RetrogeneDB ID: retro_mmus_2253

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:54810386..54811250(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000069011
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tra2b
• Ensembl ID: ENSMUSG00000022858
• Aliases: None
• Description: transformer 2 beta homolog (Drosophila) [Source:MGI Symbol;Acc:MGI:106016]

Sequence

>retro_mmus_2253
ATGAGCGACAGCGGCGAGCAGAACTACGGCGAGCGGGAATCCCGTTCTGCTTCCCGAAGTGGAAGTGCTCACGGATCGGG
GAAATCTGCACGGCATACACCTGCAAGGTCTCGCTCCAAGGAAGACTCAAGGCGTTCTAGATCAAAGTCCAGGTCCAGGT
CTGAATCTAGGTCTAGATCCAGAAGAAGTTCTAGAAGGCATTATACAAGGTCACGATCACGATCTCGCTCGCATAGACGA
TCCCGGAGCAGGTCTTACAGCCGAGATTATCGCAGGCGCCACAGCCACAGCCATTCTCCCATGTCTACTCGAAGGCGTCA
TGTTGGGAACCGGGCAAATCCTGACCCCAACTGTTGTCTTGGCGTGTTTGGGTTGAGCTTATACACCACAGAAAGAGACC
TAAGAGAAGTGTTCTCTAAATATGGCCCCATTGCTGATGTGTCTATTGTATATGACCAGCAATCTAGACGTTCAAGAGGA
TTTGCCTTTGTATATTTTGAAAATGTAGATGATGCCAAGGAAGCTAAAGAACGTGCCAATGGAATGGAGCTTGATGGGCG
TCGAATTAGAGTCGATTTCTCTATAACAAAAAGGCCCCATACCCCAACACCAGGAATTTATATGGGGAGAGCCATTTATG
GCAGTTCTCGCCGCCGAGACTATTATGACAGAGGATACGATCGGGGGTATGATGGCGGGGGCTATTACAGCAGATCACAC
AGAGGAGGAGGTGGTGGAGGAGGTGGATGGAGAGCAGCTCAAGACAGGGATCAGATTTACAGAAGACGGTCATCTTCTCC
TTACTACAGTCGTGGAGGATACAGGTCACGTTCTCGATCACGATCCTACTCACCTTGTCGCTAC

Alignment

ORF - retro_mmus_2253 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.75 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDSGEQNYGERESRSASRSGSAHGSGKSARHTPARSRSKEDSRRSRSKSRSRSESRSRSRRSSRRHYTR
          MSDSGEQNYGERESRSASRSGSAHGSGKSARHTPARSRSKEDSRRSRSKSRSRSESRSRSRRSSRRHYTR
Retrocopy MSDSGEQNYGERESRSASRSGSAHGSGKSARHTPARSRSKEDSRRSRSKSRSRSESRSRSRRSSRRHYTR

Parental  SRSRSRSHRRSRSRSYSRDYRRRHSHSHSPMSTRRRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSK
          SRSRSRSHRRSRSRSYSRDYRRRHSHSHSPMSTRRRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSK
Retrocopy SRSRSRSHRRSRSRSYSRDYRRRHSHSHSPMSTRRRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSK

Parental  YGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHTPTPGIYMGR
          YGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHTPTPGIYMGR
Retrocopy YGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHTPTPGIYMGR

Parental  PTYGSSRRRDYYDRGYDRGYDDRDYYSRSYRGGGGGGGGWRAAQDRDQIYRRRSPSPYYSRGGYRSRSRS
          ..YGSSRRRDYYDRGYDRGYD...YYSRS.R..........AAQDRDQIYRRRS.SPYYSRGGYRSRSRS
Retrocopy AIYGSSRRRDYYDRGYDRGYDGGGYYSRSHRXXXXXXXXXXAAQDRDQIYRRRSSSPYYSRGGYRSRSRS

Parental  RSYSPRRY
          RSYSP.RY
Retrocopy RSYSPCRY

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	0.14 RPM	36.47 RPM
SRP007412_cerebellum	0.17 RPM	41.08 RPM
SRP007412_heart	0.03 RPM	31.25 RPM
SRP007412_kidney	0.12 RPM	45.26 RPM
SRP007412_liver	0.03 RPM	29.14 RPM
SRP007412_testis	0.27 RPM	82.19 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2253 was not detected

EST

No EST(s) were mapped for retro_mmus_2253 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_95142	435 libraries	563 libraries	71 libraries	1 library	2 libraries

The graphical summary, for retro_mmus_2253 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_2253 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2253 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001697	2 retrocopies	retro_btau_1245, retro_btau_850,
Myotis lucifugus	ENSMLUG00000005781	2 retrocopies	retro_mluc_2565, retro_mluc_2567,
Mustela putorius furo	ENSMPUG00000003157	1 retrocopy	retro_mputfur_673,
Mus musculus	ENSMUSG00000022858	6 retrocopies	retro_mmus_1187, retro_mmus_2253 , retro_mmus_2313, retro_mmus_3139, retro_mmus_3617, retro_mmus_756,
Mus musculus	ENSMUSG00000031134	2 retrocopies	retro_mmus_170, retro_mmus_187,
Mus musculus	ENSMUSG00000031167	4 retrocopies	retro_mmus_2044, retro_mmus_2963, retro_mmus_3019, retro_mmus_501,
Ochotona princeps	ENSOPRG00000007990	2 retrocopies	retro_opri_24, retro_opri_930,
Rattus norvegicus	ENSRNOG00000001783	4 retrocopies	retro_rnor_1130, retro_rnor_1915, retro_rnor_2156, retro_rnor_2807,
Tarsius syrichta	ENSTSYG00000000388	1 retrocopy	retro_tsyr_1632,