RetrogeneDB ID: retro_chof_2583

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_87632:8104..8707(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LHX9
• Ensembl ID: ENSCHOG00000000991
• Aliases: None
• Description: LIM homeobox 9 [Source:HGNC Symbol;Acc:14222]

Sequence

>retro_chof_2583
CCTGCCGGTTCCACCACGATGCTGTTCCACAGTCTGTCGGTCCCCGAGGTGCACAGGATCATCAACGAGATGGACTGCAG
GGCCAAGAGTGAGGCTCCCGCCATCAGTTCCGCCATTGACCATGGTGACGTGGAGATGACCGTGCCTTCCATCAGCAGTG
ACTGTGCTGCACTGTGTGCTGGCTGCATGGGCAAGATTTCGGACCACTACTACCTGCTGGCAGTGGATAAACAGTGGCAC
ATGCACTGCCTCAAGTGCTGCGAGTGCAAGTTCAATCTAGAGTCAGAGCTCACCTGTTTTAGCAAGGACAGCAGCATCTA
CTGCAAGGAAGACTACTACAGGTAGTTCTCTGTGCAGCATTGCGCCCGCTGCCATCTGGGCATCTCGGCCTCAGAGATGG
TGATGTGCACCCAGAACTTGGTTTATCACCTCAACTGCTTCACTTGCACCACGTGTAACAAAATGCTGACCACCGGCAAC
CACTTTGGTATGAAGGACAGCCTGGTCTACTGCCGCTTGCACTTCGAGGCACTGCTGCAAGGTGAGTATCCCACTCATTT
TAACCATGCTGACGTGGCAGCCACAGCCAAGAGCGTGGGGCTG

Alignment

ORF - retro_chof_2583 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.69 %
• Parental protein coverage: 50.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PFRPPAMLFHGISGGHIQGIMEEMERRSKTEARLAKGSQLNGR-DAGMPPLSPEKPALCAGCGGKISDRY
          P.....MLFH..S......I..EM..R.K.EA.........G......P..S....ALCAGC.GKISD.Y
Retrocopy PAGSTTMLFHSLSVPEVHRIINEMDCRAKSEAPAISSAIDHGDVEMTVPSISSDCAALCAGCMGKISDHY

Parental  YLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDYYRRFSVQRCARCHLGISASEMVMRARDS
          YLLAVDKQWH..CLKCCECK..LESELTCF.KD.SIYCKEDYYR.FSVQ.CARCHLGISASEMVM.....
Retrocopy YLLAVDKQWHMHCLKCCECKFNLESELTCFSKDSSIYCKEDYYR*FSVQHCARCHLGISASEMVMCTQNL

Parental  VYHLSCFTCSTCNKTLTTGDHFGMKDSLVYCRAHFETLLQGEYPPQLSYTELAAKSGGLAL
          VYHL.CFTC.TCNK.LTTG.HFGMKDSLVYCR.HFE.LLQGEYP........AA......L
Retrocopy VYHLNCFTCTTCNKMLTTGNHFGMKDSLVYCRLHFEALLQGEYPTHFNHADVAATAKSVGL

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_2583 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	ENSCHOG00000000991	1 retrocopy	retro_chof_2583 ,