RetrogeneDB ID: retro_mmus_2602

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:123066241..123066607(+)
• Located in intron of: ENSMUSG00000097213

Retrocopy information

• Ensembl ID: ENSMUSG00000080836
• Aliases: Gm6444, EG623672
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ndufb11
• Ensembl ID: ENSMUSG00000031059
• Aliases: Ndufb11, D5Bwg0566e, D5Bwg0577e, NP15.6, Np15
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 11 [Source:MGI Symbol;Acc:MGI:1349919]

Sequence

>retro_mmus_2602
ATGGCGGCCAGGCTGTTAAGCTTGTATGGTCGATGCCTGTCAGCAGCGGGGGTGATGAGAGGGCTCCAGGCTGCCCTCGT
TCGCTGGGAGTCCTCCAGGGCTGTAATCGCCCTATCCGGTGTGGAGAAAAAGCGGCAACGAGAACCGACCATGCAGTGGC
AGGAGGACCCAGAACCCGAGGACGAAAACGTCTACGCAAAGAACCCTGACTTTCATGGTTATGATAGTGACCCTGTGGTG
GACATCTGGAATATGCGAGCTGTCTTCTTCTTTGGTTTTTCCATCGTCCTGGTCTTTGGGACCACCTTCGTGGCTTATGT
GCCTGATTATAGGATGCAAGAGTGGGCCCGCCGGGAAGCTGAGAGA

Alignment

ORF - retro_mmus_2602 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.9 %
• Parental protein coverage: 80.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAARLLSLYGRCLSAAGAMRGLPAARVRWESSRAVIAPSGVEKKRQREPTMQWQEDPEPEDENVYAKNPD
          MAARLLSLYGRCLSAAG.MRGL.AA.VRWESSRAVIA.SGVEKKRQREPTMQWQEDPEPEDENVYAKNPD
Retrocopy MAARLLSLYGRCLSAAGVMRGLQAALVRWESSRAVIALSGVEKKRQREPTMQWQEDPEPEDENVYAKNPD

Parental  FHGYDSDPVVDVWNMRAVFFFGFSIVLVFGTTFVAYVPDYRMQEWARREAER
          FHGYDSDPVVD.WNMRAVFFFGFSIVLVFGTTFVAYVPDYRMQEWARREAER
Retrocopy FHGYDSDPVVDIWNMRAVFFFGFSIVLVFGTTFVAYVPDYRMQEWARREAER

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	0.02 RPM	47.12 RPM
SRP007412_cerebellum	0.04 RPM	55.75 RPM
SRP007412_heart	0.28 RPM	287.39 RPM
SRP007412_kidney	0.29 RPM	173.27 RPM
SRP007412_liver	0.27 RPM	121.77 RPM
SRP007412_testis	0.00 RPM	6.63 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2602 was not detected

EST

No EST(s) were mapped for retro_mmus_2602 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_109630	324 libraries	135 libraries	282 libraries	224 libraries	107 libraries

The graphical summary, for retro_mmus_2602 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_2602 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2602 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000147123	1 retrocopy	retro_hsap_912,
Macaca mulatta	ENSMMUG00000017422	2 retrocopies	retro_mmul_1116, retro_mmul_830,
Monodelphis domestica	ENSMODG00000018491	1 retrocopy	retro_mdom_1063,
Mus musculus	ENSMUSG00000031059	2 retrocopies	retro_mmus_245, retro_mmus_2602 ,
Pongo abelii	ENSPPYG00000020284	1 retrocopy	retro_pabe_788,
Pan troglodytes	ENSPTRG00000021836	1 retrocopy	retro_ptro_633,
Rattus norvegicus	ENSRNOG00000008329	1 retrocopy	retro_rnor_151,
Ictidomys tridecemlineatus	ENSSTOG00000026821	1 retrocopy	retro_itri_1084,