RetrogeneDB ID: retro_chof_1512

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_31148:993..1799(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EMC2
• Ensembl ID: ENSCHOG00000011271
• Aliases: None
• Description: ER membrane protein complex subunit 2 [Source:HGNC Symbol;Acc:28963]

Sequence

>retro_chof_1512
ATGGCGAAGGTCTCAGAGCTTATGATGTCACTTGGGAAGAAATGCGAGATAAAATGAGAAAATGGAGAGAAGAAAACTCA
CGAAATAGTGAGCAAATTGTGGAAGTTGGAGAGGAGTTAATTAATGAATATGTGTCTAAGCTTGGAGATGATATTTGGAT
CATATATGAACAAGTGATGATTGCAGCCCTAGACTATGGTCGCGATGACTTGGCATTGTTTTGTCTTCAGGAATTGAGAA
GACAATTCCCTGGCAGTCACAGAGTCAAGCGACTAACTGGCATGAGATTTGAAGCCATGGAAAGATATGATGATGCTATA
CAGCTATATGACCGAATTTTACAAGAGGATCCAACTAACACGGCTGCAAGAAAGCGTAAGATTGCTATTCGAAAAGCCCA
GGAGAAAAATGTGGAGGCCATTCGGGAGCTGAATGAGTATCTGGAACAATTTGTTGGAGACCAAGAAGCATGGCATGAAC
TTGCAGAGCTTTATATCAATGAACATGACTATGCAAAAGCAGCCTTTTGTTTAGAGGAGCTTATGATGACTAATCCACAC
AACCACTTATACTGCCAGCAGTATGCTGAAGTTAAATATACCCAGGGTGGACTTGAAAACCTCGAACTTTCAAGAAAGTA
TTTTGCACAGGCATTGAAACTTAACAACAGAAATATGAGAGCTTTGTTTGGGCTGTACATGTCTGCAAGTCATATTGCTT
CTAATCCAAAAGCAAGTGCGAAAACGAAAAAGGACAACATGAAATATGCTAGTTGGGCAGCTAGTCGAATAAACAGTGCT
TATCAG

Alignment

ORF - retro_chof_1512 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.96 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAKVSEL-YDVTWEXXXXXXXXXXXXXXXNSEQIVEVGEELINEYASKLGDDIWIIYEQVMIAALDYGRD
          MAKVSEL.YDVTWE...............NSEQIVEVGEELINEY.SKLGDDIWIIYEQVMIAALDYGRD
Retrocopy MAKVSEL<YDVTWEEMRDKMRKWREENSRNSEQIVEVGEELINEYVSKLGDDIWIIYEQVMIAALDYGRD

Parental  DLALFCLQELRRQFPGSHRVKRLTGMRFEAMERYDDAIQLYDRILQEDPTNTAARKRKIAIRKAQGKNVE
          DLALFCLQELRRQFPGSHRVKRLTGMRFEAMERYDDAIQLYDRILQEDPTNTAARKRKIAIRKAQ.KNVE
Retrocopy DLALFCLQELRRQFPGSHRVKRLTGMRFEAMERYDDAIQLYDRILQEDPTNTAARKRKIAIRKAQEKNVE

Parental  AIRELNEYLEQFVGDQEAWHELAELYINEHDYAKAAFCLEELMMTNPHNHLYCQQYAEVKYTQGGLENLE
          AIRELNEYLEQFVGDQEAWHELAELYINEHDYAKAAFCLEELMMTNPHNHLYCQQYAEVKYTQGGLENLE
Retrocopy AIRELNEYLEQFVGDQEAWHELAELYINEHDYAKAAFCLEELMMTNPHNHLYCQQYAEVKYTQGGLENLE

Parental  LSRKYFAQALKLNNRNMRALFGLYMSASHIASNPKASAKTKKDNMKYASWAASQINSAYQ
          LSRKYFAQALKLNNRNMRALFGLYMSASHIASNPKASAKTKKDNMKYASWAAS.INSAYQ
Retrocopy LSRKYFAQALKLNNRNMRALFGLYMSASHIASNPKASAKTKKDNMKYASWAASRINSAYQ

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_1512 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012826	1 retrocopy	retro_amel_600,
Canis familiaris	ENSCAFG00000000713	1 retrocopy	retro_cfam_726,
Choloepus hoffmanni	ENSCHOG00000011271	3 retrocopies	retro_chof_1512 , retro_chof_1990, retro_chof_851,
Callithrix jacchus	ENSCJAG00000006437	2 retrocopies	retro_cjac_3295, retro_cjac_3867,
Myotis lucifugus	ENSMLUG00000013258	2 retrocopies	retro_mluc_2369, retro_mluc_2452,
Mustela putorius furo	ENSMPUG00000005915	1 retrocopy	retro_mputfur_1647,
Mus musculus	ENSMUSG00000022337	1 retrocopy	retro_mmus_1262,
Oryctolagus cuniculus	ENSOCUG00000002461	1 retrocopy	retro_ocun_1251,
Pongo abelii	ENSPPYG00000018820	1 retrocopy	retro_pabe_1600,