RetrogeneDB ID: retro_chof_797

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_149334:2220..2840(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000007073
• Aliases: None
• Description: None

Sequence

>retro_chof_797
GTGGAGGATGGCTGGGGAAGCGAAAACAAAACCACAGTGGGCTTGGCCAGCTTTTTTGGAGCCAGCGGAGCAGTTTACTT
GCACACTGACATGCCAGTGTCCCCCTAACTGGTATGAACCCTCTGTCTCCTTATTTATATGTGGATCCTTGTTATGTCAT
GCAGGATACAGATGAGTTTATTTTACCTACCAGAGCTAATAAAGCCCAGGGCAGATTTGAACTTACCTTTTTTTCCTTTG
GAGGGTGTTGCATGACAGGGGCTGCATTTGGGGCAATGAACGGTCTATGACTAGGATTGAAGGAAACCCAAACCATGACC
TGGTCTAAACCAAAAAATGTACAGATTTTGAATACAGTGACCAGGCAAGGGGCACTTTGAGCTAATACTCTAGGTTCTCT
GGCTTTGCTCTACAGTGCATTTGGCGTCGTTATCAAGCAAACACGAGGTGCAGAAGATGATCTCAACACAGTAGCAGCTG
GAACCATGACAGGTATTCACAGGTGTTCTTTGGGGAGGGAGGTAGCATGAGATGGTTTAGCAGGACTAACCCTTACCACC
CTCTATGCACTATATAATAACTGGGAGTACTTGAGAGGGTCCCTGCTCCGACTGTCACTG

Alignment

ORF - retro_chof_797 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.05 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEGGGGSGNKTTGGLAGFFGAGGAGYSHADL-AGVPXXXXXXXXXXXXXXXXXXXXDTDEFILPTGANKT
          .E.G.GS.NKTT.GLA.FFGA.GA.Y.H.D..A.VP....................DTDEFILPT.ANK.
Retrocopy VEDGWGSENKTTVGLASFFGASGAVYLHTDM<ASVPLTGMNPLSPYLYVDPCYVMQDTDEFILPTRANKA

Parental  RGRFELAFFTIGGCCMTGAAFGAINGLRLGLKETQTMAWSKPRNVQILNMVTRQGALWANTLGSLALLYS
          .GRFEL.FF..GGCCMTGAAFGA.NGL.LGLKETQTM.WSKP.NVQILN.VTRQGAL.ANTLGSLALLYS
Retrocopy QGRFELTFFSFGGCCMTGAAFGAMNGL*LGLKETQTMTWSKPKNVQILNTVTRQGAL*ANTLGSLALLYS

Parental  AFGVIIEKTRGAEDDLNTIAAGTMTGMLYKCTGGLRGVARGGLAGLTLTSLYALYNNWEHMKGSLLQQSL
          AFGV.I..TRGAEDDLNT.AAGTMTG....C..G.R.VA..GLAGLTLT.LYALYNNWE...GSLL..SL
Retrocopy AFGVVIKQTRGAEDDLNTVAAGTMTG-IHRCSLG-REVA*DGLAGLTLTTLYALYNNWEYLRGSLLRLSL

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_797 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 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007501	1 retrocopy	retro_amel_1488,
Canis familiaris	ENSCAFG00000029477	1 retrocopy	retro_cfam_329,
Choloepus hoffmanni	ENSCHOG00000007073	1 retrocopy	retro_chof_797 ,
Callithrix jacchus	ENSCJAG00000013336	1 retrocopy	retro_cjac_2965,
Cavia porcellus	ENSCPOG00000019917	2 retrocopies	retro_cpor_1013, retro_cpor_321,
Monodelphis domestica	ENSMODG00000002661	2 retrocopies	retro_mdom_1202, retro_mdom_860,
Mus musculus	ENSMUSG00000013701	1 retrocopy	retro_mmus_2,
Oryctolagus cuniculus	ENSOCUG00000000525	1 retrocopy	retro_ocun_73,
Otolemur garnettii	ENSOGAG00000015393	1 retrocopy	retro_ogar_2627,
Ochotona princeps	ENSOPRG00000005255	2 retrocopies	retro_opri_520, retro_opri_920,
Procavia capensis	ENSPCAG00000015914	1 retrocopy	retro_pcap_181,
Rattus norvegicus	ENSRNOG00000019811	3 retrocopies	retro_rnor_1804, retro_rnor_225, retro_rnor_661,
Sorex araneus	ENSSARG00000010335	1 retrocopy	retro_sara_86,
Sus scrofa	ENSSSCG00000025276	1 retrocopy	retro_sscr_404,
Ictidomys tridecemlineatus	ENSSTOG00000007041	1 retrocopy	retro_itri_1043,