RetrogeneDB ID: retro_mmus_2128

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:168983266..168983642(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

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_2128
GTTTCTCCAGTTCTGATCGGCTCCTGTGTGAGGAGTCTGATTAGGCCTGTGTCTGTCTCGGTCCTGAGTATTCCAGAGGC
CTCATCAAACAGCCTTCCTGCGGCAGCTCCCCTCTCCAGATGGCCAGACAGGGATTCCAGACCAGTGATTCTTCCAGGAC
ATTGACACAGCAGCCAGGTTTACTGGTGCTGAGGCCATGACAGTGGTGTGGCTGGATCGAGGGCTGACATTGGAACGGTG
TTTGATTGACTATCAGTATGCCAGGAACTCATCTCTCAAGAAGCAGCTCTTCTCCTATGCCATTCTGGGCTTTGCCCTTT
CAGGGGCCACGGGGCTCTTCTGTTTGATGGTCACCTTCCTCAGCCTCTTTGCCATT

Alignment

ORF - retro_mmus_2128 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.08 %
• Parental protein coverage: 94.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ISPALIRSCTRGLIRPVSASLLSRPEAPS-KQPSCSSSPLQVARREFQTSVISR-DIDTAAKFIGAGAAT
          .SP.LI.SC.R.LIRPVS.S.LS.PEA.S.KQPSC.SSPLQ.AR..FQTS..SR.DIDTAA.F...GA..
Retrocopy VSPVLIGSCVRSLIRPVSVSVLSIPEASS<KQPSCGSSPLQMARQGFQTSDSSR<DIDTAARF--TGAEA

Parental  VGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMVAFLILFAM
          ..V.....G...........YARN.SLK.QLFSYAILGFALS.A.GLFCLMV.FL.LFA.
Retrocopy MTVVWLDRGLTLERCLIDYQYARNSSLKKQLFSYAILGFALSGATGLFCLMVTFLSLFAI

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	0.05 RPM	41.24 RPM
SRP007412_cerebellum	0.09 RPM	40.69 RPM
SRP007412_heart	0.00 RPM	473.96 RPM
SRP007412_kidney	0.02 RPM	174.27 RPM
SRP007412_liver	0.05 RPM	57.73 RPM
SRP007412_testis	0.78 RPM	17.43 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2128 was not detected

EST

No EST(s) were mapped for retro_mmus_2128 retrocopy.

TSS

No TSS is located nearby retro_mmus_2128 retrocopy 5' end.

Lab

retro_mmus_2128 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2128 has 0 orthologous retrocopies within eutheria group .

---

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,