RetrogeneDB ID: retro_chof_1831

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_398677:0..1047(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNF4G
• Ensembl ID: ENSCHOG00000000938
• Aliases: None
• Description: hepatocyte nuclear factor 4, gamma [Source:HGNC Symbol;Acc:5026]

Sequence

>retro_chof_1831
TTCGGGGCATCGAGCTGCAATGGGTGCAAGGGCTTCTTCAGACGCAGCATACGCAAGAGTCACGTTTATTCCTGCAGGTT
CAGTCGTCAATGTGTTGTTGACAAGGACAAAAGGAATCAATGTAGATATTGTCGATTAAGAAAATGTTTTAGTGCAGGAA
TGAAAAAAGAAGCTGTGCAAAATGAACGCGATAGAATAAGCACCAGAAGAAGCACGTTTGATGGCAGCAATATTCCTTCC
ATTAACACGCTGGCACAGGCCGAAGCTCTGTCTCGCCAGATCCCTGTCTCAAGCCCTGGGGCAAGCACTGACATAAATGT
GAAGAAAATTGCAAGTATTGCTGATGTCTGTGAATCTATGAAACAGCAACTCTTAGTCTTGGTGGAATGGGCTAAATATA
TCCCTGCCTTCTGTGAGTTACCATTGGATGATCAGGTGGCACTGTTGAGAGCTCATGCAGGGGAACATTTATTGCTTGGA
GCTACCAAGCGATCCATGGTGTATAAAGATATTTTGCTTTTGGGAAACAACTACGTTATCCACCACAACAGCTGTGAAGT
AGAGATCAGTCGTGTGGCCAATCGGATTCTAGATGAGCTAGTCAGACCATTTCAAGAAATTCAGATTGATGACAATGAAT
ACGCTTGTTTGAAGGCAATTGTATTTTTCGACCCAGATGCAAAAGGACTCAGTGACCCAGTAAAAATTAAGAACATGTGA
TTCCAAGTTCAGATTGGTTTGGAGGACTACATCAATGACCGGCAGTACGACTCCCGGGGGAGATTTGGGGAGCTGCTTCT
GCTTCTGCCCACCCTGCAGAGCATCACCTGGCAGATGATTGAACAAATACAGTTTGTTAAACTTTTTGGGATGGTTAAAA
TTGACAGCCTACTTCAGGAGATGCTACTGGGTGGTGCTTCCAACGATGCTGGCCATCTCCATCATCCAATGCACCCACAT
TTGTCTCAAGATCCATTAACTGGACAGACTATCCTTATAAGTTCCCTGTCAACACTGGTTCATACAGACCAGATCTCAAC
TCCTGAA

Alignment

ORF - retro_chof_1831 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.71 %
• Parental protein coverage: 78.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YGASSCDGCKGFFRRSIRKSHVYSCRFSRQCVVDKDKRNQCRYCRLRKCFRAGMKKEAVQNERDRISTRR
          .GASSC.GCKGFFRRSIRKSHVYSCRFSRQCVVDKDKRNQCRYCRLRKCF.AGMKKEAVQNERDRISTRR
Retrocopy FGASSCNGCKGFFRRSIRKSHVYSCRFSRQCVVDKDKRNQCRYCRLRKCFSAGMKKEAVQNERDRISTRR

Parental  STFDGSNIPSINTLAQAEALSRQIPVSSPGASTDINVKKIASIADVCESMKQQLLVLVEWAKYIPAFCEL
          STFDGSNIPSINTLAQAEALSRQIPVSSPGASTDINVKKIASIADVCESMKQQLLVLVEWAKYIPAFCEL
Retrocopy STFDGSNIPSINTLAQAEALSRQIPVSSPGASTDINVKKIASIADVCESMKQQLLVLVEWAKYIPAFCEL

Parental  PLDD-VALLRAHAGEHLLLGATKRSMVYKDILLLGNNYVIHRNSCEVEISRVANRILDELVRPFQDIQID
          PLDD.VALLRAHAGEHLLLGATKRSMVYKDILLLGNNYVIH.NSCEVEISRVANRILDELVRPFQ.IQID
Retrocopy PLDDQVALLRAHAGEHLLLGATKRSMVYKDILLLGNNYVIHHNSCEVEISRVANRILDELVRPFQEIQID

Parental  DNEYACLKAIVFFDPDAKGLSDPVKIKNMRFQVQIGLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMI
          DNEYACLKAIVFFDPDAKGLSDPVKIKNM.FQVQIGLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMI
Retrocopy DNEYACLKAIVFFDPDAKGLSDPVKIKNM*FQVQIGLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMI

Parental  EQIQFVKLFGMVKIDSLLQEMLLGGASNDAGHLHHPMHPHLSQDPLTGQTILISSMSTLVHTDQISTPE
          EQIQFVKLFGMVKIDSLLQEMLLGGASNDAGHLHHPMHPHLSQDPLTGQTILISS.STLVHTDQISTPE
Retrocopy EQIQFVKLFGMVKIDSLLQEMLLGGASNDAGHLHHPMHPHLSQDPLTGQTILISSLSTLVHTDQISTPE

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_1831 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000938	1 retrocopy	retro_chof_1831 ,
Pan troglodytes	ENSPTRG00000020357	1 retrocopy	retro_ptro_869,