RetrogeneDB ID: retro_chof_1201

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_224062:518..1037(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL15
• Ensembl ID: ENSCHOG00000001114
• Aliases: None
• Description: ribosomal protein L15 [Source:HGNC Symbol;Acc:10306]

Sequence

>retro_chof_1201
ATGGGTGCTTACAAGTACATACAGCAGTTATGGAGGAAGAAGCAGTCCGATGTGATGCGCTTTCTTCTGAGGGTCCGCTG
CTGGCAATACCGCCAGCTCTCTGCACTCCACAGGGCCCCGCGTCCCACCCGGCCAGATGAAGTGCGCGGGCTGGGATACA
AGGCCAAGCAAGGTTATGTCATCTGTAGGATTCGAGTATGCTGTGGTGGCCACAAATGCCCGGTTCCTAAGGTTGCAACC
TATGGCAAGCCTGTCCATCCTAGTGTTAACCAGCTGAAATTTGCTCGAAGCCTTCAGTCTGTTGCTGAGGAGTGAGCTGG
ACGCCACTGTGGGGTGCTGAGAATCTTGAATTCTTACTGAGTTGATGAAGATTCCACATGCAAATTCTTTGAGGTTATCC
TCATTGATCCATTCCATAAAGCTATCAGAAGAAATCCTGACAGCCAGTGGATCACCAAGCCCTTCCATAAGCACAGGGAG
ATGCGTGGGCTGACTTCTGCAGGCCGCAAGAGCCGTGGC

Alignment

ORF - retro_chof_1201 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGAYKYIQELWRKKQSDVMRFLLRVRCWQYRQLSALHRAPRPTRPDKARRLGYKAKQGYVIYRIRVRRGG
          MGAYKYIQ.LWRKKQSDVMRFLLRVRCWQYRQLSALHRAPRPTRPD..R.LGYKAKQGYVI.RIRV..GG
Retrocopy MGAYKYIQQLWRKKQSDVMRFLLRVRCWQYRQLSALHRAPRPTRPDEVRGLGYKAKQGYVICRIRVCCGG

Parental  RKRPVPKGATYGKPVHHGVNQLKFARSLQSVAEERAGRHCGALRVLNSYWVGEDSTYKFFEVILIDPFHK
          .K.PVPK.ATYGKPVH..VNQLKFARSLQSVAEE.AGRHCG.LR.LNSY.V.EDST.KFFEVILIDPFHK
Retrocopy HKCPVPKVATYGKPVHPSVNQLKFARSLQSVAEE*AGRHCGVLRILNSY*VDEDSTCKFFEVILIDPFHK

Parental  AIRRNPDTQWITKPVHKHREMRGLTSAGRKSRG
          AIRRNPD.QWITKP.HKHREMRGLTSAGRKSRG
Retrocopy AIRRNPDSQWITKPFHKHREMRGLTSAGRKSRG

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_1201 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 4 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001114	6 retrocopies	retro_chof_1201 , retro_chof_1253, retro_chof_1323, retro_chof_2246, retro_chof_357, retro_chof_877,
Equus caballus	ENSECAG00000010157	1 retrocopy	retro_ecab_38,
Procavia capensis	ENSPCAG00000011995	1 retrocopy	retro_pcap_265,
Tursiops truncatus	ENSTTRG00000007244	5 retrocopies	retro_ttru_1305, retro_ttru_1358, retro_ttru_280, retro_ttru_920, retro_ttru_987,