RetrogeneDB ID: retro_chof_141

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_3201:17414..18283(+)
• Located in intron of: ENSCHOG00000002633

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000007548
• Aliases: None
• Description: None

Sequence

>retro_chof_141
AATGAAGAGGATTGGAGGAGAGCAGTGTGGGAGAAGAATATGAAAATGACTGAACTGCACAATGTGGAATACAGCCTGAG
GCAACACAGCTTCAAGTTGGGAATGAATGCCTTTGGTGGCATGACCAATGAAGAATTCAGGTAGGTGATGAATGGCTTTC
AAAACTAGGAACCCAAGAAGGGGGAAATGTTCTTTGAATTTCCCTCTGAGGTCCCCACATCTGTGGATTGGAGGGATAAA
GACTATGTGACTCCCGTGAAGAATCAGGGTCACTGTGGTCCTTGTTGGGCTTTCAGTACAACCAGTTCCCTGGAAGGACA
GATGTTCCAGAAAACTGGCATACTTGTTTCACTCAGTGAGCAGAAGCTGGTGGACTGCTCACAGGCTGAGGGCAATAGCA
GCTGCAATGGCGGCCTAATGGACAATGCTTTTCAGTATGTCCAGGACAACAAAGGCCTCAATTCAAAGGAATTTTATCCA
TATGTTGGAAAGGACATGACCTGTAGCTACAAGCCTGAGTATTCTGCTGCCAACGACACTGGCTTTGTAGAGTCTCTCTA
CTGGAGAAGGCACTTATGGTGGCATTGGCAACTGTAGGTCCCATCTCGATTGCTATTGATGCAAGCCATGACTCCTTCCA
GTTCTATGAATCAGGCATTTATTATGAGCCACACTGCAGTAGCAGAGACCCGGATCACGGGGTCCTGGTGGTTGGCTATG
GCTTTGAAGGAACAGATTCAGATAACAATAAATACTGGCTCATCAAGAACAACTGGGGTGAAAGTTGGGGCATGGACGGC
TATGTAAAGACGGCCAGAGACCAGAACAACCACTGTGGAGTTGCCACAAAAGCCAGCTATCCCACCGTG

Alignment

ORF - retro_chof_141 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.19 %
• Parental protein coverage: 92.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SEEDWRRAVWEKNMKIIEVHNQEYSLGQHSFKLGMNAFGDMTSEEFRQVMNGFQNKEHKKGEMFSESPSE
          .EEDWRRAVWEKNMK..E.HN.EYSL.QHSFKLGMNAFG.MT.EEFR.VMNGFQN.E.KKGEMF.E.PSE
Retrocopy NEEDWRRAVWEKNMKMTELHNVEYSLRQHSFKLGMNAFGGMTNEEFR*VMNGFQN*EPKKGEMFFEFPSE

Parental  VPTSVDWRDKGYVTPVKNQGHCGSCWAFSAAGSLEGQMFRKTGILVSLSEQNLVDCSRAEGNSGCNGGLM
          VPTSVDWRDK.YVTPVKNQGHCG.CWAFS...SLEGQMF.KTGILVSLSEQ.LVDCS.AEGNS.CNGGLM
Retrocopy VPTSVDWRDKDYVTPVKNQGHCGPCWAFSTTSSLEGQMFQKTGILVSLSEQKLVDCSQAEGNSSCNGGLM

Parental  DNAFQYVQDNKGLDSEESYPYVGKDMNCSYKPEYSAANDTGFVE-VAPLEKTLMAAVAAVGPISVAIDAS
          DNAFQYVQDNKGL.S.E.YPYVGKDM.CSYKPEYSAANDTGFVE.V..LEK.LM.A.A.VGPIS.AIDAS
Retrocopy DNAFQYVQDNKGLNSKEFYPYVGKDMTCSYKPEYSAANDTGFVE<VSLLEKALMVALATVGPISIAIDAS

Parental  HESFQFYESGIYYEPDCSSKDLDHGVLVVGYGFEETDSDNNKYWLVKNSWGESWGMEGYVKMARDRDNHC
          H.SFQFYESGIYYEP.CSS.D.DHGVLVVGYGFE.TDSDNNKYWL.KN.WGESWGM.GYVK.ARD..NHC
Retrocopy HDSFQFYESGIYYEPHCSSRDPDHGVLVVGYGFEGTDSDNNKYWLIKNNWGESWGMDGYVKTARDQNNHC

Parental  GIATKASYPTV
          G.ATKASYPTV
Retrocopy GVATKASYPTV

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_141 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 10 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007548	8 retrocopies	retro_chof_1227, retro_chof_1332, retro_chof_1345, retro_chof_141 , retro_chof_1464, retro_chof_2392, retro_chof_383, retro_chof_424,
Dasypus novemcinctus	ENSDNOG00000012037	1 retrocopy	retro_dnov_2387,
Macropus eugenii	ENSMEUG00000002168	2 retrocopies	retro_meug_1349, retro_meug_1567,
Macropus eugenii	ENSMEUG00000014293	1 retrocopy	retro_meug_1873,
Macropus eugenii	ENSMEUG00000016209	2 retrocopies	retro_meug_159, retro_meug_1727,
Monodelphis domestica	ENSMODG00000002844	1 retrocopy	retro_mdom_1101,
Otolemur garnettii	ENSOGAG00000001349	2 retrocopies	retro_ogar_1053, retro_ogar_1373,
Ochotona princeps	ENSOPRG00000001030	2 retrocopies	retro_opri_186, retro_opri_499,
Petromyzon marinus	ENSPMAG00000003453	1 retrocopy	retro_pmar_7,
Tupaia belangeri	ENSTBEG00000016406	1 retrocopy	retro_tbel_2841,