RetrogeneDB ID: retro_chof_1457

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_29958:14906..15550(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNI2
• Ensembl ID: ENSCHOG00000000600
• Aliases: None
• Description: cyclin I family, member 2 [Source:HGNC Symbol;Acc:33869]

Sequence

>retro_chof_1457
CAGGAAGTCGTGCCATGGCTTCTGAGGCTCGATAACACATCGGCTTCTCCCGGGCCACTTTTAACCTGGCTCTCACCATC
ATCAGCCGCCTCCTTGCGTCAGCAAAGATAAAAAAGAGGTACCTCCAGTGTGTCACAATTACTTCCTTGAGACTTGCTGC
AAAAGTTAACGAAGAAGAGGAGTTAATTCCACGCATAAAAGACTTCATAAAGCACTATGGCTCTGCCTATACCCCGAATG
AGCTGCTGAGGATGGAGCTGGCTATTCTGGACATACTGCGGTGGGACCTCTATATCGGGACACCGCTGGACTTCTTGACT
ATATTCCACGCCCTGGTGGTCCTGGGCTGGCCCCACGTGGTGGAGCTGCTGCCTCAGAGGAATCCTTCCCTCCACGTCGC
GTCCCTGACCAGACAGCTGCAGCACTGTATGGCCGGCCACCAGCTGCTGCAGTTCAAGGGCTCCACACTGGCCTTGGTCA
TCATCACCTTAGAGTTGGAGAGGCTCATGCCCGACTGGTTGACTCCTACATCTGATCTGCTAAAGAAAGCACAGATCAAT
ATTGACCAGTTCAGCTACTGCAAGAAACTTGCGAAACAGCAGCTAAGAAGTTTCTAGTCATCCTTCTGCATGGACACCTT
CTTG

Alignment

ORF - retro_chof_1457 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.15 %
• Parental protein coverage: 59.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QEVVPWLLRLDNT-FGFSRATFNLALTIISRLLASAKIKKRYLQCVTITSLRLAAKVNEEEELIPRIKDF
          QEVVPWLLRLDNT..GFSRATFNLALTIISRLLASAKIKKRYLQCVTITSLRLAAKVNEEEELIPRIKDF
Retrocopy QEVVPWLLRLDNT<IGFSRATFNLALTIISRLLASAKIKKRYLQCVTITSLRLAAKVNEEEELIPRIKDF

Parental  IKHYGSAYTPNELLRMELAILDILRWDLYIGTPLDFLTIFHALVVLGWPHVVELLPQRNPSLHVASLTRQ
          IKHYGSAYTPNELLRMELAILDILRWDLYIGTPLDFLTIFHALVVLGWPHVVELLPQRNPSLHVASLTRQ
Retrocopy IKHYGSAYTPNELLRMELAILDILRWDLYIGTPLDFLTIFHALVVLGWPHVVELLPQRNPSLHVASLTRQ

Parental  LQHCMAGHQLLQFKGSTLALVIITLELERLMPDWLTPTSDLLKKAQINIDQFSYCKKLAKQQLRSF-SSF
          LQHCMAGHQLLQFKGSTLALVIITLELERLMPDWLTPTSDLLKKAQINIDQFSYCKKLAKQQLRSF.SSF
Retrocopy LQHCMAGHQLLQFKGSTLALVIITLELERLMPDWLTPTSDLLKKAQINIDQFSYCKKLAKQQLRSF*SSF

Parental  CMDTFV
          CMDTF.
Retrocopy CMDTFL

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_1457 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 4 parental genes, and 5 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,
Callithrix jacchus	ENSCJAG00000013222	1 retrocopy	retro_cjac_3834,
Dasypus novemcinctus	ENSDNOG00000001502	1 retrocopy	retro_dnov_2629,