RetrogeneDB ID: retro_chof_1748

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_374071:141..969(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ABT1
• Ensembl ID: ENSCHOG00000005188
• Aliases: None
• Description: activator of basal transcription 1 [Source:HGNC Symbol;Acc:17369]

Sequence

>retro_chof_1748
ATGGAGGCCAAGGAATCGGGGAAGGAAGCGGCGAAGCAGGAGCCGCTGGAAGGGGAAGACCAGAAACCGGGGCCGGAGGA
AGAGCAGGAGGATCCTGGAGACGAGGCTTGCGTCGGCAAAAAGCGGGTGGTGCCGGGTATTGTGTACTTGGGCCACATCC
CGCCGCGCTTCCGGCCCCTGCACGTGCACAACCTTCTCAGCGCCTACGGCGAAGTCGGGCGCGTTTTCTTTCAGCCTGAG
GACGGGTTTGTGCGGCGCAAGACGAAGGCGGCGGCGGCTGCTGGGGCCACGGGAGGAAAGAAAGGGTCCAGGTACAGCAA
GGACTACACTGAGGGCTGGGTGGAGTTCCGGGACAAGCGCGTGGCGAAGCGCGTGGCAGCCAGTCTACACAACACGCCCA
TGGGTTCCCGAAGGCGCAGCCCCTTCCGCTATGATCTGTGGAATCTTAAGTACCCGCATCGGTTCACCTGGTCCCACCTC
AGCGAGCACCTGGCCTTTGAGCACCAGGTGCACCGACAGCACCTGAGAGCTGAGGTTGCTCAGGCTAAGTGTGAGACTGA
CTTTTATCTTCGAAGTGTGGAGCGGGGACAACGCTTCCTCGCTGCTGATGGTGACCCTGCCCGCCCCAATGGCTCTTGGG
CCTTTGCCCAGCACCCCACTGAGCAGGAGCTGAGGGCCCGTCGTTTGGCCCGACCAGGAGGGCGCGAACGGGCTCGCCTG
ACTACTGCCCAGGACCAGGCCCGCTCCAACCAAGGACTTCTTGCCAGGATCTTTGGAGCTCCACCACCCTCGGAGGACAT
GTAGGGACCTGCTGTGGCCAGGGACAAC

Alignment

ORF - retro_chof_1748 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.84 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEAEESGKEAAKQEPLEGEDQKPGPEEEQEDPGEEACVGKKRVVPGIVYLGHIPPRFRPLHVRNLLSAYG
          MEA.ESGKEAAKQEPLEGEDQKPGPEEEQEDPG.EACVGKKRVVPGIVYLGHIPPRFRPLHV.NLLSAYG
Retrocopy MEAKESGKEAAKQEPLEGEDQKPGPEEEQEDPGDEACVGKKRVVPGIVYLGHIPPRFRPLHVHNLLSAYG

Parental  EVGRVFFQPEDGFVRRKKKKAAAAGATGGKKGSRYSKDYTEGWVEFRDKRVAKRVAASLHNTPMGARRRS
          EVGRVFFQPEDGFVRRK.K.AAAAGATGGKKGSRYSKDYTEGWVEFRDKRVAKRVAASLHNTPMG.RRRS
Retrocopy EVGRVFFQPEDGFVRRKTKAAAAAGATGGKKGSRYSKDYTEGWVEFRDKRVAKRVAASLHNTPMGSRRRS

Parental  PFRYDLWNLKYLHRFTWSHLSDHLAFERQVRRQRLRAEVAQAKRETDFYLRSVERGQRFLAADGDPARPN
          PFRYDLWNLKY.HRFTWSHLS.HLAFE.QV.RQ.LRAEVAQAK.ETDFYLRSVERGQRFLAADGDPARPN
Retrocopy PFRYDLWNLKYPHRFTWSHLSEHLAFEHQVHRQHLRAEVAQAKCETDFYLRSVERGQRFLAADGDPARPN

Parental  GSWAFAQHPTEQELRARRLA-PGGRERTHLATAQDQARSNQGLLARIFGAPPPSEDM-GPAVARDN
          GSWAFAQHPTEQELRARRLA.PGGRER..L.TAQDQARSNQGLLARIFGAPPPSEDM.GPAVARDN
Retrocopy GSWAFAQHPTEQELRARRLARPGGRERARLTTAQDQARSNQGLLARIFGAPPPSEDM*GPAVARDN

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_1748 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005188	1 retrocopy	retro_chof_1748 ,
Cavia porcellus	ENSCPOG00000008937	1 retrocopy	retro_cpor_1386,
Gorilla gorilla	ENSGGOG00000024149	1 retrocopy	retro_ggor_2106,
Macaca mulatta	ENSMMUG00000006914	1 retrocopy	retro_mmul_1959,
Otolemur garnettii	ENSOGAG00000026316	1 retrocopy	retro_ogar_2895,
Pongo abelii	ENSPPYG00000016335	1 retrocopy	retro_pabe_2541,
Rattus norvegicus	ENSRNOG00000017585	1 retrocopy	retro_rnor_841,
Sarcophilus harrisii	ENSSHAG00000003493	1 retrocopy	retro_shar_97,