RetrogeneDB ID: retro_chof_1624

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_344561:442..1316(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MCU
• Ensembl ID: ENSCHOG00000003454
• Aliases: None
• Description: mitochondrial calcium uniporter [Source:HGNC Symbol;Acc:23526]

Sequence

>retro_chof_1624
AATTTGGGAGTTGTTTATTGCAGTACTGTTGTGCCCTCTGATGATTTGACAGTGGTTTATCGAAACAGCTTACCTGTGAT
ATCTGTGAGGTTACCATCCCGGCGTGAACGCTGCCAGTTCACACTCAAACCTATCTCAGACTCTGTTGGTGTCTTTTTAC
AACTCCAAGAAGAGGATCGAGGAATTGACAGAGTCGCAATCTATTCGCCAGATGGTGTTCGAGTTGCTGCCTCAACAGGG
ATAGACCTGCTCCTCCTCGACGACTTTAAGCTGGTCATTAATGACTTAACATATCATGTCAGACCACCAAAGAGAGACCT
CTTAAGCCATGAAAATGCAGCAACGCTGAATGATGTAAAGACACTGGTCCAGCAGCTATACACTACACTGTGCATTGGGC
AGCACCAGTTAAATAAGGAAAGAGAGCTTATAGAACGATTAGAGGATCTCAAAGAGCAACTGGCTCCCTTGGAAAAGGTA
TGAATTGAGATTAGCAAAAAAGCTGAGAAGAGGACCACTCTGGTGCTATGGGGTGGACTTGCCTACATGGCCACACAGTT
TGGCATTTTGGCCCGGCTTACCTGGTGGGAATATTCCTGGGATATCATGGAGCCGGTCACCTACTTCATCACTTATGGAA
GTGCCACGGCAATGTATGCATATTTTGTAATGACACGTCAGGAATATGTTTATCCAGAAGCCAGAGACAGACAATACTTA
TTATTTTTCCATAAAGGAGCCAAAAAGTCACGTTTTGACTTACAGAAATATAATCAACTCAAGGATGCAGTTGCTCAGGC
AGAAATGGACCTTAAGAGACTGAGAGGACCCATTGCAAGTACATCTGCCCCTCCGACAAATTGGTGAAAAAGAT

Alignment

ORF - retro_chof_1624 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.25 %
• Parental protein coverage: 97.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NLGVVYCSTVVPSDDVTVVYQNGLPVISVRLPSRRERCQFTLKPISDSVGVFLQQLQEEDRGIDRVAIYS
          NLGVVYCSTVVPSDD.TVVY.N.LPVISVRLPSRRERCQFTLKPISDSVGVFL.QLQEEDRGIDRVAIYS
Retrocopy NLGVVYCSTVVPSDDLTVVYRNSLPVISVRLPSRRERCQFTLKPISDSVGVFL-QLQEEDRGIDRVAIYS

Parental  PDGVRVAASTGIDLLLLDDFKLVINDLTYHVRPPKRDLLSHENAATLNDVKTLVQQLYTTLCIEQHQLNK
          PDGVRVAASTGIDLLLLDDFKLVINDLTYHVRPPKRDLLSHENAATLNDVKTLVQQLYTTLCI.QHQLNK
Retrocopy PDGVRVAASTGIDLLLLDDFKLVINDLTYHVRPPKRDLLSHENAATLNDVKTLVQQLYTTLCIGQHQLNK

Parental  ERELIERLEDLKEQLAPLEKVRIEISKKAEKRTTLVLWGGLAYMATQFGILARLTWWEYSWDIMEPVTYF
          ERELIERLEDLKEQLAPLEKV.IEISKKAEKRTTLVLWGGLAYMATQFGILARLTWWEYSWDIMEPVTYF
Retrocopy ERELIERLEDLKEQLAPLEKV*IEISKKAEKRTTLVLWGGLAYMATQFGILARLTWWEYSWDIMEPVTYF

Parental  ITYGSAMAMYAYFVMTRQEYVYPEARDRQYLLFFYKGAKKSRFDLEKYNQLKDAIAQAEMDLKRLR-DPL
          ITYGSA.AMYAYFVMTRQEYVYPEARDRQYLLFF.KGAKKSRFDL.KYNQLKDA.AQAEMDLKRLR.DPL
Retrocopy ITYGSATAMYAYFVMTRQEYVYPEARDRQYLLFFHKGAKKSRFDLQKYNQLKDAVAQAEMDLKRLR>DPL

Parental  QVHLPLRQIGEKD
          QVHLPLRQIGEKD
Retrocopy QVHLPLRQIGEKD

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_1624 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003454	1 retrocopy	retro_chof_1624 ,
Macropus eugenii	ENSMEUG00000001448	1 retrocopy	retro_meug_327,