RetrogeneDB ID: retro_chof_2262

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_61808:6265..7397(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNI
• Ensembl ID: ENSCHOG00000003915
• Aliases: None
• Description: cyclin I [Source:HGNC Symbol;Acc:1595]

Sequence

>retro_chof_2262
ATGAAGTTTCCAGGATCTTTGGAAAACCAGAGATTGTCTTTCCTGTTGGAAAAGGCAATCTCTAGGGAAGCCCAGATGTG
GAAGGTGAATGTGCCCAAAACGCCTACAAATCAGAATGTTTCCCCATCCCAGAGAGATGAAGTGATTCAGTGGTTGGCCA
AACTCAAGTACCAATTCAACCTTTACCCAGAAACGTTTGCCCTGGCTAGCAGTCTTTTGGACAGGTTTTTAGCTACTGTA
AAGGCTCACCCAAAATACTTGAGTTGTATTGCAATCAGCTGTTTTTTCCTAGCTGCCAAGACTGTTGAGGAGGATGAGAG
AATTCCAGTACTGAAGGTATTGGCAAGAGACAGTTTCTGTGGATGTTCTTCCTCTGAAATTCTGAGAATGGAGAGAATTA
TTCTGGATAAGCTGAATTGGGATCTTCACACAGCTACACCATTGGATTTTCTTCACATTTTCCATGCCATTGCAGTGTCA
ACTAGGCCTCAGTTACTCTTCAGTTTGCCCAAACTGAGCCCATCCCAACATTTGGCGGCCCTTACCAAGCAACTAGTTAA
GTGTATGGCCTGCAATCAACTTTTGCAGTTCAAAGGATCTATGCTTGCTCTGGCCATGGTTAGTTTGGAAATGGAGAAAC
TTATTCCTGATTGGCTCTCTCTTACAATTGAATTGCTTCAGAAAGCACAGATGGATAGCTCCCAGTTGATCCACTGTCGG
GAGTTTGTGGCACATCACCTTTTCTACTCTGCAGTCTTCTCTGCCTCTAAATTCCGTTTATGTCTACCGTCCCCTCAAGC
ACACCCTGGTGACCTGTGACAAAGGAGTGTTCAGATTACATCCCTCCTCTGTCCCAGGCCCAGACTTCTCCAAGGACAAC
AGCAAACCAGAAGTGCCAGTCAGAAGTACAGCAGCCTTATGCCATCATCTCCCAGCTGCCAGTGGGTGCAAACATACCTC
TGCTAAACGCAAAGTAGAGGAAATGGAAGTGGATGATTTCTATGATGGAATCAAGCGGCTCTATAATGAAGACAGTGCTT
CAGAAAACGTGGGTTCTGTGTGTGGCACTGATTTATCAAGGCAAGAGGGACATGGTTCCCCTTGCCCACCTCTGCAACCT
GTTTCTGTCATG

Alignment

ORF - retro_chof_2262 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.88 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKFPGSLENQRLSFLLEKAISREAQMWKVNVPKTPTNQNVSPSQRDEVIQWLAKLKYQFNLYPETFALAS
          MKFPGSLENQRLSFLLEKAISREAQMWKVNVPKTPTNQNVSPSQRDEVIQWLAKLKYQFNLYPETFALAS
Retrocopy MKFPGSLENQRLSFLLEKAISREAQMWKVNVPKTPTNQNVSPSQRDEVIQWLAKLKYQFNLYPETFALAS

Parental  SLLDRFLATVKAHPKYFFCIAISCFFLAAKTVEEDERIPVLKVLARDSFCGCSSSEILRMERIMLDKLNW
          SLLDRFLATVKAHPKY..CIAISCFFLAAKTVEEDERIPVLKVLARDSFCGCSSSEILRMERI.LDKLNW
Retrocopy SLLDRFLATVKAHPKYLSCIAISCFFLAAKTVEEDERIPVLKVLARDSFCGCSSSEILRMERIILDKLNW

Parental  -LHTATPLDFLHIFHAIAVSTRPQLLFSLPKLSPSQHLAALTKQLLKCMACNQLLQFKGSMLALAMVSLE
          .LHTATPLDFLHIFHAIAVSTRPQLLFSLPKLSPSQHLAALTKQL.KCMACNQLLQFKGSMLALAMVSLE
Retrocopy DLHTATPLDFLHIFHAIAVSTRPQLLFSLPKLSPSQHLAALTKQLVKCMACNQLLQFKGSMLALAMVSLE

Parental  MEKLIPDWLSLTIELLQKAQMDSSQLIHCREFVAHYL-STLQSSLPLNSVYVYRPLKHTLVTCDKGVFRL
          MEKLIPDWLSLTIELLQKAQMDSSQLIHCREFVAH.L.STLQSSLPLNSVYVYRPLKHTLVTCDKGVFRL
Retrocopy MEKLIPDWLSLTIELLQKAQMDSSQLIHCREFVAHHL>STLQSSLPLNSVYVYRPLKHTLVTCDKGVFRL

Parental  HPSSVPGPDFSKDNSKPEVPVRSTAAFCHHLPAASGCKHTSAKRKVEEMEVDDFYDGIKRLYNEDSASEN
          HPSSVPGPDFSKDNSKPEVPVRSTAA.CHHLPAASGCKHTSAKRKVEEMEVDDFYDGIKRLYNEDSASEN
Retrocopy HPSSVPGPDFSKDNSKPEVPVRSTAALCHHLPAASGCKHTSAKRKVEEMEVDDFYDGIKRLYNEDSASEN

Parental  VGSVCGTDLSRQEGHGSPCPPLQPVSVM
          VGSVCGTDLSRQEGHGSPCPPLQPVSVM
Retrocopy VGSVCGTDLSRQEGHGSPCPPLQPVSVM

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_2262 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	ENSCHOG00000000600	1 retrocopy	retro_chof_1457,
Choloepus hoffmanni	ENSCHOG00000003915	2 retrocopies	retro_chof_2262 , retro_chof_26,