RetrogeneDB ID: retro_chof_1080

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_19529:9069..10014(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GAB1
• Ensembl ID: ENSCHOG00000004704
• Aliases: None
• Description: GRB2-associated binding protein 1 [Source:HGNC Symbol;Acc:4066]

Sequence

>retro_chof_1080
ATGAGCGGCGGCGAGGTGGTATGCTCGGGATGGCCCCGCAAATCCCCCCCGGAGAAAAAGTTGAAGCGTTATGCATGGAA
GAAGAGATGGTTTGTGTTACACAGTGGCCATTTAACTGGAGATCCAGATGTCTTGGAATATTACAAAAATGATTATTCCA
AGAAGCCTATTCGTATTATTGATTTAAATTTATGTCAGCAAGTTGATGCTGGATTGACATTTAACAAAAAAGAGTTTGAA
AACAGCTACATTTTTTGTATCAACACTATTGACCGGATTTTCTACTTGGTAGCAAACAGTGAAGAGGAGATGAATAAGTA
CGTTCTTGTATTTGTGATATCTGTGGGTTTAATCCTACAGAAGATGCTGTGAAGCCACTGGACAACTCCTTACAAGCAGC
AGCTGATTTATCTTTATCTGTAAATACAGTCCCGTCGTCCACCCGGGTGGATTCTTCTTCAGCTACTCTACTTCCTCCAT
ATCAGCTAATTAACCTTCCACCACACCTGGAAACTCTTGGCATCCAGGAGCATCCTCAAGACTACCTCTCGCTAATCAAC
TTTCAAAGCAAGAAGCCTGAACCCAGGAGAACACATGCTGACTTTGAAAAATCCATCTCCTTTGCAACAGACTGCAATGA
TAACGTCCCTTCTTATAAAAATCCTGCTTCTTCCCTGAACAAACAAGGAGTGAATGGCTTTTTTTCAGCAGCAAATAATG
TATGACTCTCCACCATCACATACTGCATTGCTTTCTGCAGACTCCAGCCTTTATAATCTGCCCAGGAGTTATTCCTGTGA
TATTTTACCAAAGGTATCTCCATTGAATGCCGAAGCAGATGGAGAATTCTATGTTTTTAATACCCCATCAGGGACATCAA
ATGCAGAGTCTCAAATGAGGCATGTGTCTATTAGTTATGACATTCCTCCAATACCTGGTAATTCC

Alignment

ORF - retro_chof_1080 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.42 %
• Parental protein coverage: 54.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNRGEVVCSGWFRKS-PPEKKLKHYAWKKRWFVLRSDL--DPDV-EYTKNDHAKKPR--IDLNLCQQVDA
          M..GEVVCSGW.RKS.P..K.......K.........L..DPDV.EY.KND..KKP...IDLNLCQQVDA
Retrocopy MSGGEVVCSGWPRKSPPEKKLKRYAWKKRWFVLHSGHLTGDPDVLEYYKNDYSKKPIRIIDLNLCQQVDA

Parental  GLTFNKKEFENSYIFDINTIDRIFYLVADSEEEMNKWV-RCICDICGFNPTEEDAVKPPGNSLQAPADLP
          GLTFNKKEFENSYIF.INTIDRIFYLVA.SEEEMNK.V..CICDICGFNPTE.DAVKP..NSLQA.ADL.
Retrocopy GLTFNKKEFENSYIFCINTIDRIFYLVANSEEEMNKYV<SCICDICGFNPTE-DAVKPLDNSLQAAADLS

Parental  LAINTAPLSTQVDSSSATLPPPYQLINLPPHLETLGIQEDPQDYLLLINCQSKKPEPTRTHADPAKSTSS
          L..NT.P.ST.VDSSSATL.PPYQLINLPPHLETLGIQE.PQDYL.LIN.QSKKPEP.RTHAD..KS.S.
Retrocopy LSVNTVPSSTRVDSSSATLLPPYQLINLPPHLETLGIQEHPQDYLSLINFQSKKPEPRRTHADFEKSISF

Parental  ETDCNDNVPSHKNPASSLNKQGVNG-FFQQQMMYDSPLSRAASISVDSSLYNLPRSYSHDVLPKVSPSST
          .TDCNDNVPS.KNPASSLNKQGVNG.FFQQQ.MYDSP.S..A..S.DSSLYNLPRSYS.D.LPKVSP...
Retrocopy ATDCNDNVPSYKNPASSLNKQGVNG>FFQQQIMYDSPPSHTALLSADSSLYNLPRSYSCDILPKVSPLNA

Parental  EADGELYVFNTPSGTSSVETQMRHVSISYDIPPIPGNT
          EADGE.YVFNTPSGTS..E.QMRHVSISYDIPPIPGN.
Retrocopy EADGEFYVFNTPSGTSNAESQMRHVSISYDIPPIPGNS

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_1080 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004704	2 retrocopies	retro_chof_1080 , retro_chof_2144,
Ochotona princeps	ENSOPRG00000015330	1 retrocopy	retro_opri_1086,