RetrogeneDB ID: retro_mmus_192

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:87756354..87757578(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000069324
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Bhmt
• Ensembl ID: ENSMUSG00000074768
• Aliases: None
• Description: betaine-homocysteine methyltransferase [Source:MGI Symbol;Acc:MGI:1339972]

Sequence

>retro_mmus_192
ATGGCACCAGTTGCTGGCAAGAAGGCCAAGAAGGGGATCTTAGAACGCTTAAATGCCGGAGAAGTTGTGATTGGAGATGG
AGGATTTGTCTTTGCACTGGAAAAGAGGGGCTATGTAAAGGCTGGACCCTGGACCCCAGAAGCTGCCGTGGAGCACCCTG
AGGCAGTTCGTCAGCTTCATCGGGAGTTCCTCAGAGCTGGATCGAACGTCATGCAGACCTTCACTTTCTATGCAAGTGAA
GACAAGCTGGAAAACAGAGGAAACTATGTGGCAGAGAAGATTTCTGGGCAGAAAGTCAACGAAGCTGCTTGTGACATTGC
ACGGCAAGTGGCTGATGAAGGAGACGCCTTGGTTGCAGGAGGCGTGAGCCAGACGCCTTCATACCTTAGCTGCAAGAGTG
AGGTAGAAGTGAAAAAGATATTTCGCCAACAGCTAGAGGTGTTCATGAAGAAGAACGTGGACTTCCTCATTGCAGAGTAT
TTTGAACATGTTGAAGAAGCCGTGTGGGCAGTGGAAGCCTTAAAAGCATCTGGTAAGCCCGTAGCAGCTACCATGTGCAT
CGGGCCCGAGGGAGATCTGCATGGCGTGCCCCCTGGAGAGTGTGCCGTGCGTCTGGTGAAAGCAGGCGCCTCCATTGTCG
GCGTGAACTGCCACTTCGACCCCAGCGTCAGCTTACAGACTGTGAAGCTCATGAAGGAGGGTTTGGAGGCTGCGCGGTTG
AAAGCTTACCTGATGAGCCAGCCCCTGGCCTACCATACCCCTGACTGTGGCAAACAGGGATTTATTGATCTCCCAGAATT
CCCCTTTGGATTGGAACCCCGAGTTGCCACTAGATGGGATATTCAAAAATATGCCAGAGAGGCCTACAACCTGGGGGTTA
GGTACATTGGCGGCTGCTGCGGATTTGAGCCCTACCACATCAGGGCGATTGCAGAGGAGTTGGCCCCAGAAAGGGGATTT
TTGCCACCGGCTTCAGAAAAACATGGCAGCTGGGGAAGTGGTTTGGACATGCACACCAAACCCTGGATCAGAGCAAGGGC
CAGAAAGGAATACTGGCAGAATCTGCGAATAGCTTCCGGCAGGCCGTACAACCCTTCCATGTCCCGGCCAGATGCTTGGG
GCGTGACTAAGGGAGCAGCCGAGCTGATGCAGCAGAAGGAGGCCACTACTGAGCAGCAGCTGAGGGAGCTCTTTGAAAAA
CAAAAATTCAAGTCTGCACAGTAG

Alignment

ORF - retro_mmus_192 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  MAPVAGKKAKKGILERLNAGEVVIGDGGFVFALEKRGYVKAGPWTPEAAVEHPEAVRQLHREFLRAGSNV
          MAPVAGKKAKKGILERLNAGEVVIGDGGFVFALEKRGYVKAGPWTPEAAVEHPEAVRQLHREFLRAGSNV
Retrocopy MAPVAGKKAKKGILERLNAGEVVIGDGGFVFALEKRGYVKAGPWTPEAAVEHPEAVRQLHREFLRAGSNV

Parental  MQTFTFYASEDKLENRGNYVAEKISGQKVNEAACDIARQVADEGDALVAGGVSQTPSYLSCKSEVEVKKI
          MQTFTFYASEDKLENRGNYVAEKISGQKVNEAACDIARQVADEGDALVAGGVSQTPSYLSCKSEVEVKKI
Retrocopy MQTFTFYASEDKLENRGNYVAEKISGQKVNEAACDIARQVADEGDALVAGGVSQTPSYLSCKSEVEVKKI

Parental  FRQQLEVFMKKNVDFLIAEYFEHVEEAVWAVEALKASGKPVAATMCIGPEGDLHGVPPGECAVRLVKAGA
          FRQQLEVFMKKNVDFLIAEYFEHVEEAVWAVEALKASGKPVAATMCIGPEGDLHGVPPGECAVRLVKAGA
Retrocopy FRQQLEVFMKKNVDFLIAEYFEHVEEAVWAVEALKASGKPVAATMCIGPEGDLHGVPPGECAVRLVKAGA

Parental  SIVGVNCHFDPSVSLQTVKLMKEGLEAARLKAYLMSQPLAYHTPDCGKQGFIDLPEFPFGLEPRVATRWD
          SIVGVNCHFDPSVSLQTVKLMKEGLEAARLKAYLMSQPLAYHTPDCGKQGFIDLPEFPFGLEPRVATRWD
Retrocopy SIVGVNCHFDPSVSLQTVKLMKEGLEAARLKAYLMSQPLAYHTPDCGKQGFIDLPEFPFGLEPRVATRWD

Parental  IQKYAREAYNLGVRYIGGCCGFEPYHIRAIAEELAPERGFLPPASEKHGSWGSGLDMHTKPWIRARARKE
          IQKYAREAYNLGVRYIGGCCGFEPYHIRAIAEELAPERGFLPPASEKHGSWGSGLDMHTKPWIRARARKE
Retrocopy IQKYAREAYNLGVRYIGGCCGFEPYHIRAIAEELAPERGFLPPASEKHGSWGSGLDMHTKPWIRARARKE

Parental  YWQNLRIASGRPYNPSMSRPDAWGVTKGAAELMQQKEATTEQQLRELFEKQKFKSAQ
          YWQNLRIASGRPYNPSMSRPDAWGVTKGAAELMQQKEATTEQQLRELFEKQKFKSAQ
Retrocopy YWQNLRIASGRPYNPSMSRPDAWGVTKGAAELMQQKEATTEQQLRELFEKQKFKSAQ

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	0.09 RPM
SRP007412_cerebellum	0.00 RPM	0.04 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	1.12 RPM	13.44 RPM
SRP007412_liver	26.30 RPM	429.84 RPM
SRP007412_testis	0.59 RPM	7.68 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_192 was not detected

EST

1 EST(s) were mapped to retro_mmus_192 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AI530322	87756286	87756889	99.8	449	1	447

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_61924	960 libraries	46 libraries	17 libraries	6 libraries	43 libraries

The graphical summary, for retro_mmus_192 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_192 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_192 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000007560	1 retrocopy	retro_cint_30,
Monodelphis domestica	ENSMODG00000019726	1 retrocopy	retro_mdom_1533,
Mus musculus	ENSMUSG00000074768	1 retrocopy	retro_mmus_192 ,
Rattus norvegicus	ENSRNOG00000011200	1 retrocopy	retro_rnor_2137,