RetrogeneDB ID: retro_mmus_873

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:69123100..69123777(+)
• Located in intron of: None

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_873
ATGGAAGGTAATGGATCCGTCGACATGTTCTCAGAAGTCCTGGAGAATCAGTTCCTCCAGGCCGCTAAGCTGGTGAGAAT
CACTTGGACTCTGAAATTCAGAAACTGGATCAGATTGGTGAAGATGAACTGGAGCTGCTCAAAGAAAAGAGGCTGGCGGC
GCTCAGGCAGGCTCAGCAGCAGAAAGAAGAGTGGCTTTCCAAAGGGCACGGGGAGTACAGAGAAATCGGCAGCGAGAGAG
ACTTCTTTCAAGAAGTCAAGGAGAGTGAGAAAGTGGTTTGCCATTTCTACAGAGACACCACATTCAGGTGTAAAATACTA
GACAGACATTTGGCAATTCTGGCCAAAAAACATCTTGAAACCAAGTTTTTGAAGCTGAATGTGGAAAAGGCACCATTCCT
CTGTGAGAGACTGCGGATCAAGGTCATCCCCACGCTAGCTCTCTTAAGAGATGGCAAGACACAAGATTATGTTGTTGGAT
TCACCGACCTAGGAAATACAGACGACTTCACTACAGAAACTTTAGAATGGAGACTTGGTTGTTCTGATGTTATCAATTAC
AGTGGAAATTTAATGGAGCCACCATTTCAGAGCCAAAAGAAATTTGGGACAAACTTCACAAAGCTGGAAAAGAAAACTAT
CCGAGGAAAGAAATACGATTCCGATTCTGATGATGAC

Alignment

ORF - retro_mmus_873 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEGNGSVDMFSEVLENQFLQAAKLV-ENHLDSEIQKLDQIGEDELELLKEKRLAALRKAQQQKQEWLSKG
          MEGNGSVDMFSEVLENQFLQAAKLV.ENHLDSEIQKLDQIGEDELELLKEKRLAALR.AQQQK.EWLSKG
Retrocopy MEGNGSVDMFSEVLENQFLQAAKLV<ENHLDSEIQKLDQIGEDELELLKEKRLAALRQAQQQKEEWLSKG

Parental  HGEYREIGSERDFFQEVKESEKVVCHFYRDTTFRCKILDRHLAILAKKHLETKFLKLNVEKAPFLCERLR
          HGEYREIGSERDFFQEVKESEKVVCHFYRDTTFRCKILDRHLAILAKKHLETKFLKLNVEKAPFLCERLR
Retrocopy HGEYREIGSERDFFQEVKESEKVVCHFYRDTTFRCKILDRHLAILAKKHLETKFLKLNVEKAPFLCERLR

Parental  IKVIPTLALLRDGKTQDYVVGFTDLGNTDDFTTETLEWRLGCSDVINYSGNLMEPPFQSQKKFGTNFTKL
          IKVIPTLALLRDGKTQDYVVGFTDLGNTDDFTTETLEWRLGCSDVINYSGNLMEPPFQSQKKFGTNFTKL
Retrocopy IKVIPTLALLRDGKTQDYVVGFTDLGNTDDFTTETLEWRLGCSDVINYSGNLMEPPFQSQKKFGTNFTKL

Parental  EKKTIRGKKYDSDSDDD
          EKKTIRGKKYDSDSDDD
Retrocopy EKKTIRGKKYDSDSDDD

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	0.02 RPM	25.21 RPM
SRP007412_cerebellum	0.00 RPM	25.79 RPM
SRP007412_heart	0.06 RPM	23.32 RPM
SRP007412_kidney	0.10 RPM	33.78 RPM
SRP007412_liver	0.03 RPM	23.70 RPM
SRP007412_testis	0.14 RPM	49.22 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_873 was not detected

EST

No EST(s) were mapped for retro_mmus_873 retrocopy.

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_23951	367 libraries	78 libraries	163 libraries	229 libraries	235 libraries

The graphical summary, for retro_mmus_873 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_873 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_873 has 0 orthologous retrocopies within eutheria group .

---

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,