RetrogeneDB ID: retro_chof_2144

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_53137:6026..6918(-)
• 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_2144
AAGTTGAAGCATTATGCATGGAAGAGGCGATGGTTTTTGTTATGCAGTGACCGTTTAACTGGAGATCCAGATGTCTTGGA
ATATTACAAAAATGATCATGACAAGAAGCCTATTCGCATTGTTGATTTAAATTTATGTCAGCAAGTCGATGCAGAATTGA
CATTTAACAAAAAAGAGTTTGAAAACAGCTACATTTTTGACACCAACACTGTTGACCAGTTTTTCTGCTTGGTAGCCGAC
AGTGAAGAGGAGATAAGTGGATTCCTTGTATTTGTGACATCTGTGCGTTTAATCCTACAGAAGAAGATGCTGTGAAGCCA
CCTGGCAACTCCTTACAAGCACCAGCTGATTTATCTTCAGCTGTAAATACAGTCTTGTCGTCCACCCGGGTGGATTCTTC
CACGGCTACTTTACCTTCTGCATATCAGCTAATTAACCTCCCACCACACCTGGAAACTGGTAGCATCCATGAGGATCCTC
AAGACTGATCCTCTTACTAATCAACTCTCAAAGCAAGAAGACTGAACCCACAAGAACACATGCTGATCCTGCAAAATCCA
CCTCCTCTGAAATAGCTACAACCATAATGTCCCTTCTTATAAAAATCCTGCTTCCTTCCTGAACAAACAAGGAGTGAATG
GCTTTTTTTTTCAGCAGCAAATGATGTGTGACTGTCCACTATCACGTACTGCATCGATTTCTGTAGACTCCAGCCTTTAT
AATCTGCCCAGGAGTTATTCCCATGATATCTTACCAAAGGTATCTCCATTGAATACCGAAGCAGATGGAGAACTCTTATG
TTTTTAATACCCCATCAGGGACATCAAATGTAGAGACTCAAATAAGGCATGTGTCTATTAGTTATGACATTCCCCTAATA
CCTGGTAATACC

Alignment

ORF - retro_chof_2144 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.22 %
• Parental protein coverage: 51.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KLKHYAWKKRWFVLRSDL---DPDV-EYTKNDHAKKPR--IDLNLCQQVDAGLTFNKKEFENSYIFDINT
          KLKHYAWK.RWF.L.SD....DPDV.EY.KNDH.KKP....DLNLCQQVDA.LTFNKKEFENSYIFD.NT
Retrocopy KLKHYAWKRRWFLLCSDRLTGDPDVLEYYKNDHDKKPIRIVDLNLCQQVDAELTFNKKEFENSYIFDTNT

Parental  IDRIFYLVADSEEEM-NKWVRCICDICGFNPTEEDAVKPPGNSLQAPADLPLAINTAPLSTQVDSSSATL
          .D..F.LVADS.EE...KW..CICDIC.FNPTEEDAVKPPGNSLQAPADL..A.NT...ST.VDSS.ATL
Retrocopy VDQFFCLVADS-EEE<DKWIPCICDICAFNPTEEDAVKPPGNSLQAPADLSSAVNTVLSSTRVDSSTATL

Parental  PPPYQLINLPPHLETLGIQEDPQD-YLLL-INCQSKKPEPTRTHADPAKSTSSE-TDCNDNVPSHKNPAS
          P..YQLINLPPHLET..I.EDPQD...LL.IN.QSKK.EPTRTHADPAKSTSSE....N.NVPS.KNPAS
Retrocopy PSAYQLINLPPHLETGSIHEDPQD<LILLLINSQSKKTEPTRTHADPAKSTSSE<NSYNHNVPSYKNPAS

Parental  SLNKQGVNG-FFQQQMMYDSPLSRAASISVDSSLYNLPRSYSHDVLPKVSPSSTEADGEL-YVFNTPSGT
          .LNKQGVNG...QQQMM.D.PLSR.ASISVDSSLYNLPRSYSHD.LPKVSP..TEADGEL.YVFNTPSGT
Retrocopy FLNKQGVNGXXXQQQMMCDCPLSRTASISVDSSLYNLPRSYSHDILPKVSPLNTEADGEL>YVFNTPSGT

Parental  SSVETQMRHVSISYDIPPIPGNT
          S.VETQ.RHVSISYDIP.IPGNT
Retrocopy SNVETQIRHVSISYDIPLIPGNT

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_2144 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,