RetrogeneDB ID: retro_chof_216

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_4699:72901..73679(+)
• Located in intron of: ENSCHOG00000012695

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000010080
• Aliases: None
• Description: None

Sequence

>retro_chof_216
TCAACATCCTCTGGAGTTTTAATGGTTGTACCTAATGTTAGAGTTGGAAAAAAAATGGATGTGGTAATTTTGCATAATTA
TGATTAGGTAAAAATGTATACACAAATGGATATATGGCAATTTAGCTGGAACCCACGAAATCGAGAGCACAACAGCTACA
TTTTGAAAACAGACTCTATAAGCAATTAGGATTAGGAGATGGTATATCTCAAGTTTAGTATTTTCGCCCTTGTGGTAAGT
ATCATGCTATGGTGCTACAGCTGCTGGGATCTAGTTTGGAGACTTGTTTGACTTGTGTGACACAACATTTTCTCTTAAAA
CAGCTCCCATGATAACTATCCAACTGATTTCTCATATGGAACATGTAAATTAAAAGAATTTAATATACAGAGATGTAAAA
CATGAGAAATTCTTAACAGGACAACCAGGAAACAAAACCCCAAAAGTTATTCACACAGATTTCAATTTGGCAAAGGATAT
ATTGATCCAGAGACAAAGAAACACATACCATACAGGGAACACAAGATCCTTATGGGAACAAATAACATATATGAACATAA
ACACAGTTTTAGGAAAGAAAAATAGAAGGGATGATTCAGAAGCTTTAGGAAACACATTTATGCATTTTATGAGAAGACAT
CATCCTTGGCAAGTCTTAAAGGCTGACACATTAAAAAAGAGGTATCATAAAATTGGAGATATAAAACAAGCCACACCAAT
AGAACTGGTATGTGAAAATTTTCCAGAAGAAATGGCAACATATGTTTGCTATGTAAGA

Alignment

ORF - retro_chof_216 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.66 %
• Parental protein coverage: 65.1 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  STSSGVLMVGPNFRVGKKI-GCGNFGELRLGKNLYTNEYVAIKLEPIKSRAPQLHLEYRFYKQLGSAGEG
          STSSGVLMV.PN.RV.....GCGNF..L.LGKN.YTN.Y.AI.LEP.KSRA.QLH.E.R.YKQLG..G.G
Retrocopy STSSGVLMVVPNVRVXXXX<GCGNFA*L*LGKNVYTNGYMAI*LEPTKSRAQQLHFENRLYKQLG-LGDG

Parental  LPQVYYFGPCGKYNAMVLELLGPSLE-DLFDLCDRTFTLKTVLMIAIQLLSRMEYVHSKNLIYRDVKPEN
          ..QV.YF.PCGKY.AMVL.LLG.SLE.DLFDLCD.TF.LKT..MI.IQL.S.ME.V..KNLIYRDVK.E.
Retrocopy ISQV*YFRPCGKYHAMVLQLLGSSLE<DLFDLCDTTFSLKTAPMITIQLISHMEHVN*KNLIYRDVKHEK

Parental  FLIGRQGNKKEHVIHIIDFGLAKE-YIDPETKKHIPYREHKSLTGTAR-YMSINTHLGKEQSRRDDLEAL
          FL.G..GNK...VIH..DF.LAK..YIDPETKKHIPYREHK.L.GT...YM.INT.LGK...RRDD.EAL
Retrocopy FLTGQPGNKTPKVIHT-DFNLAKD<YIDPETKKHIPYREHKILMGTNN>YMNINTVLGKK-NRRDDSEAL

Parental  GHMFMYFLRGSLPWQGLKADTLKERYQKIGDTKRNTPIEALCENFPEEMATYLRYVR
          G..FM.F.R...PWQ.LKADTLK.RY.KIGD.K..TPIE..CENFPEEMATY..YVR
Retrocopy GNTFMHFMRRHHPWQVLKADTLKKRYHKIGDIKQATPIELVCENFPEEMATYVCYVR

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_216 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003299	1 retrocopy	retro_chof_753,
Choloepus hoffmanni	ENSCHOG00000010080	3 retrocopies	retro_chof_1577, retro_chof_2058, retro_chof_216 ,
Dasypus novemcinctus	ENSDNOG00000018857	1 retrocopy	retro_dnov_2386,
Rattus norvegicus	ENSRNOG00000016620	1 retrocopy	retro_rnor_2267,
Tupaia belangeri	ENSTBEG00000003013	1 retrocopy	retro_tbel_17,