RetrogeneDB ID: retro_chof_2538

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_83537:7524..8104(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAK16
• Ensembl ID: ENSCHOG00000009081
• Aliases: None
• Description: MAK16 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:13703]

Sequence

>retro_chof_2538
CATAAATGTAAACAGAGATTCACCAGGATTACCCGGTAGCTAATTTGAATTCGAAAACTTACGCTAAAGAGACAGAGAAA
ACTTGTTCCTTTGAGTAAGAAGGTAGAACAGAGGGAAAAAAGGAGCGAGGAAAAGGCATTGATAGCTGCTCAGCTGGACA
ACAACATTGAAAAGGAATTACTAGAAAGACTGAAACAAGATACATATGGCGACATCTACAACTTCCCTGTTCATGCGTTC
GACAAGGCCCTGGAACAGCAGGAGGCAGAGAGTGGCTCTTCAGATGCTGAGGAAAAAGACAACAATGAAGAAGAAGAAGA
AGATGTGGGAACAAGAGAATTTGTGGAAGATGATGAGGTGGATGAGAGTGACATAAGTGACTTTGAGGACATGAATAAAT
TGGATATCAGCAGTAATGAAGATCAGGATCAGAGATCATCCAGTGAGGACGAAGAAAAGGCCCTGGATGCCAGACACAAA
AGCAAAAACACCTTTGAAAGGACCTTTGCGGAGAAAATGAGCCTATGTAGAGATAGGGTATGAGCAGGAGACAGAGCCCA
TGGCTAAGGCCAAAACCACG

Alignment

ORF - retro_chof_2538 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.05 %
• Parental protein coverage: 64.19 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HKCKQRFTKITQYLIRIRKLTLKRQRKIVPLSKKVERREKRREEKALIAAQLDNAIEKELLERLKQDTYS
          HKCKQRFT.IT..LI.IRKLTLKRQRK.VPLSKKVE.REKR.EEKALIAAQLDN.IEKELLERLKQDTY.
Retrocopy HKCKQRFTRITR*LI*IRKLTLKRQRKLVPLSKKVEQREKRSEEKALIAAQLDNNIEKELLERLKQDTYG

Parental  DIYNFPIHAFDKALEQQEAESDSSDAEEKDDEEEEVDE--TREFLEDDEVDESDIK-LEDMDKLDISGSE
          DIYNFP.HAFDKALEQQEAES.SSDAEEKD..EEE.....TREF.EDDEVDESDI...EDM.KLDIS..E
Retrocopy DIYNFPVHAFDKALEQQEAESGSSDAEEKDNNEEEEEDVGTREFVEDDEVDESDISDFEDMNKLDISSNE

Parental  DQDQRSSSEDEEKALDARH-KGKTPLKGPLRRKRAYVEIEYEQETEPMAKAKTT
          DQDQRSSSEDEEKALDARH.K.KTPLKGPLRRK.AYVEI.YEQETEPMAKAKTT
Retrocopy DQDQRSSSEDEEKALDARH>KAKTPLKGPLRRK*AYVEIGYEQETEPMAKAKTT

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_2538 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 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009081	5 retrocopies	retro_chof_2336, retro_chof_2538 , retro_chof_531, retro_chof_867, retro_chof_948,
Dasypus novemcinctus	ENSDNOG00000008424	1 retrocopy	retro_dnov_624,
Latimeria chalumnae	ENSLACG00000018758	1 retrocopy	retro_lcha_67,
Macropus eugenii	ENSMEUG00000006945	1 retrocopy	retro_meug_1291,
Myotis lucifugus	ENSMLUG00000002758	1 retrocopy	retro_mluc_590,
Oryctolagus cuniculus	ENSOCUG00000008735	3 retrocopies	retro_ocun_1053, retro_ocun_1298, retro_ocun_908,
Sus scrofa	ENSSSCG00000015832	1 retrocopy	retro_sscr_917,