDGYEQT..EMP........SH.F.AL.KLQEYFSV.AGAGDH
Retrocopy PGC----WDFAFQPDGYEQTCVEMP<RLRRTPFSHLFQALLKLQEYFSVTAGAGDH

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	18.69 RPM
SRP007412_cerebellum	0.00 RPM	9.73 RPM
SRP007412_heart	0.00 RPM	9.96 RPM
SRP007412_kidney	0.00 RPM	12.59 RPM
SRP007412_liver	0.00 RPM	9.53 RPM
SRP007412_testis	0.00 RPM	10.25 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3604 was not detected

EST

No EST(s) were mapped for retro_mmus_3604 retrocopy.

TSS

No TSS is located nearby retro_mmus_3604 retrocopy 5' end.

Lab

retro_mmus_3604 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3604 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011021	1 retrocopy	retro_amel_476,
Canis familiaris	ENSCAFG00000031613	1 retrocopy	retro_cfam_1841,
Felis catus	ENSFCAG00000013414	1 retrocopy	retro_fcat_1776,
Microcebus murinus	ENSMICG00000013833	1 retrocopy	retro_mmur_1207,
Mustela putorius furo	ENSMPUG00000008868	1 retrocopy	retro_mputfur_971,
Mus musculus	ENSMUSG00000074797	3 retrocopies	retro_mmus_2063, retro_mmus_3369, retro_mmus_3604 ,