RetrogeneDB ID: retro_chof_982

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_179986:3736..4321(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPH
• Ensembl ID: ENSCHOG00000011338
• Aliases: None
• Description: centromere protein H [Source:HGNC Symbol;Acc:17268]

Sequence

>retro_chof_982
CAGCAACTTTTGGAATATAAATCAATGGTTGTTGCAATTCAAGAAAAATCTCCAGAACAAATGCATGAAAAGCAAATTGA
GGCTAAAATTGAGGACTTGGAAAATGAAATTGAAGAGTCCAAAATTGCCTTTGAAATGAAAAGTCTTGCATTAGACAGGT
TGCAGCTTTCATCGGCACATAAAAGAAACCTGGAGAAAACTGACACCAAAACTAGTTTACTCATGGATGACCTGAAACAT
GTATTAAAGCTAAATAAATTAATAATGAAATCACAGCAGAAATCTTGGGACTTTGAGGAAAAACTGCTGGATGTTAGAAA
GAAGAGACTGCAATTAAAACAAGCGTCAGAAAGTAAACTTTTAGAAATACAAACTGAAAAGAACAAACAAAAAGATGATT
TGGACAGTATGGAAAATTCAGACAAGATAAAGACCGTATGACAAAACCTACAGGTGGAGATACAGATTACTACAGTTATT
CAACATGTGTTTCAGAACCTCATTTTGGGGAGCAAAGTCCATTGGGCAGAAGATTGTGCCTTGAAGGAAACTGTTCTGCA
ACTTGAGAGGAATCTACCCATGATC

Alignment

ORF - retro_chof_982 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.63 %
• Parental protein coverage: 79.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QQLLEYKSMVDANEEKTPEQIMQEKQIEAKIEDLENEIEESKIAFEMTSLALHRMQLSSALKRNLEKTDT
          QQLLEYKSMV.A..EK.PEQ.M.EKQIEAKIEDLENEIEESKIAFEM.SLAL.R.QLSSA.KRNLEKTDT
Retrocopy QQLLEYKSMVVAIQEKSPEQ-MHEKQIEAKIEDLENEIEESKIAFEMKSLALDRLQLSSAHKRNLEKTDT

Parental  KTSLLMDNMKHVLKLNKLIMKSQQKSWDLEEKLLDVRKKRLQLKQASESKLLEIQTEKNKQKDDLDSMEN
          KTSLLMD..KHVLKLNKLIMKSQQKSWD.EEKLLDVRKKRLQLKQASESKLLEIQTEKNKQKDDLDSMEN
Retrocopy KTSLLMDDLKHVLKLNKLIMKSQQKSWDFEEKLLDVRKKRLQLKQASESKLLEIQTEKNKQKDDLDSMEN

Parental  SDKIKTIQQXXXXXXXXXXXXXXXXXNLILGSKVNWAEDSALKETVLQLEKNLSMI
          SDKIKT..Q.................NLILGSKV.WAED.ALKETVLQLE.NL.MI
Retrocopy SDKIKTV*QNLQVEIQITTVIQHVFQNLILGSKVHWAEDCALKETVLQLERNLPMI

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_982 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 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007717	1 retrocopy	retro_cfam_961,
Choloepus hoffmanni	ENSCHOG00000011338	2 retrocopies	retro_chof_1939, retro_chof_982 ,
Monodelphis domestica	ENSMODG00000025601	1 retrocopy	retro_mdom_1859,
Mustela putorius furo	ENSMPUG00000014646	1 retrocopy	retro_mputfur_240,
Sarcophilus harrisii	ENSSHAG00000007822	4 retrocopies	retro_shar_805, retro_shar_806, retro_shar_807, retro_shar_809,
Tupaia belangeri	ENSTBEG00000011867	2 retrocopies	retro_tbel_4318, retro_tbel_4535,
Tarsius syrichta	ENSTSYG00000002098	1 retrocopy	retro_tsyr_199,