RetrogeneDB ID: retro_chof_2474

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_78519:3094..4060(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTBP3
• Ensembl ID: ENSCHOG00000002039
• Aliases: None
• Description: polypyrimidine tract binding protein 3 [Source:HGNC Symbol;Acc:10253]

Sequence

>retro_chof_2474
GTGTTGAAATGAAAAGGCCAGGCTCTTTTAGAAATGGCTTTTGAGGAAGCTGCTGTTACTTTGGTGAATTATTACACTCC
TATTATTCCTCACCTTCAAAACTGGCCTGTTCATATTCAGTATTTCAATCAGAGAGCTCAAGACTGACAACCCAATTAAG
CTAGAACCCAAGCTGCACTACAGGCCATCAATGCTGTCCAGCCAGGATGTCTGGCCCTCACTGGAGCTCCTGCTAGTGAA
AGCAGTGTAGCTGGACAAAGCCCTGTGCTCTGAGTAATCATTAAAAAACTCTTTTATCCTGTTAATCTAAATCCTTCATC
AGATATTTTCTAAATATGGCTCCATCTTGAGGATCATTACCTTTATAGAGAATAATCAGTTTCAAGCCTTGTTTCAGTAT
GCTGACCTAATGAATGCACATTATGCCATAATGGGTGTGAATGGCCAGAATATCTATAATGCACACTGCACTCTGCTTAT
TGACTTCTCCAAGCTCACCAGTCTTAAATGTGAAATAAAATAATGACAAAAGTAGAGTTTTCACTTGCTTAGATCTTACT
GGTGGTAGCCAGCCATTCTCTGACCTCCAATGGCTGCTGCTTTCATGGCACCCATTATAATTTCCTCACCATGTCCAGGG
GCTTTTGGATTTGCCCCTGGCATTGGGTTTCCTCAAGCTACAGGCCTTTCAGTCCCAGGTGTTCCTGAAACTCTTGGTCT
ACTCACAGTTACCTCCTCTGCTGTCACTGGAAGGATGGCCATTCTTGGAACAATGGCATGCCAGGAAATCCTGTTCTCCT
GGTCACCAATTTCAATTCTGATCTTATCACACAACATGGCTTTTTATCCTGTATGGAGTGAGTGTATGGTGATATACATC
AAGTGAAGTTTATGTTTAACAAGGAAGTAAATGCTTTGGTTCAGATGGGAGATACAATTCAAGCTCAGCTAGCGATAAAT
CAAATA

Alignment

ORF - retro_chof_2474 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.98 %
• Parental protein coverage: 56.6 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MLKGKSQAFLEMASEEAAVTMVNYYTPVTPHLRSQPVYIQYSNHRELKTDNLPNQARTQAALQAISAVQS
          .LK.K.QA.LEMA.EEAAVT.VNYYTP..PHL...PV.IQY.N.R....D..PN.ARTQAALQAI.AVQ.
Retrocopy VLK*KGQALLEMAFEEAAVTLVNYYTPIIPHLQNWPVHIQYFNQRA--QD*QPN*ARTQAALQAINAVQP

Parental  GNLALTGTATNEGTVLPGQSPVLRIII-ENLFYPVTLEVLHQIFSKFGAVLKIITFTKNNQFQALLQYAD
          G.LALTG....E..V..GQSPVL..II..N.F.......LHQIFSK.G..L.IITF..NNQFQAL.QYAD
Retrocopy GCLALTGAPASESSVA-GQSPVL*VII>KNSFI-LLI*ILHQIFSKYGSILRIITFIENNQFQALFQYAD

Parental  PMNAHYAKMALDGQNIYNACCTLRIDFSKLTSL-NVKYNNDKSRDFTRLDLPTGDGQPSLE-PPMAAAFG
          .MNAHYA.M...GQNIYNA.CTL.IDFSKLTSL.NVK.NNDKSR.FT.LDL.TG..QP....PPMAAAF.
Retrocopy LMNAHYAIMGVNGQNIYNAHCTLLIDFSKLTSL>NVK*NNDKSRVFTCLDL-TGGSQPFSD<PPMAAAFM

Parental  APGIISSPYAGAAGFAPAIGFPQATGLSVPAVPGALGPLTITPSAVTGRMAIPGA-SGMPGNSVLLVTNL
          AP.IISSP..GA.GFAP.IGFPQATGLSVP.VP..LG.LT.T.SAVTGRMAI.G...GMPGN.VLLVTN.
Retrocopy APIIISSPCPGAFGFAPGIGFPQATGLSVPGVPETLGLLTVTSSAVTGRMAILGT<NGMPGNPVLLVTNF

Parental  NPDLITPHG-LFILFGVYGDVHRVKIMFNKKENALVQMADANQAQLAMNHL
          N.DLIT.HG.L.....VYGD.H.VK.MFNK..NALVQM.D..QAQLA.N..
Retrocopy NSDLITQHGFLSCME*VYGDIHQVKFMFNKEVNALVQMGDTIQAQLAINQI

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_2474 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002039	2 retrocopies	retro_chof_1487, retro_chof_2474 ,
Ciona savignyi	ENSCSAVG00000007421	1 retrocopy	retro_csav_17,
Loxodonta africana	ENSLAFG00000011358	1 retrocopy	retro_lafr_1050,