RetrogeneDB ID: retro_mmus_154

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:87078270..87079158(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000071035
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Tmx2
• Ensembl ID: ENSMUSG00000050043
• Aliases: Tmx2, 2310042M24Rik, AA589631, Txndc14
• Description: thioredoxin-related transmembrane protein 2 [Source:MGI Symbol;Acc:MGI:1914208]

Sequence

>retro_mmus_154
ATGGCTGTCCTTGCGCCTCTGATTGCTTTGGTGTACTCGGTGCCGAGGCTTTCTCGATGGCTGGCCCGACCTTATTGCCT
TCTGTCTGCTCTGCTTTCCATTGCTTTCCTCCTCGTGAGGAAACTGCCACCGATTTGCAATGGTCTCCCCACGCAACGCG
AAGATGGCAACCCGTGTGACTTTGACTGGAGAGAAGTGGAGATCCTGATGTTCCTCAGTGCCATTGTGATGATGAAGAAC
CGCAGATCCATCACTGTGGAGCAACACGTAGGCAACATCTTTATGTTTAGTAAAGTGGCCAACGCCATCCTTTTCTTCCG
ACTGGATATTCGAATGGGTCTGCTATACCTCACACTCTGCATAGTGTTCCTGATGACCTGCAAGCCCCCGCTGTACATGG
GTCCTGAGTATATCAAGTACTTCAATGATAAAACCATTGATGAGGAGCTGGAGCGAGACAAGAGGGTCACTTGGATTGTG
GAGTTCTTTGCCAACTGGTCTAATGATTGCCAGTCCTTTGCTCCCATCTATGCGGACTTGTCCCTCAAGTACAACTGTTC
AGGGCTAAATTTTGGGAAGGTAGATGTTGGACGCTACACTGACGTTAGCACACGGTACAAAGTAAGCACATCACCCCTCA
CCAGACAGCTCCCTACCCTGATTCTGTTCCAAGGCGGCAAGGAGGTCATTCGTCGGCCGCAGATTGACAAGAAAGGACGA
GCTGTCTCTTGGACCTTTTCTGAAGAGAATGTGATTCGAGAATTCAACTTGAATGAGCTATACCAACGAGCCAAGAAGCA
CTCAAAGGGTGGAGACATGTCAGAAGAGAAGCCTGTGGACCCTGCTCCCACTACTGTGCCAGATGGGGAAAACAAGAAGG
ACAAATAG

Alignment

ORF - retro_mmus_154 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MAVLAPLIALVYSVPRLSRWLARPYCLLSALLSIAFLLVRKLPPICNGLPTQREDGNPCDFDWREVEILM
          MAVLAPLIALVYSVPRLSRWLARPYCLLSALLSIAFLLVRKLPPICNGLPTQREDGNPCDFDWREVEILM
Retrocopy MAVLAPLIALVYSVPRLSRWLARPYCLLSALLSIAFLLVRKLPPICNGLPTQREDGNPCDFDWREVEILM

Parental  FLSAIVMMKNRRSITVEQHVGNIFMFSKVANAILFFRLDIRMGLLYLTLCIVFLMTCKPPLYMGPEYIKY
          FLSAIVMMKNRRSITVEQHVGNIFMFSKVANAILFFRLDIRMGLLYLTLCIVFLMTCKPPLYMGPEYIKY
Retrocopy FLSAIVMMKNRRSITVEQHVGNIFMFSKVANAILFFRLDIRMGLLYLTLCIVFLMTCKPPLYMGPEYIKY

Parental  FNDKTIDEELERDKRVTWIVEFFANWSNDCQSFAPIYADLSLKYNCSGLNFGKVDVGRYTDVSTRYKVST
          FNDKTIDEELERDKRVTWIVEFFANWSNDCQSFAPIYADLSLKYNCSGLNFGKVDVGRYTDVSTRYKVST
Retrocopy FNDKTIDEELERDKRVTWIVEFFANWSNDCQSFAPIYADLSLKYNCSGLNFGKVDVGRYTDVSTRYKVST

Parental  SPLTRQLPTLILFQGGKEVIRRPQIDKKGRAVSWTFSEENVIREFNLNELYQRAKKHSKGGDMSEEKPVD
          SPLTRQLPTLILFQGGKEVIRRPQIDKKGRAVSWTFSEENVIREFNLNELYQRAKKHSKGGDMSEEKPVD
Retrocopy SPLTRQLPTLILFQGGKEVIRRPQIDKKGRAVSWTFSEENVIREFNLNELYQRAKKHSKGGDMSEEKPVD

Parental  PAPTTVPDGENKKDK
          PAPTTVPDGENKKDK
Retrocopy PAPTTVPDGENKKDK

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	0.44 RPM	79.18 RPM
SRP007412_cerebellum	0.56 RPM	87.88 RPM
SRP007412_heart	0.28 RPM	44.20 RPM
SRP007412_kidney	0.37 RPM	52.28 RPM
SRP007412_liver	0.22 RPM	21.71 RPM
SRP007412_testis	0.18 RPM	33.62 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_154 was not detected

EST

1 EST(s) were mapped to retro_mmus_154 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA052431	87078588	87078764	100	176	0	176

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_57468	428 libraries	222 libraries	402 libraries	16 libraries	4 libraries

The graphical summary, for retro_mmus_154 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_154 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_154 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000035426	1 retrocopy	retro_cjac_3263,
Homo sapiens	ENSG00000213593	1 retrocopy	retro_hsap_4158,
Gorilla gorilla	ENSGGOG00000001519	1 retrocopy	retro_ggor_2792,
Monodelphis domestica	ENSMODG00000020112	1 retrocopy	retro_mdom_924,
Mus musculus	ENSMUSG00000050043	1 retrocopy	retro_mmus_154 ,
Pan troglodytes	ENSPTRG00000033702	1 retrocopy	retro_ptro_2827,