RetrogeneDB ID: retro_chof_1939

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_42720:4049..4549(-)
• 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_1939
GCTAAATTGAGTGACCTGGAGATGAATTGAAGAGCAAAAATGCTTTTGAAATATAAAGTCTTGCATTAAACAGTATGCAG
CTTTCATCGGCACTTAAAAGAAACCTGGAGGAAACTGACACCAAAACTAGTTTACTCATGGATGACATGAAACATGTATT
AAAGCTAAATAAATTAATAATGAAATCACAGCAGAAATCTCGGGACTTTGAGGAAAAACTGCTGGATGTTAGAAAGACAA
GACTGCAATTAAAATAAGCTTCAGAAAGTAAACTTCTAGAAATACAAATTGAAAAGAACAAACAAAAAGATGATTTGGAC
AGTATGGAAAATTCAGACAAGATAAAGACCATATGACAAAACCTACAGGTGGAGATATAGATTATTACAGTTACTCAACA
TGTGTTTCAGAACCTCATTTTGGGGAGTGAAGTCCATTGGGCAGAAGATTGTGCCTTGGAGGAAACTGTTCTGCAACTCG
AGAGGAATCTATCCATGATT

Alignment

ORF - retro_chof_1939 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.15 %
• Parental protein coverage: 68.02 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AKIEDLE-NEIEESKIAFEMTSLALHRMQLSSALKRNLEKTDTKTSLLMDNMKHVLKLNKLIMKSQQKSW
          AK..DLE..E...SK.AFE..SLAL..MQLSSALKRNLE.TDTKTSLLMD.MKHVLKLNKLIMKSQQKS.
Retrocopy AKLSDLE<DELK-SKNAFEI*SLALNSMQLSSALKRNLEETDTKTSLLMDDMKHVLKLNKLIMKSQQKSR

Parental  DLEEKLLDVRKKRLQLKQASESKLLEIQTEKNKQKDDLDSMENSDKIKTIQQXXXXXXXXXXXXXXXXXN
          D.EEKLLDVRK.RLQLK.ASESKLLEIQ.EKNKQKDDLDSMENSDKIKTI.Q.................N
Retrocopy DFEEKLLDVRKTRLQLK*ASESKLLEIQIEKNKQKDDLDSMENSDKIKTI*QNLQVEI*IITVTQHVFQN

Parental  LILGSKVNWAEDSALKETVLQLEKNLSMI
          LILGS.V.WAED.AL.ETVLQLE.NLSMI
Retrocopy LILGSEVHWAEDCALEETVLQLERNLSMI

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_1939 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,