RetrogeneDB ID: retro_mmus_829

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:100361718..100362126(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000091478
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Atp5g1
• Ensembl ID: ENSMUSG00000006057
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial F0 complex, subunit c1 (subunit 9) [Source:MGI Symbol;Acc:MGI:107653]

Sequence

>retro_mmus_829
ATGCAGACCACCAAGGCACTGCTCATTTCTCCAGCTCTGATTCGCTCCTGTACCAGGGGTCTAATCAGGCCTGTGTCTGC
CTCCCTCCTGAGCAGACCAGAGGCCCCATCTAAGCAGCCTTCCTGCAGCAGCTCCCCTCTCCAGGTGGCCCGACGGGAAT
TCCAGACCAGTGTCATTTCCCGGGACATCGACACAGCAGCCAAGTTCATTGGTGCTGGGGCCGCCACAGTTGGTGTGGCT
GGATCAGGAGCTGGCATTGGCACAGTGTTTGGTAGCTTGATTATTGGCTATGCCAGGAACCCATCTCTCAAGCAGCAGCT
CTTCTCCTATGCCATTCTGGGGTTTGCCCTGTCTGAGGCCATGGGACTCTTCTGTTTGATGGTCACCTTCCTCATCCTCT
TCGCCATG

Alignment

ORF - retro_mmus_829 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.26 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQTTKALLISPALIRSCTRGLIRPVSASLLSRPEAPSKQPSCSSSPLQVARREFQTSVISRDIDTAAKFI
          MQTTKALLISPALIRSCTRGLIRPVSASLLSRPEAPSKQPSCSSSPLQVARREFQTSVISRDIDTAAKFI
Retrocopy MQTTKALLISPALIRSCTRGLIRPVSASLLSRPEAPSKQPSCSSSPLQVARREFQTSVISRDIDTAAKFI

Parental  GAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMVAFLILFAM
          GAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMV.FLILFAM
Retrocopy GAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMVTFLILFAM

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	0.42 RPM	41.24 RPM
SRP007412_cerebellum	0.48 RPM	40.69 RPM
SRP007412_heart	3.74 RPM	473.96 RPM
SRP007412_kidney	2.16 RPM	174.27 RPM
SRP007412_liver	0.33 RPM	57.73 RPM
SRP007412_testis	0.18 RPM	17.43 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_829 was not detected

EST

No EST(s) were mapped for retro_mmus_829 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_7872	350 libraries	68 libraries	379 libraries	219 libraries	56 libraries

The graphical summary, for retro_mmus_829 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_829 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_829 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006341	1 retrocopy	retro_acar_9,
Canis familiaris	ENSCAFG00000016880	5 retrocopies	retro_cfam_1583, retro_cfam_1621, retro_cfam_1882, retro_cfam_336, retro_cfam_647,
Callithrix jacchus	ENSCJAG00000007352	7 retrocopies	retro_cjac_1190, retro_cjac_1549, retro_cjac_161, retro_cjac_1878, retro_cjac_289, retro_cjac_4060, retro_cjac_679,
Cavia porcellus	ENSCPOG00000009017	2 retrocopies	retro_cpor_43, retro_cpor_550,
Equus caballus	ENSECAG00000019908	1 retrocopy	retro_ecab_463,
Felis catus	ENSFCAG00000002344	2 retrocopies	retro_fcat_1165, retro_fcat_1346,
Loxodonta africana	ENSLAFG00000004537	2 retrocopies	retro_lafr_341, retro_lafr_522,
Macropus eugenii	ENSMEUG00000005744	2 retrocopies	retro_meug_1650, retro_meug_1973,
Myotis lucifugus	ENSMLUG00000011738	4 retrocopies	retro_mluc_1276, retro_mluc_1508, retro_mluc_1885, retro_mluc_2498,
Macaca mulatta	ENSMMUG00000013395	1 retrocopy	retro_mmul_173,
Mustela putorius furo	ENSMPUG00000015341	3 retrocopies	retro_mputfur_1575, retro_mputfur_479, retro_mputfur_497,
Mus musculus	ENSMUSG00000006057	5 retrocopies	retro_mmus_1523, retro_mmus_1726, retro_mmus_2128, retro_mmus_725, retro_mmus_829 ,
Mus musculus	ENSMUSG00000062683	1 retrocopy	retro_mmus_6,
Rattus norvegicus	ENSRNOG00000007235	5 retrocopies	retro_rnor_1342, retro_rnor_2240, retro_rnor_529, retro_rnor_64, retro_rnor_880,
Tupaia belangeri	ENSTBEG00000003575	5 retrocopies	retro_tbel_2765, retro_tbel_3270, retro_tbel_3540, retro_tbel_387, retro_tbel_4002,