RetrogeneDB ID: retro_mmus_1929

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:68554554..68554926(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000075312
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tax1bp3
• Ensembl ID: ENSMUSG00000040158
• Aliases: Tax1bp3, 1300011C24Rik, TIP-1
• Description: Tax1 (human T cell leukemia virus type I) binding protein 3 [Source:MGI Symbol;Acc:MGI:1923531]

Sequence

>retro_mmus_1929
ATGTCCTACACCCCGGGCCAGCCTGTCACCGCCGTAGTGCAAAGAGTTGAAATTCATAAGTTGCGTCAAGGTGAGAACTT
AATCTTGGGCTTCAGTATTGGAGGTGGGATCGACCAGGACCCGTCTCAGAATCCCTTCTCGGAAGATAAAACAGACAAGG
GCATTTACGTCACACGAGTATCAGAGGGAGGTCCTGCTGAAATTGCTGGGCTGCAGATTGGAGACAAGATCATGCAGGTG
AATGGCTGGGACATGACCATGGTCACTCACGACCAGGCTCGGAAGCGGCTCACCAAGCGCTCGGAGGAGGTGGTCCGCCT
GCTGGTGACTCGGCAGTCTCTACAAAAGGCTGTACAGCAGTCCATGCTGTCT

Alignment

ORF - retro_mmus_1929 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  MSYTPGQPVTAVVQRVEIHKLRQGENLILGFSIGGGIDQDPSQNPFSEDKTDKGIYVTRVSEGGPAEIAG
          MSYTPGQPVTAVVQRVEIHKLRQGENLILGFSIGGGIDQDPSQNPFSEDKTDKGIYVTRVSEGGPAEIAG
Retrocopy MSYTPGQPVTAVVQRVEIHKLRQGENLILGFSIGGGIDQDPSQNPFSEDKTDKGIYVTRVSEGGPAEIAG

Parental  LQIGDKIMQVNGWDMTMVTHDQARKRLTKRSEEVVRLLVTRQSLQKAVQQSMLS
          LQIGDKIMQVNGWDMTMVTHDQARKRLTKRSEEVVRLLVTRQSLQKAVQQSMLS
Retrocopy LQIGDKIMQVNGWDMTMVTHDQARKRLTKRSEEVVRLLVTRQSLQKAVQQSMLS

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	1.52 RPM
SRP007412_cerebellum	0.00 RPM	1.00 RPM
SRP007412_heart	0.09 RPM	7.88 RPM
SRP007412_kidney	0.15 RPM	8.60 RPM
SRP007412_liver	0.00 RPM	3.11 RPM
SRP007412_testis	0.05 RPM	1.69 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1929 was not detected

EST

No EST(s) were mapped for retro_mmus_1929 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_88285	505 libraries	428 libraries	137 libraries	2 libraries	0 libraries

The graphical summary, for retro_mmus_1929 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_1929 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1929 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000013801	2 retrocopies	retro_dord_56, retro_dord_728,
Myotis lucifugus	ENSMLUG00000026421	1 retrocopy	retro_mluc_221,
Mus musculus	ENSMUSG00000040158	1 retrocopy	retro_mmus_1929 ,
Oryctolagus cuniculus	ENSOCUG00000023903	1 retrocopy	retro_ocun_781,
Sus scrofa	ENSSSCG00000017866	1 retrocopy	retro_sscr_365,
Ictidomys tridecemlineatus	ENSSTOG00000022920	1 retrocopy	retro_itri_134,