RetrogeneDB ID: retro_mmus_1451

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:22230390..22230918(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000043870
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tmem97
• Ensembl ID: ENSMUSG00000037278
• Aliases: Tmem97, 1810014L12Rik, AI115531, AL022956, D11Bhm182e
• Description: transmembrane protein 97 [Source:MGI Symbol;Acc:MGI:1916321]

Sequence

>retro_mmus_1451
ATGGGGGCCCTGGCAGCTAGGCGCTGTGTTGAGTGGCTCTTGGGCCTCTACTTCGTCTCGCACATCCCCATCACGCTGTT
CATCGACCTGCAGGCGGTGCTGCCGCCCGAACTCTACCCGCAGGAGTTCAGCAACCTGTTGTGGTGGTACTCAAAGGAGT
TCAAAGACCCTCTGATGCAGGAGCCCCCAGTGTGGTTCAAGTCCTTCCTGCTCTGTGAGCTTGTGTTCCAGCTGCCTTTC
TTTCCCATTGCGGCATATGCCTTCTTCAAAGGAAGCTGCCGGTGGATCCGAATCCCTGCAATCATCTATGCAGCTCACAC
CATAACGACTTTAATTCCAATCCTCTACACACTCCTGTTTGAGGATTTCTCTAAAGCCGTTGCTTTCAAGGGACAAAGAC
CCGAGAGTTTCCGTGAATGACTGACCCTCGTAGGTGTCTACGCCCCCTATTTAATAATCCCCCTCATACTCCTCCTGTTC
ATGTTTCAGAACCCGTACTACAAGTATGAGGAGAAAAGAAAGAAAAAA

Alignment

ORF - retro_mmus_1451 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.73 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGALAARRCVEWLLGLYFVSHIPITLFIDLQAVLPPELYPQEFSNLLRWYSKEFKDPLMQEPPVWFKSFL
          MGALAARRCVEWLLGLYFVSHIPITLFIDLQAVLPPELYPQEFSNLL.WYSKEFKDPLMQEPPVWFKSFL
Retrocopy MGALAARRCVEWLLGLYFVSHIPITLFIDLQAVLPPELYPQEFSNLLWWYSKEFKDPLMQEPPVWFKSFL

Parental  LCELVFQLPFFPIAAYAFFKGSCRWIRIPAIIYAAHTITTLIPILYTLLFEDFSKAVAFKGQRPESFRER
          LCELVFQLPFFPIAAYAFFKGSCRWIRIPAIIYAAHTITTLIPILYTLLFEDFSKAVAFKGQRPESFRE.
Retrocopy LCELVFQLPFFPIAAYAFFKGSCRWIRIPAIIYAAHTITTLIPILYTLLFEDFSKAVAFKGQRPESFRE*

Parental  LTLVGVYAPYLIIPLILLLFMLRNPYYKYEEKRKKK
          LTLVGVYAPYLIIPLILLLFM..NPYYKYEEKRKKK
Retrocopy LTLVGVYAPYLIIPLILLLFMFQNPYYKYEEKRKKK

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	6.54 RPM
SRP007412_cerebellum	0.00 RPM	3.13 RPM
SRP007412_heart	0.03 RPM	2.37 RPM
SRP007412_kidney	0.02 RPM	7.99 RPM
SRP007412_liver	0.05 RPM	48.83 RPM
SRP007412_testis	0.23 RPM	216.53 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1451 was not detected

EST

No EST(s) were mapped for retro_mmus_1451 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_45725	589 libraries	310 libraries	160 libraries	9 libraries	4 libraries

The graphical summary, for retro_mmus_1451 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_1451 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1451 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011105	1 retrocopy	retro_chof_566,
Homo sapiens	ENSG00000109084	1 retrocopy	retro_hsap_4027,
Gorilla gorilla	ENSGGOG00000004565	1 retrocopy	retro_ggor_2703,
Macaca mulatta	ENSMMUG00000019142	1 retrocopy	retro_mmul_2323,
Mus musculus	ENSMUSG00000037278	1 retrocopy	retro_mmus_1451 ,
Nomascus leucogenys	ENSNLEG00000001868	1 retrocopy	retro_nleu_1574,
Otolemur garnettii	ENSOGAG00000003329	1 retrocopy	retro_ogar_1913,
Pongo abelii	ENSPPYG00000008086	1 retrocopy	retro_pabe_3307,
Pan troglodytes	ENSPTRG00000008909	1 retrocopy	retro_ptro_2731,
Ictidomys tridecemlineatus	ENSSTOG00000007542	2 retrocopies	retro_itri_341, retro_itri_758,
Tupaia belangeri	ENSTBEG00000005125	2 retrocopies	retro_tbel_2160, retro_tbel_2221,