RetrogeneDB ID: retro_chof_311

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_7094:138814..139862(+)
• Located in intron of: ENSCHOG00000004370

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC62
• Ensembl ID: ENSCHOG00000011521
• Aliases: None
• Description: coiled-coil domain containing 62 [Source:HGNC Symbol;Acc:30723]

Sequence

>retro_chof_311
AATAAAGTCACTCACGAAGAAGAGGAGCTGAATGAAAAGACAATGGAAAATAATGAACAACGAGAAGAAATCATTCGCCT
CAAACAAGAGCAAAGTTGCCTGCATGATGAATTGGTTTTTACTGTAGAGAGAGAAAAAAGGAAAGATGAGTTACTTGACA
TTGCAAAGTCAAAGCAAGAGCGTACAAACACTGAACTGCATAATCTGAGACAGATTTATGTAAAGCAACAGAGTGATCTG
CAGTTTCTTCATTTCAATGTGGAAAATTCTCAGGAATTAATACAGATATATGACTCAAAGATGGAGGAGTCAAAGGCTCT
CGAATCCAGCAGAGACATGTGTCTAGCAGACCTTGAAAATCACCACCCAAGATTCGATGTTAAGAGGGAGAAAAATCAGA
AATTACTGGTTAAGGACCAAAAATTTGAGACCATGATGGTTCACCAAAATACATCAGACAAGAGCTCTTGCAATGTATGT
GAAGAGAAGAAATCACAGGTTAATCCTTCATTTGGGGAAAAAAATATCACTGCTAGTTCATATCTATTTACCAAAGACTC
AGTGGAGAAACAAAAATCCTAGTCTCTGGAAGGAAAAATTCAGATTGAACCTGAAAACAAAAGTACGTTGTGCAAGACCC
ATGCAAAGTCACCAAAAGGTAATGAAATTGGAATTCAGAATGGAAAGAAACAAGTATCTGAAGTATCTTTAACTAATGAA
AAACAGTGGCATGATTTCAGTGTTTACCTGGATCTGGCCAATTGTTCTGGTTCAAAACAACCAAAAAAGCTGGATGTTGA
ATGTCAAGATCAGATGGAAAGGTCTCAAGTCTTGTGTTGCCAGAAAAATGAAGCCTGTCTGGGTGACAGTGACATTTGTG
AAGCTAAGTGCTGCCACCCTAGTAACTTCATAATTGAAGCCCCAGGCCACATATCTGATACAGAGTGGATGAGTATTTTC
AAGCCTTCTAAGGTGGAAAGAATTGTTCGCCACAATCTGTCTGCACTTGTTCAGAAACATCAGTGGAACAAAATCTAACT
CCTCCACA

Alignment

ORF - retro_chof_311 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.02 %
• Parental protein coverage: 51.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SEISKLKEELNEKTMENNEQREEIIRLKQEQSCLHDELVFTVEREKRKDELLDIAKSKQERTNTELHNLR
          .......EELNEKTMENNEQREEIIRLKQEQSCLHDELVFTVEREKRKDELLDIAKSKQERTNTELHNLR
Retrocopy NKVTHEEEELNEKTMENNEQREEIIRLKQEQSCLHDELVFTVEREKRKDELLDIAKSKQERTNTELHNLR

Parental  QIYVKQQSDLQFLHFNVENSQELIQIYDSKMEESKALESSRDMCLADLENHHPRFDVKREKNQKLLVKDQ
          QIYVKQQSDLQFLHFNVENSQELIQIYDSKMEESKALESSRDMCLADLENHHPRFDVKREKNQKLLVKDQ
Retrocopy QIYVKQQSDLQFLHFNVENSQELIQIYDSKMEESKALESSRDMCLADLENHHPRFDVKREKNQKLLVKDQ

Parental  KFETMMVHQNTSDKSSCSVCEEKKSQINPSFGEKNITASSYLFTKDSVEKQKSWSLEGKIQIEPENKSTL
          KFETMMVHQNTSDKSSC.VCEEKKSQ.NPSFGEKNITASSYLFTKDSVEKQKS.SLEGKIQIEPENKSTL
Retrocopy KFETMMVHQNTSDKSSCNVCEEKKSQVNPSFGEKNITASSYLFTKDSVEKQKS*SLEGKIQIEPENKSTL

Parental  CKIHAKSPKGNEIGIQNGKKQVSEVSLTNEKQWHDFSVYLDLANCSGSKQPKKLDVECQDQMERSQVLCC
          CK.HAKSPKGNEIGIQNGKKQVSEVSLTNEKQWHDFSVYLDLANCSGSKQPKKLDVECQDQMERSQVLCC
Retrocopy CKTHAKSPKGNEIGIQNGKKQVSEVSLTNEKQWHDFSVYLDLANCSGSKQPKKLDVECQDQMERSQVLCC

Parental  QKNEACLGDSDICEAKCCHPSNFIIEAPGHISDTEWMSIFKPSKVERIVRH-KSVCTCSE-NISGTKSNS
          QKNEACLGDSDICEAKCCHPSNFIIEAPGHISDTEWMSIFKPSKVERIVRH..SVCTCSE.NISGTKSNS
Retrocopy QKNEACLGDSDICEAKCCHPSNFIIEAPGHISDTEWMSIFKPSKVERIVRH<QSVCTCSE<NISGTKSNS

Parental  ST
          ST
Retrocopy ST

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_311 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011521	2 retrocopies	retro_chof_311 , retro_chof_894,
Ictidomys tridecemlineatus	ENSSTOG00000014132	1 retrocopy	retro_itri_673,