RetrogeneDB ID: retro_chof_2016

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_456439:1..627(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000001829
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SDHB
• Ensembl ID: ENSCHOG00000005664
• Aliases: None
• Description: succinate dehydrogenase complex, subunit B, iron sulfur (Ip) [Source:HGNC Symbol;Acc:10681]

Sequence

>retro_chof_2016
ATGGTACTGGATGCTTAATCAAGATAAAAAAATGAAACGGATGCTTCCTTGACATTCCGAAGATAGTGCAGAGAAGGTAT
CTGTGGCTCTTGTGCAATGAACATCAATGGAAACAACACTCTAGCTTGCACCCAAAGGATTGACACCAACCTCAATAAAG
TCTCAAAAATCTACCCCTTTCCGCATAAGTATGTGATAAAGGATCTTGTTCCTGATTTGAGCAAATTCTTTGCTCAGTAC
AAATCCGTTGAATCTTATCTGAAGAAAAAGGATGAGTCCCAGAAAGGCAAGCCGTATACACAGTCCTTAGAAGATTGTGA
GAAACTGGATGGTCTGTACAAGTACATTCTCTGTGCCTGCTGAGCACCAGCTGCCCCAGCTACTGGTGGAACGGAGATAA
ATATTTGGGACTGGCAGTTCTTATGCAGGCTTATCACTGGATGATCAACCCCAGAGATGACTTCAGGGCAGAGCACCTGG
CCAAGCTGCAGGACCCATTCTCTATGTACCACTGCCACACCATCATGAACTGCACCTTGACCTGTCCCAAGGGTCTAAAT
CCAGCAAAAGCTATTGCTGAAATCAAGAAAATGATGGTAACCTATACGGAGAAGAAGGCTTCAGCC

Alignment

ORF - retro_chof_2016 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.1 %
• Parental protein coverage: 74.91 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVLDALIKIKNEMDASLTFRRSCREGICGSCAMNINGNNTLACTQKIDTNLNKVSKIYPLPHMYVIKDLV
          MVLDA....KNE.DASLTFRR.CREGICGSCAMNINGNNTLACTQ.IDTNLNKVSKIYP.PH.YVIKDLV
Retrocopy MVLDA*SR*KNETDASLTFRR*CREGICGSCAMNINGNNTLACTQRIDTNLNKVSKIYPFPHKYVIKDLV

Parental  PDLSNFFAQYKSIEPYLKKKDESQKGKPYTQSLEDREKLDGLYECILCAC-CSTSCPSYWWNGDKYLGPA
          PDLS.FFAQYKS.E.YLKKKDESQKGKPYTQSLED.EKLDGLY..ILCAC..STSCPSYWWNGDKYLG.A
Retrocopy PDLSKFFAQYKSVESYLKKKDESQKGKPYTQSLEDCEKLDGLYKYILCAC<LSTSCPSYWWNGDKYLGLA

Parental  VLMQAYRWMIDSRDDFRAERLAKLQDPFSLYRCHTIMNCTLTCPKGLNPGKAIAEIKKMMVTYTEKKASA
          VLMQAY.WMI..RDDFRAE.LAKLQDPFS.Y.CHTIMNCTLTCPKGLNP.KAIAEIKKMMVTYTEKKASA
Retrocopy VLMQAYHWMINPRDDFRAEHLAKLQDPFSMYHCHTIMNCTLTCPKGLNPAKAIAEIKKMMVTYTEKKASA

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_2016 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 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015832	1 retrocopy	retro_cfam_587,
Choloepus hoffmanni	ENSCHOG00000005664	1 retrocopy	retro_chof_2016 ,
Callithrix jacchus	ENSCJAG00000007927	1 retrocopy	retro_cjac_2988,
Loxodonta africana	ENSLAFG00000018475	1 retrocopy	retro_lafr_454,
Macropus eugenii	ENSMEUG00000004817	1 retrocopy	retro_meug_1106,
Microcebus murinus	ENSMICG00000016629	1 retrocopy	retro_mmur_1062,
Myotis lucifugus	ENSMLUG00000000032	1 retrocopy	retro_mluc_150,
Nomascus leucogenys	ENSNLEG00000013264	1 retrocopy	retro_nleu_1640,
Sorex araneus	ENSSARG00000013780	1 retrocopy	retro_sara_577,
Tupaia belangeri	ENSTBEG00000004803	2 retrocopies	retro_tbel_2480, retro_tbel_2875,
Xenopus tropicalis	ENSXETG00000013435	1 retrocopy	retro_xtro_60,