RetrogeneDB ID: retro_chof_263

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_5800:14352..15130(+)
• Located in intron of: ENSCHOG00000012810

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLCCI1
• Ensembl ID: ENSCHOG00000012559
• Aliases: None
• Description: glucocorticoid induced transcript 1 [Source:HGNC Symbol;Acc:18713]

Sequence

>retro_chof_263
CAAAATCATGTTTCACGTGTACCCTGCAATGTAGAAGGAATTAAGTCCTGAATTAGAAAAGGTATTCATTAAAGAAAATA
ACAGGAAGGAGGAAGTGACCAAGCCTTTGGACATACCAGATGGCCGAAGAGCTCCCCTCCGTGCTCACTACCAGAGCAGT
AGGCCTCGCAGCACTGACACTGACTCCCTCTGTCCAGGAGTGCAGCAGCAGCTGCAGCGGTAATTCACCCTGTGTCTCCC
CATTTTGTCCCCCGGAATCCCAGGATGGCAGCCCTTGCTCAACTGAAGATTTGCCCTATGATCATGATAAAGACAGTGGG
AGTAGCTCACCATTACCCAAGAATGCTTCATCTCCCAAACCAAACAACAGCTACATGTCAAACGGGAGCCCCCGGAGGGA
TGTGAGCAAGTGAAGGTCTTTCAGGAAATGGTGTCTGGTCAGCCTATCTCAGTCCTTCTCTTTTCATGTCCTGACAAAAA
CAAGGTTAATTTCATCCCAGCTGGTTCAGCTTTCTGTCCTGTAAAAGTTCTAGGCCCTCTCTTACCTGCCTCCGACCTGA
TGCTCAAGAACTCTCCTAACTCTGGCCAGACCTCAGCTCTGGCCACTCTGACTGTTGAACAGCTCTCACCCTGGGTTTCC
TTTGCATCTCCTTCCAATGACACCAGCACAGTGGGTCCCACAGAGGTCTCTACTCAACAGCCATCCCAGCAGCAGCAGCA
GCTTCTGCAGGAACTGCAGGCTGAAGAGCTCATCTCTGCTCAGAACTATGTGATCATC

Alignment

ORF - retro_chof_263 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.55 %
• Parental protein coverage: 65.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KSSVSRVSCNVEGI-SPELEKVFIKENNGKEEVTKPLDIPDGRRAPLPAHYRSSSTRSIDTQT-PSVQER
          ...VSRV.CNVEGI.SPELEKVFIKENN.KEEVTKPLDIPDGRRAPL.AHY.SS..RS.DT...P.....
Retrocopy QNHVSRVPCNVEGI>SPELEKVFIKENNRKEEVTKPLDIPDGRRAPLRAHYQSSRPRSTDTDS<PLSRSA

Parental  SSSCSSHSPCVSPFCP-PESQDGSPCSAEDLLYDRDKDSGSSSPLPKYASSPKPNNSYM-FKREPPEGCE
          ........P....F.P.PESQDGSPCS.EDL.YD.DKDSGSSSPLPK.ASSPKPNNSYM..KREPPEGCE
Retrocopy AAAAAVIHPVSPHFVP<PESQDGSPCSTEDLPYDHDKDSGSSSPLPKNASSPKPNNSYM<VKREPPEGCE

Parental  RVKVFEEMASRQPISAPLFSCPDKNKVNFIPTGSAFCPVKLLGPLLPASDLMLKNSPNSGQSSALSTLTV
          .VKVF.EM.S.QPIS..LFSCPDKNKVNFIP.GSAFCPVK.LGPLLPASDLMLKNSPNSGQ.SAL.TLTV
Retrocopy QVKVFQEMVSGQPISVLLFSCPDKNKVNFIPAGSAFCPVKVLGPLLPASDLMLKNSPNSGQTSALATLTV

Parental  EQLSSRVSFASLSNDTSTVGPTESSTQQPSQQQQQLLQELQAEEHISAQNYVII
          EQLS..VSFAS.SNDTSTVGPTE.STQQPSQQQQQLLQELQAEE.ISAQNYVII
Retrocopy EQLSPWVSFASPSNDTSTVGPTEVSTQQPSQQQQQLLQELQAEELISAQNYVII

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_263 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012559	1 retrocopy	retro_chof_263 ,
Mus musculus	ENSMUSG00000029638	1 retrocopy	retro_mmus_1583,