RetrogeneDB ID: retro_chof_2113

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_50269:7430..8732(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000003460
• Aliases: None
• Description: None

Sequence

>retro_chof_2113
GACCCCTCTGGTAAGCCGCCTTGCCGAGGCTGCTCCTCCTACCTCATGGAGCCTTATATCAAGTGTGCTGAATGTGGACC
ACCTCTTTTCTTTCTCTGCTTACAGTGTTTCACTCGAGGATTTGAGTACAAGAAACATCAAAGTGATCATACTTATGAAA
TAATGACCTCAGATTTTCCTGTTCTTGATCCAAGCTGGACTGCTCAAGAAGAAATGGCCCTTTTAGAAGCTGTGATGGAC
TGTGGCTTTGGAAATTGGCAGAATGTAACCAATCAAATGTGTACCAAGACCAAGGAGGAGTGTGAGAAGCAGTATATGAA
ACATTTCATCAACAACCCTCTGTTCGCATCTACCTTGCTGAACCTGAAGTAAGCAGACGAAGCAAAAACTGCTGACACAG
CGATTCCATTTCACTCTACAAACTACCTTCCCTGGCCTAACTTTGACTCCCTGCTTTCTCGGGACATGGCAGGATACATG
CCAGCTCGAGCAGACTTCATTGAGGAGTTTGACAATTATGCAGAATGGGACTTGAGAGACATCGATTTTGTTGAAGATGA
CTTGGACATTTTACATGCTCTGAAGATGGCTGTGGAAGATATCTATCATTCCAGGTTAAAAGAGAGACAAAGGCGAAAAA
ACATTGTAAGAGACCATGGATTAATCAACCTTAGAAAATTTCAGTTAATGGAATGGCGGTATCCCAAGGAGGTCCAAGAC
CTTTAAGAAACAAAGAGGCGATTTGCAAGGATTGTGGGGCCAGTGGAGCATGACAAGTTCATTGAAAGCCATGCATTGGA
ATTTGAACTCCGAAGGGAAATTAAGAAGCTCTAGGAATATAGGACAGCAGGCATTACCAGTTTTTGTAGTGCCAGAACCT
ATGATCACCTCAAGAAGACACAAGAGGAGGAACGCCTTAAACGCACCATACTCTCCGAAGTTCTCCAGTATATCCAGGAA
AGTAGTGCTTGCTGGCAGTGGCTCCGCCGACAAGCTGACATTGACTCTGGCCTCGGTCCTTCCATTCCAATGTCTTCAAA
TTCAGGTAGATGGAGTGCACCACCCTTGAACCTCACTGGCCTCCCTGGCACAGAGAAGCTGAATGAAAAAGAAAAAGAGC
ACTGTCAGATGGTGAGGTTGGTCCCTGGAGCCTATTTAGAATACAAATCTGCTCTATTGAATGAACGTAACAAGCAAGGA
GGCTTGAGACTGGCACGGGCAAGAGCACTGATCAAGATAGACATGAACAAAAGCCAGAAAATCTATGATTTCCTCATCCA
AGAAGGATACATCACTAAAGCC

Alignment

ORF - retro_chof_2113 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.4 %
• Parental protein coverage: 99.09 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DPSGKPPCRGCSSYLMEPYIKCAECGPPPFFLCLQCFTRGFEYKKHQSDHTYEIMTSDFPVLDPSWTAQE
          DPSGKPPCRGCSSYLMEPYIKCAECGPP.FFLCLQCFTRGFEYKKHQSDHTYEIMTSDFPVLDPSWTAQE
Retrocopy DPSGKPPCRGCSSYLMEPYIKCAECGPPLFFLCLQCFTRGFEYKKHQSDHTYEIMTSDFPVLDPSWTAQE

Parental  EMALLEAVMDCGFGNWQDVANQMCTKTKEECEKHYMKHFINNPLFASTLLNLKQAEEAKTADTAIPFHST
          EMALLEAVMDCGFGNWQ.V.NQMCTKTKEECEK.YMKHFINNPLFASTLLNLK.A.EAKTADTAIPFHST
Retrocopy EMALLEAVMDCGFGNWQNVTNQMCTKTKEECEKQYMKHFINNPLFASTLLNLK*ADEAKTADTAIPFHST

Parental  DDPPRPNFDSLLSRDMAGYMPARADFIEEFDNYAEWDLRDIDFVEDDSDILHALKMAVVDIYHSRLKERQ
          ...P.PNFDSLLSRDMAGYMPARADFIEEFDNYAEWDLRDIDFVEDD.DILHALKMAV.DIYHSRLKERQ
Retrocopy NYLPWPNFDSLLSRDMAGYMPARADFIEEFDNYAEWDLRDIDFVEDDLDILHALKMAVEDIYHSRLKERQ

Parental  RRKKIIRDHGLINLRKFQLMERRYPKEVQDLYETMRRFARIVGPVEHDKFIESHALEFELRREIKRLQEY
          RRK.I.RDHGLINLRKFQLME.RYPKEVQDL.ET.RRFARIVGPVEHDKFIESHALEFELRREIK.L.EY
Retrocopy RRKNIVRDHGLINLRKFQLMEWRYPKEVQDL*ETKRRFARIVGPVEHDKFIESHALEFELRREIKKL*EY

Parental  RTAGITSFCSARTYDHLKKTREEERLKRTMLSEVLQYIQDSSACQQWLRRQADIDSGLSPSIPMASNSGR
          RTAGITSFCSARTYDHLKKT.EEERLKRT.LSEVLQYIQ.SSAC.QWLRRQADIDSGL.PSIPM.SNSGR
Retrocopy RTAGITSFCSARTYDHLKKTQEEERLKRTILSEVLQYIQESSACWQWLRRQADIDSGLGPSIPMSSNSGR

Parental  RSAPPLNLTGLPGTEKLNEKEKELCQMVRLVPGAYLEYKSALLNECNKQGGLRLAQARALIKIDVNKTRK
          .SAPPLNLTGLPGTEKLNEKEKE.CQMVRLVPGAYLEYKSALLNE.NKQGGLRLA.ARALIKID.NK..K
Retrocopy WSAPPLNLTGLPGTEKLNEKEKEHCQMVRLVPGAYLEYKSALLNERNKQGGLRLARARALIKIDMNKSQK

Parental  IYDFLIREGYITKA
          IYDFLI.EGYITKA
Retrocopy IYDFLIQEGYITKA

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_2113 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	ENSCHOG00000003460	2 retrocopies	retro_chof_15, retro_chof_2113 ,
Nomascus leucogenys	ENSNLEG00000002646	1 retrocopy	retro_nleu_930,