RetrogeneDB ID: retro_mmus_3369

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:95675427..95676019(-)
• Located in intron of: ENSMUSG00000015354

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

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_3369
GTGGCCACACCTTTGGTGGGGAAGAAGATACGTGTTTGTGAGGAGAAGTGCAAAGAAGCTGGAGGAGCTCATTCAGATTC
TAGGAGATAAGTTTCCACGCCCTTTGGTGGCACAGGAACATTGACCTTCCTGAGTACCAGGGAGAGCCAGGTGAAATTTC
CATACAGAAGTGACTGGAGGCAGCTTGCTAGGTGCAGGGCTCTGTACTGGTGGAGAATACGTGTCCAGGCTTTAATGCAC
TTGGGGGACTCCCTGGACCCTACCTAAGATGGTTCCTGCAGAAGCTGAAGCCTAAAGGTCTCCACTAGCTCCTGACTAGC
TTTGCAGACGAATCAGCCTATGCACTCTGCACTATGCTCTCAGCACTGGGGACCCAAGCCAGCCAGTGCTCCTGTTCAGA
GGCCAGACCTCGGGACAGATTATGATACCACGAGGCTGCCGGGACTTTGGCTGGGATCCCTGCTTTCCGCCTGATGGATA
TGAACAAATATATACAGAGATACCAAAGGCTGAGAACACCATTTCTCGTCGGTTCCGAGCCCTGCTCAAGCTGCAGGAGT
ACTTTAGTGTGGCTGCTGGGACTGGTGACCAC

Alignment

ORF - retro_mmus_3369 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.61 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAASLVGKKI-VFVTGNAKKLEEVIQILGDNFPCTLEAQK-IDLPEYQGEPDEISIQKCREAARQVQGPV
          .A..LVGKKI.VFV...AKKLEE.IQILGD.FP..L.AQ..IDLPEYQGEP.EISIQK..EAA..VQG.V
Retrocopy VATPLVGKKI>VFVRRSAKKLEELIQILGDKFPRPLVAQE>IDLPEYQGEPGEISIQK*LEAAC*VQGSV

Parental  LVEDTCLCFNALGGLPGPYIKWFLQKLKPEGLHQLLAGFEDKSAYALCT-FALSTGDPSQPVLLFRGQTS
          LVE.TC..FNALGGLPGPY..WFLQKLKP.GLH.LL..F.D.SAYALCT..ALSTGDPSQPVLLFRGQTS
Retrocopy LVENTCPGFNALGGLPGPYLRWFLQKLKPKGLH*LLTSFADESAYALCT<YALSTGDPSQPVLLFRGQTS

Parental  GQIVMPRGSRDFGWDPCFQPDGYEQTYAEMPKSEKNTISHRFRALHKLQEYFSVAAGAGDH
          GQI..PRG.RDFGWDPCF.PDGYEQ.Y.E.PK.E.NTIS.RFRAL.KLQEYFSVAAG.GDH
Retrocopy GQIMIPRGCRDFGWDPCFPPDGYEQIYTEIPKAE-NTISRRFRALLKLQEYFSVAAGTGDH

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	0.09 RPM	9.73 RPM
SRP007412_heart	0.00 RPM	9.96 RPM
SRP007412_kidney	0.02 RPM	12.59 RPM
SRP007412_liver	0.03 RPM	9.53 RPM
SRP007412_testis	0.05 RPM	10.25 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3369 was not detected

EST

No EST(s) were mapped for retro_mmus_3369 retrocopy.

TSS

No TSS is located nearby retro_mmus_3369 retrocopy 5' end.

Lab

retro_mmus_3369 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3369 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,