RetrogeneDB ID: retro_mmus_2791

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:128883851..128884352(+)
• Located in intron of: ENSMUSG00000090164

Retrocopy information

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

Parental gene information

• Parental gene symbol: Txndc9
• Ensembl ID: ENSMUSG00000058407
• Aliases: Txndc9, AI098020, APACD
• Description: thioredoxin domain containing 9 [Source:MGI Symbol;Acc:MGI:2138153]

Sequence

>retro_mmus_2791
ATGGAAGGTAATGGATCCATCGACATGTTCTCAGAAGTCCTAGAGAAGCAGTTCCTCCAGGCTGCTAAGCTAGTGGAAAA
TCACTTGGACTCTGAAATTCAGAAACTGGATCAGATTGGTGAAGATGAACTGGAGCTGCTCAAAGAAAACTGGTGACGCT
CAGGCAGGCTCAGCAGCAGAAACAAGAGTGGCATTCCAAAGGGCACTGGGGTGTACAGAGAAATCGGCAGCGAGAGAGAC
TTCTTTTAAGAAGTCAAGGAGAGTGAGAAAGTGGTTTGCCATTTCTACAGAGACACCGCATTCAGGTGTAAAATACTAGA
CAGACATTTGCCAATTCCGGCCAAAAACCATCTTGAAACCAAGTTTTTGAAGCTGAATGTGGAAAAGACACCATTCCCCT
GTGAGAGACTGCAGATCAAGGTCACCCCCACACTAGCTCTCTTGAGAGATGGCAAGACACAAGATTATGTTGTTGGATTC
ACCGCCCTAAGAAATACAGAT

Alignment

ORF - retro_mmus_2791 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.71 %
• Parental protein coverage: 74.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEGNGSVDMFSEVLENQFLQAAKLVENHLDSEIQKLDQIGEDELELLKE-KRLAALRKAQQQKQEWLSKG
          MEGNGS.DMFSEVLE.QFLQAAKLVENHLDSEIQKLDQIGEDELELLKE.K........QQ.KQEW.SKG
Retrocopy MEGNGSIDMFSEVLEKQFLQAAKLVENHLDSEIQKLDQIGEDELELLKE<KLVTLRQAQQQ-KQEWHSKG

Parental  H-GEYREIGSERDFFQEVKESEKVVCHFYRDTTFRCKILDRHLAILAKKHLETKFLKLNVEKAPFLCERL
          H.G.YREIGSERDFF.EVKESEKVVCHFYRDT.FRCKILDRHL.I.AK.HLETKFLKLNVEK.PF.CERL
Retrocopy H>GVYREIGSERDFF*EVKESEKVVCHFYRDTAFRCKILDRHLPIPAKNHLETKFLKLNVEKTPFPCERL

Parental  RIKVIPTLALLRDGKTQDYVVGFTDLGNTD
          .IKV.PTLALLRDGKTQDYVVGFT.L.NTD
Retrocopy QIKVTPTLALLRDGKTQDYVVGFTALRNTD

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	25.21 RPM
SRP007412_cerebellum	0.00 RPM	25.79 RPM
SRP007412_heart	0.00 RPM	23.32 RPM
SRP007412_kidney	0.04 RPM	33.78 RPM
SRP007412_liver	0.00 RPM	23.70 RPM
SRP007412_testis	0.05 RPM	49.22 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2791 was not detected

EST

No EST(s) were mapped for retro_mmus_2791 retrocopy.

TSS

No TSS is located nearby retro_mmus_2791 retrocopy 5' end.

Lab

retro_mmus_2791 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2791 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009936	1 retrocopy	retro_cjac_500,
Dipodomys ordii	ENSDORG00000013557	1 retrocopy	retro_dord_141,
Homo sapiens	ENSG00000115514	1 retrocopy	retro_hsap_3042,
Gorilla gorilla	ENSGGOG00000024615	1 retrocopy	retro_ggor_2096,
Myotis lucifugus	ENSMLUG00000008110	1 retrocopy	retro_mluc_717,
Mus musculus	ENSMUSG00000058407	2 retrocopies	retro_mmus_2791 , retro_mmus_873,
Pan troglodytes	ENSPTRG00000012278	1 retrocopy	retro_ptro_1996,