RetrogeneDB ID: retro_chof_586

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_124303:6043..6629(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS31
• Ensembl ID: ENSCHOG00000008470
• Aliases: None
• Description: mitochondrial ribosomal protein S31 [Source:HGNC Symbol;Acc:16632]

Sequence

>retro_chof_586
GCTTCAAAGACAAAAAATAGTATCCAAAGATATTTTGGTACAATGATCTATATAGTAAGAAAGATGAGCAGTGTGTTCCA
ACCAAAAGATTTCCAAGGAAACTTCAAAGAACCAAAGGAATGTAAAAAGAATATGAAAAAAGGCTTGTAAATATTATTAA
AGGCATGGAAGTTGCATTAAGCTCACTGAATGTACAAACAACCAAGGCATCCAAAAGAAGACCAGTTAAAAGTTCGGAGG
CTACAACTGGTAGGCATTAAAAAGCTACAGATGATACCGCAAAGAAGAGAAATGAGCCTCTAAGTACCGAGTTACAGGAG
GCTGCACCTGCTGTTGCAGAGTTTGTCCCTTTTGACAAGCAGGGGACCAGGTCAGAGCTGCTCAGGCAGCTTCAGCCACA
CAAGGAAGACCTGAGGGCACAGAAAGATGGGGAAAGACAGAAAGTTAGTTTCAGTAACATAATATCAGAGATGAAAGTTG
GCAGATCAGCTATAGCTAGAAATAGTATGAGACCAAGCATCAGATGCAATTTGATGAAGTATCAGAAAACCATATTGACA
AGGGAGAGACCACTGATCTTAGAAAA

Alignment

ORF - retro_chof_586 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.75 %
• Parental protein coverage: 51.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SAPTKNNIQRY-FGTNSVICSKKDEQQSVPTN-ELSKGTSKNQDNVKG-NMKKDL-LTIIKGMKVELSKV
          ...TKN.IQRY.F..N....SKKDEQ..VPT....SK.TSKNQ.NVK..NMKK.L...IIKGM.V.LS..
Retrocopy ASKTKNSIQRY<FWYNDLY-SKKDEQ-CVPTK<KISKETSKNQRNVKR<NMKKGL<VNIIKGMEVALSSL

Parental  NVQTTKPPNRRPLRSLEATVGRLQKPTENTTSKRNESLSPELVAAASAVAESLPFDKQMTKSELLRQLRQ
          NVQTTK...RRP..S.EAT.GR..K.T..T..KRNE.LS.EL..AA.AVAE..PFDKQ.T.SELLRQL..
Retrocopy NVQTTKASKRRPVKSSEATTGRH*KATDDTAKKRNEPLSTELQEAAPAVAEFVPFDKQGTRSELLRQLQP

Parental  HEEKWRAQKDEERRKVSFSNIISDMKVAKSAIARINRRP-EHQIQFDEGPENFVDEEKTADLRK
          H.E..RAQKD.ER.KVSFSNIIS.MKV..SAIAR...RP..HQ.QFDE..EN..D...T.DLRK
Retrocopy HKEDLRAQKDGERQKVSFSNIISEMKVGRSAIARNSMRP<KHQMQFDEVSENHIDKGETTDLRK

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_586 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008470	1 retrocopy	retro_chof_586 ,
Equus caballus	ENSECAG00000003600	1 retrocopy	retro_ecab_1028,
Nomascus leucogenys	ENSNLEG00000001164	1 retrocopy	retro_nleu_1999,
Oryctolagus cuniculus	ENSOCUG00000021467	1 retrocopy	retro_ocun_1747,
Otolemur garnettii	ENSOGAG00000024374	1 retrocopy	retro_ogar_914,
Ochotona princeps	ENSOPRG00000014606	1 retrocopy	retro_opri_1137,
Pongo abelii	ENSPPYG00000005306	1 retrocopy	retro_pabe_3785,
Sorex araneus	ENSSARG00000004428	1 retrocopy	retro_sara_594,
Sarcophilus harrisii	ENSSHAG00000007140	1 retrocopy	retro_shar_591,
Tarsius syrichta	ENSTSYG00000002170	1 retrocopy	retro_tsyr_238,
Tursiops truncatus	ENSTTRG00000012556	1 retrocopy	retro_ttru_1285,