RetrogeneDB ID: retro_chof_102

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_1990:1277..1897(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5C1
• Ensembl ID: ENSCHOG00000011229
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1 [Source:HGNC Symbol;Acc:833]

Sequence

>retro_chof_102
AAAACACCACTTATCATTGGTATATCCTTGGATCGAGGACTTTGTGGTACTATACAGTTGCTCAACAGATGAAAAACAGA
GGTGGCCTCAAACTCAGCAGCTGGAAGAGATGTTATGCTTGTTGGAATTGGTGATAAGGTCAGGGGCATACTTTATAGGA
CTCATTCTGATCAGTTTCTGGTGACATTCAAAGAAGTGGGAAGGAAACCCCCCACATTTGGAGTTGCATCAGTCATTGCC
CTTGAATTATTAAATTCTGGCTATGAATTTAATGAAGGATCTATTGTCTTTAATAAAGTCAGGTCCGTCATCTTCTGTAA
GAGAGAAGACAAGCCTGTTTTTTCCCTAATACCATTGCAAGTGCCGAGAGCATGAGTATCTATGACGATATTGATGTTGA
TGTGCTGCAAAATTACCAAGAATACAATGTGGCAAACATCATCTACTACTCAAAGGAGTCTGCTACTAGCGAGCAAAGTA
CACAGATGGTGGCCATGGACAATGCTACTAAGAATGCTTCTGAGATGACTGACAAATTGACTTTGACATTCAATCGCACC
CACCAAGCTGTCATCATGAAAGAGTTGATTGAAATCATCTCTGGTGCAGCAGCTCTGGAT

Alignment

ORF - retro_chof_102 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.15 %
• Parental protein coverage: 75.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKHLIIGVSSDRGLCGAIHSSVAKQMKSEVAALTAAGKDVMIVGVGDKIRGILHRTHSDQFLVTFKEVGR
          K..LIIG.S.DRGLCG.I........K.EVA...AAG.DVM.VG.GDK.RGIL.RTHSDQFLVTFKEVGR
Retrocopy KTPLIIGISLDRGLCGTI--QLLNR*KTEVASNSAAGRDVMLVGIGDKVRGILYRTHSDQFLVTFKEVGR

Parental  KPPTFGDASVIALELLNSGYEFDEGSIIFNKFRSVISYKTEEKPIFSL-NTIASAESMSIYDDIDADVLQ
          KPPTFG.ASVIALELLNSGYEF.EGSI.FNK.RSVI..K.E.KP.FSL.NTIASAESMSIYDDID.DVLQ
Retrocopy KPPTFGVASVIALELLNSGYEFNEGSIVFNKVRSVIFCKREDKPVFSL<NTIASAESMSIYDDIDVDVLQ

Parental  NYQEYSLANIIYYSLKESTTSEQSARMTAMDNASKNASEMIDKLTLTFNRTRQAVITKELIEIISGAAAL
          NYQEY..ANIIYYS.KES.TSEQS..M.AMDNA.KNASEM.DKLTLTFNRT.QAVI.KELIEIISGAAAL
Retrocopy NYQEYNVANIIYYS-KESATSEQSTQMVAMDNATKNASEMTDKLTLTFNRTHQAVIMKELIEIISGAAAL

Parental  D
          D
Retrocopy D

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_102 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,