RetrogeneDB ID: retro_chof_2078

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_47786:6576..7306(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMAA
• Ensembl ID: ENSCHOG00000003897
• Aliases: None
• Description: methylmalonic aciduria (cobalamin deficiency) cblA type [Source:HGNC Symbol;Acc:18871]

Sequence

>retro_chof_2078
ATTTCCATGCTTCTGCAATACCCTCACCAACATTTCCTAAAAGGCCTTTTAAGAACACCTTTCTGACATTACCACTTCAT
CTTTCTCTCAAGTACTCATCTTGGATCGAGAATCCCATCTGCTCAGCCATTTAATTATCTTGGACTCCATTGTACAAAGT
GGATGCTGCTGTCAATAGGTTTAAAGAGAAAATTATGTGTACAGACAACCTTAAAAGAACACACAGAAGGACTTTCTGAC
AAAGAACAGATTTGTGGATAAACTTTACTCTGGTTTAATCCAAGGACAAAGGGCCTGCTTAGCAGAGTCCATAACTCTTA
TAGAGTCAACTCATGACAGGAAAAAAGAGTTAGCCCAGGTGATTCCTCAGAAAGTATTAGTCTTCTACAGGGAACAAGAA
CAATTAAACAAAGGAAAACCACTAGCATTTCAAGTGGGATTGCCTGGCCCTCCTGGTGATGGAAAATAGATATTTATAGA
ATATTTTGGAAAAATGCTTACTGAGAGAGGGCACAAAGTATCTGTGCTAGCTGTGGACCCTTCTTCTTGCACCAGTGGTG
GCTCACTCTTAGGTGATAAAACCCGAATGACTGCATTATCAAGAGATATGAATGCAAACATCAGGCCATCTCCTACTAGA
GGGACTTTAGGAGGTATGACAAGGACCACAAATGAAGCTATTCTGTTGTGTGAAGGAGGGGGGTATGACATCATTCTTAT
TGAAACTGTA

Alignment

ORF - retro_chof_2078 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.52 %
• Parental protein coverage: 58.51 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ISMLLQCAHQHFLKGLLRTTLRHYHFIFHSSTHHGSGIPSAQPFNSLGLHCTKWMLLSVGL-KRKLCVQT
          ISMLLQ..HQHFLKGLLRT...HYHFIF.SSTH.GS.IPSAQPFN.LGLHCTKWMLLS.GL.K.K.....
Retrocopy ISMLLQYPHQHFLKGLLRTPF*HYHFIFLSSTHLGSRIPSAQPFNYLGLHCTKWMLLSIGL<KEKIMCTD

Parental  TLK-EHTEGLSDKEQRFVDKLYSGLIQGQRACLAESITLIESTHDRKKELAQVLLQKVLVYHREREQLNK
          .LK...T........RFVDKLYSGLIQGQRACLAESITLIESTHDRKKELAQV..QKVLV..RE.EQLNK
Retrocopy NLK<KNTQKDFLTKNRFVDKLYSGLIQGQRACLAESITLIESTHDRKKELAQVIPQKVLVFYREQEQLNK

Parental  GKPLAFRVGLSGPPGAGKSTFIEYFGKMLTERGHKVSVLAVDPSSCTSGGSLLGDKTRMTELSRDMNAYI
          GKPLAF.VGL.GPPG.GK..FIEYFGKMLTERGHKVSVLAVDPSSCTSGGSLLGDKTRMT.LSRDMNA.I
Retrocopy GKPLAFQVGLPGPPGDGK*IFIEYFGKMLTERGHKVSVLAVDPSSCTSGGSLLGDKTRMTALSRDMNANI

Parental  TPSPTRGTLGGVTRTTNEAILLCEGGGYDIILIETV
          .PSPTRGTLGG.TRTTNEAILLCEGGGYDIILIETV
Retrocopy RPSPTRGTLGGMTRTTNEAILLCEGGGYDIILIETV

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_2078 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003897	1 retrocopy	retro_chof_2078 ,