RetrogeneDB ID: retro_chof_823

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_152287:2741..3659(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KPNA4
• Ensembl ID: ENSCHOG00000008565
• Aliases: None
• Description: karyopherin alpha 4 (importin alpha 3) [Source:HGNC Symbol;Acc:6397]

Sequence

>retro_chof_823
AATAAAAGAGATGAACATCTCTTAAAGAGAAGGAATGTACCACATGAAGATATCTGTGAAGACTCTGATATAGATGGTGA
TTATAGAGTGCAAAATACCTCTCTAGAAGCTATTGTTCAAAATGCTTCAAGTGATAACCAAGGAATTCAAATAAGTGCAG
TTCAAGCTGCTAGGAAACTTTTATCCAGTGACAGAAATCCACCAATTGATGACTTAATAAAATCTGGAATATTGCCTATT
TTAGTCCATTGTCTTGAAAGAGATGACAATCCTTCTTTACAGTTTGAAGCTGCATGGGCTTTGACAAACATTGCATCTGG
AACCTCTGAACAAACGCAAGCAGTCGTTCAGTCCAATGCTGTGCCACTTTTTCTGAGGCTTCTCCATTCACCCCATCAAA
ACGTTTGTGAGCAAGCAGTGTGGGCACTGGGAAATATCATAGGTGATGGGCCCCAGTGTAGAGATTATGTTATAAGTCTT
GGAGTTGTGAAACCTTTACTTTCCTTCATAAGTCCATCTATTCCTATTACATTCTTAAGAAATGTTACTTGGGTCATGGT
CAACTTATGTCGCCACAAAGACCCACCACCCCCAATGGAAACCATTCAAGAGATTCTCCCAGCCCTTTGTGTTTTAATTC
ATCACACAGATGTAAATATATTGGTAGATACTGTCTGGGCCCTCTCTTACCTTACTGATTCTGGCAATGAACAGATACAG
ATGGTAATAGACTCTGGAATAGTTCCTCATTTGGTTCCTCTACTCAGCCACCAGGAAGTAAAAGTTCAGACTGCTGCACT
TAGAGCTGTAGGGAATATTGTTACTGGAACTGATGAGCAAACACAAGTAGTTTTGAACTGTGATGCTCTTTCACACTTTC
CTGCACTTCTGACACATCCCAAAGAAAAAATTAATAAA

Alignment

ORF - retro_chof_823 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.35 %
• Parental protein coverage: 58.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NKRDEHLLKRRNVPHEDICEDSDIDGDYRVQNTSLEAIVQNASSDNQGIQLSAVQAARKLLSSDRNPPID
          NKRDEHLLKRRNVPHEDICEDSDIDGDYRVQNTSLEAIVQNASSDNQGIQ.SAVQAARKLLSSDRNPPID
Retrocopy NKRDEHLLKRRNVPHEDICEDSDIDGDYRVQNTSLEAIVQNASSDNQGIQISAVQAARKLLSSDRNPPID

Parental  DLIKSGILPILVHCLERDDNPSLQFEAAWALTNIASGTSEQTQAVVQSNAVPLFLRLLHSPHQNVCEQAV
          DLIKSGILPILVHCLERDDNPSLQFEAAWALTNIASGTSEQTQAVVQSNAVPLFLRLLHSPHQNVCEQAV
Retrocopy DLIKSGILPILVHCLERDDNPSLQFEAAWALTNIASGTSEQTQAVVQSNAVPLFLRLLHSPHQNVCEQAV

Parental  WALGNIIGDGPQCRDYVISLGVVKPLLSFISPSIPITFLRNVTWVMVNLCRHKDPPPPMETIQEILPALC
          WALGNIIGDGPQCRDYVISLGVVKPLLSFISPSIPITFLRNVTWVMVNLCRHKDPPPPMETIQEILPALC
Retrocopy WALGNIIGDGPQCRDYVISLGVVKPLLSFISPSIPITFLRNVTWVMVNLCRHKDPPPPMETIQEILPALC

Parental  VLIHHTDVNILVDTVWALSYLTDAGNEQIQMVIDSGIVPHLVPLLSHQEVKVQTAALRAVGNIVTGTDEQ
          VLIHHTDVNILVDTVWALSYLTD.GNEQIQMVIDSGIVPHLVPLLSHQEVKVQTAALRAVGNIVTGTDEQ
Retrocopy VLIHHTDVNILVDTVWALSYLTDSGNEQIQMVIDSGIVPHLVPLLSHQEVKVQTAALRAVGNIVTGTDEQ

Parental  TQVVLNCDALSHFPALLTHPKEKINK
          TQVVLNCDALSHFPALLTHPKEKINK
Retrocopy TQVVLNCDALSHFPALLTHPKEKINK

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_823 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	ENSCHOG00000004243	1 retrocopy	retro_chof_805,
Choloepus hoffmanni	ENSCHOG00000008565	2 retrocopies	retro_chof_1082, retro_chof_823 ,
Echinops telfairi	ENSETEG00000019546	1 retrocopy	retro_etel_1695,
Rattus norvegicus	ENSRNOG00000010768	1 retrocopy	retro_rnor_592,