RetrogeneDB ID: retro_mmus_2008

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:10959132..10959661(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082871
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Atp5c1
• Ensembl ID: ENSMUSG00000025781
• Aliases: Atp5c1, 1700094F02Rik
• Description: ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1 [Source:MGI Symbol;Acc:MGI:1261437]

Sequence

>retro_mmus_2008
ACAGCAGCTGCAAGAGAAGTTATATTCGCTGGAATTAGTAAAAAAAATTAGGGGCATACTTTATAGAACTTGCTCTGATC
AGTTTGGGGTACCATTCAAAGATGTAGCATGAAAGCCCCCTATTTTTTGGAGATCTGTCAATCATTGCTCTTGGGTTGTT
AAATTTTGGGTATGAGTTTGATGAAGGCTATATAATTTTTAATCAATTAAAGTCTATTATCTGCTATAAAACAAAAGAGA
AGCCCATCTTCTCTCTCAATACCGTTGCAACTGCTGAGAACATGAGCACTATGATGTCACTGATGCTGATTTGCTGCAGA
GTTATCAGGAAATCAATCTGGCCAGCATCATCTACTACACCCTGAAAGCATCCACCACTAGTGAGCAGAGTGCCAGGATG
ACCACCACAGACAACTGCAGAAAGAATGCTTCTGCCATGATTGACAAATTGGATTCGATGTACAAATGCATGCATCAGGA
TGTCATCACAAAGGAGTGGGTTGAAATCATCTCTGGGACTACTGCTCTG

Alignment

ORF - retro_mmus_2008 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.04 %
• Parental protein coverage: 59.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TAAGKEVMIVGVGEKI-KGILYRTHSDQFLVSFKDVGRKPPTF-GDASVIALELLNSGYEFDEGSIIFNQ
          TAA..EV...G.......GILYRT.SDQF.V.FKDV..KPP.F.GD.S.IAL.LLN.GYEFDEG.IIFNQ
Retrocopy TAAAREVIFAGISXXX>RGILYRTCSDQFGVPFKDVA*KPPIF>GDLSIIALGLLNFGYEFDEGYIIFNQ

Parental  FKSVISYKTEEKPIFSLNTIATAETMSI-YDDIDADVLQNYQEYNLANLIYYSLKESTTSEQSARMTAMD
          .KS.I.YKT.EKPIFSLNT.ATAE.MS..YD..DAD.LQ.YQE.NLA..IYY.LK.STTSEQSARMT..D
Retrocopy LKSIICYKTKEKPIFSLNTVATAENMST<YDVTDADLLQSYQEINLASIIYYTLKASTTSEQSARMTTTD

Parental  NASKNASDMIDKLTLTFNRTRQAVITKELIEIISGAAAL
          N..KNAS.MIDKL........Q.VITKE..EIISG..AL
Retrocopy NCRKNASAMIDKLDSMYKCMHQDVITKEWVEIISGTTAL

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	129.27 RPM
SRP007412_cerebellum	0.00 RPM	119.76 RPM
SRP007412_heart	0.00 RPM	575.78 RPM
SRP007412_kidney	0.00 RPM	361.03 RPM
SRP007412_liver	0.00 RPM	140.94 RPM
SRP007412_testis	0.00 RPM	55.62 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2008 was not detected

EST

No EST(s) were mapped for retro_mmus_2008 retrocopy.

TSS

No TSS is located nearby retro_mmus_2008 retrocopy 5' end.

Lab

retro_mmus_2008 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2008 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005024	1 retrocopy	retro_cfam_1781,
Choloepus hoffmanni	ENSCHOG00000011229	3 retrocopies	retro_chof_102, retro_chof_297, retro_chof_673,
Callithrix jacchus	ENSCJAG00000020635	7 retrocopies	retro_cjac_1079, retro_cjac_1293, retro_cjac_1381, retro_cjac_1636, retro_cjac_2506, retro_cjac_4190, retro_cjac_526,
Cavia porcellus	ENSCPOG00000010523	2 retrocopies	retro_cpor_422, retro_cpor_984,
Echinops telfairi	ENSETEG00000010549	1 retrocopy	retro_etel_1406,
Felis catus	ENSFCAG00000000196	1 retrocopy	retro_fcat_818,
Homo sapiens	ENSG00000165629	1 retrocopy	retro_hsap_1415,
Gorilla gorilla	ENSGGOG00000009719	1 retrocopy	retro_ggor_1094,
Macaca mulatta	ENSMMUG00000009207	1 retrocopy	retro_mmul_2254,
Monodelphis domestica	ENSMODG00000016720	1 retrocopy	retro_mdom_1287,
Mus musculus	ENSMUSG00000025781	4 retrocopies	retro_mmus_1122, retro_mmus_2008 , retro_mmus_3451, retro_mmus_3644,
Nomascus leucogenys	ENSNLEG00000011917	1 retrocopy	retro_nleu_1836,
Oryctolagus cuniculus	ENSOCUG00000004642	2 retrocopies	retro_ocun_1171, retro_ocun_363,
Otolemur garnettii	ENSOGAG00000015242	2 retrocopies	retro_ogar_1099, retro_ogar_2738,
Procavia capensis	ENSPCAG00000004971	1 retrocopy	retro_pcap_99,
Pongo abelii	ENSPPYG00000002076	1 retrocopy	retro_pabe_1170,
Pan troglodytes	ENSPTRG00000002277	1 retrocopy	retro_ptro_968,
Pteropus vampyrus	ENSPVAG00000006512	3 retrocopies	retro_pvam_1466, retro_pvam_51, retro_pvam_530,
Ictidomys tridecemlineatus	ENSSTOG00000026133	1 retrocopy	retro_itri_665,
Tupaia belangeri	ENSTBEG00000011530	4 retrocopies	retro_tbel_1763, retro_tbel_2023, retro_tbel_4384, retro_tbel_4406,
Tarsius syrichta	ENSTSYG00000003035	4 retrocopies	retro_tsyr_1268, retro_tsyr_1988, retro_tsyr_465, retro_tsyr_506,