RetrogeneDB ID: retro_chof_2472

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_78481:2745..3783(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000008890
• Aliases: None
• Description: None

Sequence

>retro_chof_2472
GTGAACACTCCAACAAAAACCTATGGAATGGGAAAAGGCCGGGCAGCAGATCTGAAGTACATTGAAGCTTGTGCTAGACA
CATTGTACAAAACTCACATGGGTACAAAATTGTGACTGAGAAAAGCATAGATCCTGTGCGGGCAGCAGAAAGTATCCATC
GCATATTTGACACAAACACAAAACCCAACTTGAACTTGTAAGTGCTGTCCAACCCCGAGTTCTTGGCAGAGGGAACAGCC
ATCAAGGACCTAAAGAACAGGACAGAGTACTGATTGGGGGAGATGAAACACCAGAGGGCCAGAGAGCTGTGCAGGCACTA
TGTGAGGTGTATGAGCACTGGGTTCCCAGAGAAAAGATCCTCACCACTAATAACTTGGTCTTCAGAACTTTCCAAACTGG
CAGCAAATGCTTTTCTTGCCCAAAGAATCAGCAGCATTAACTCTATAAGTGCACTACGTGAAGCAAAAGGAGCTGATGTA
GAAGAGGTAGCAACAGCCACTGGAATGGACCAGAGAATTGGAAATAAGTTTCTGAAAGCCAGTGTTGGTTTTGGTGGGAG
CTGCTTTCAAAAAGATGTTCTGAATTTAGTTTATCTCTGTGAGGCTCTGAATTTGCCTGAAGTAGCTGGTTATTGGCAGC
AGGTCATAGACATGAATGACTATCAGAGAAGGAGGTTTGCTTCCCAGATTATAGACAGTCTGTTTAATACAGTCACTGAT
GATAAGACAGCTATTTTGGGGTTTGCATTCAAAAAGGACACTGGTGATACGAGAGAATCTTCAAGTATATGTATCAGCAA
ATATTTGATGGATGACGGTGAACACCTCCATGTATATGATCCAAAAGTACCAAGGTAAAAAATCGTTGTGAATCTTTTTC
AACCAGGTGTTTCAGAGTATGACCAAGTGTCTCGACTTGTGACCATTTCCATGGATCCATATGAAGCATGTGACGGTGCC
CATGCAGTGGTTATTTGCACTGAGTGTGACATGTTTAAGGAATTGGATTATGAATGCATTCATAAAAAAATGCTGAAA

Alignment

ORF - retro_chof_2472 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.8 %
• Parental protein coverage: 69.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VNTPTKTYGMGKGRAADLKYIEACARRIVQNSHGYKIVTEKSTVPVRAAESIRRIFDANTKPNLNLQVLS
          VNTPTKTYGMGKGRAADLKYIEACAR.IVQNSHGYKIVTEKS..PVRAAESI.RIFD.NTKPNLNL.VLS
Retrocopy VNTPTKTYGMGKGRAADLKYIEACARHIVQNSHGYKIVTEKSIDPVRAAESIHRIFDTNTKPNLNL*VLS

Parental  NPEFLAEGTAIKDLKN-PDRVLIGGDETPEGQRAVQALCAVYEHWVPREKILTTN-TWSSELSKLAANAF
          NPEFLAEGTAIKDLKN..DRVLIGGDETPEGQRAVQALC.VYEHWVPREKILTTN.TWSSELSKLAANAF
Retrocopy NPEFLAEGTAIKDLKN<QDRVLIGGDETPEGQRAVQALCEVYEHWVPREKILTTN>TWSSELSKLAANAF

Parental  LAQRISSINSISALCEATGADVEEVATAIGMDQRIGNKFLKASVGFGGSCFQK-VLNLVYLCEALNLPEV
          LAQRISSINSISAL.EA.GADVEEVATA.GMDQRIGNKFLKASVGFGGSCFQK.VLNLVYLCEALNLPEV
Retrocopy LAQRISSINSISALREAKGADVEEVATATGMDQRIGNKFLKASVGFGGSCFQKDVLNLVYLCEALNLPEV

Parental  ARYWQQVIDMNDYQRRRFASRIIDSLFNTVTDKKIAILGFAFKKDTGDT-ESSSIYISKYLMDEGAHLHV
          A.YWQQVIDMNDYQRRRFAS.IIDSLFNTVTD.K.AILGFAFKKDTGDT.ESSSI.ISKYLMD.G.HLHV
Retrocopy AGYWQQVIDMNDYQRRRFASQIIDSLFNTVTDDKTAILGFAFKKDTGDTRESSSICISKYLMDDGEHLHV

Parental  YDPKVPREQIVVDLSQPGVSEDDQVSRRVTISKDPYEACDGAHAAVICTEWDMFKELDYERIHKKMLK
          YDPKVPR..IVV.L.QPGVSE.DQVSR.VTIS.DPYEACDGAHA.VICTE.DMFKELDYE.IHKKMLK
Retrocopy YDPKVPR*KIVVNLFQPGVSEYDQVSRLVTISMDPYEACDGAHAVVICTECDMFKELDYECIHKKMLK

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_2472 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008890	1 retrocopy	retro_chof_2472 ,
Monodelphis domestica	ENSMODG00000020549	1 retrocopy	retro_mdom_118,
Otolemur garnettii	ENSOGAG00000004941	1 retrocopy	retro_ogar_1145,