RetrogeneDB ID: retro_chof_1487

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_305733:542..1480(+)
• 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_1487
TCGTGGCGAGCCCGTCAGTCCCCGCATAGTGTGCTTCTTCATCTGGGCCATGGATGGCGGGGATCTGATGAGCTTCTTTC
TTCTGGCATCATTAACGGACCTTTTACCATGAACAATTCCACTCCTACCACAGGTGTGTATGCTAATGGGAATGACAACA
AGAAATTTAAAGGAGATAGAACTCCTTGTTCACCTTCCCGTGTTCTCCATCTTCGCCAAATTCCAAGTGATGTCACCGAA
GCAGAGGTCATATCATTAGGTCTACCATTCGGCAAAGTAACTAATCTTTTGATGTTGAAAGGAAAAAGCCAGGCTTTCTT
AGAAATGGCTTCTGAGGAAGCTGCTGTAACTATGGTGAATTATTACACTCCTGTTACTCCTCACCTACGAAGCCAGCCTG
TTTATATCCAGTATTCCAATCATAGAGAACTCAAGACTGACAATCTGCCTAATCAAGCTAGAACCCAAGCTGCATTGCAG
GCCATCAGTGCTGTCCAGTCAGGAAACGTGGCCCTTACTGGAAATGCTACCAATGAAGGCACAGTCCTGCCTGGGCAAAG
CCCTGTGCTCCGAATAATTATTGAAAACCTGTTTTACCCTGTTACTCTGGAAGTTCTTCATCAGATATTTTCTAAATTTG
GCGCAGTCTTGAAGATTATCACCTTTACAAAGAATAATCAGTTTCAAGCCTTGCTTCAGTATGCTGACCCAATGAATGCA
CATTATGCTAAAATGGCTCTGGATGGCCAAAATATCTATAATGCATGCTGCACTCTACGCATTGACTTCTTCAAGCTCAC
CAACCCTTAATTGTGAAAATATAATAATGACAAAAGCAGAGACTTCCCCTCGCTTTAGACCTTTCCTACTGGTGATGGCT
CAGCCCTTCCCTTTGAACCCCCTATTGGCTGCTGCTTTTTGGTGCACCGGGAATAATC

Alignment

ORF - retro_chof_1487 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.04 %
• Parental protein coverage: 53.65 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SRRARQSPHSALLHLGHGWRRSDELLSSGIINEPFTMNNSTPTTGVFANGNDNKKFKGDRTPCSPSRVLH
          S.RARQSPHS.LLHLGHGWR.SDELLSSGIIN.PFTMNNSTPTTGV.ANGNDNKKFKGDRTPCSPSRVLH
Retrocopy SWRARQSPHSVLLHLGHGWRGSDELLSSGIINGPFTMNNSTPTTGVYANGNDNKKFKGDRTPCSPSRVLH

Parental  LRQIPSDVTEAEVISLGLPFGKVTNLLMLKGKSQAFLEMASEEAAVTMVNYYTPVTPHLRSQPVYIQYSN
          LRQIPSDVTEAEVISLGLPFGKVTNLLMLKGKSQAFLEMASEEAAVTMVNYYTPVTPHLRSQPVYIQYSN
Retrocopy LRQIPSDVTEAEVISLGLPFGKVTNLLMLKGKSQAFLEMASEEAAVTMVNYYTPVTPHLRSQPVYIQYSN

Parental  HRELKTDNLPNQARTQAALQAISAVQSGNLALTGTATNEGTVLPGQSPVLRIIIENLFYPVTLEVLHQIF
          HRELKTDNLPNQARTQAALQAISAVQSGN.ALTG.ATNEGTVLPGQSPVLRIIIENLFYPVTLEVLHQIF
Retrocopy HRELKTDNLPNQARTQAALQAISAVQSGNVALTGNATNEGTVLPGQSPVLRIIIENLFYPVTLEVLHQIF

Parental  SKFGAVLKIITFTKNNQFQALLQYADPMNAHYAKMALDGQNIYNACCTLRIDFSKLTSLNV-KYNNDKSR
          SKFGAVLKIITFTKNNQFQALLQYADPMNAHYAKMALDGQNIYNACCTLRIDF.KLT.....KYNNDKSR
Retrocopy SKFGAVLKIITFTKNNQFQALLQYADPMNAHYAKMALDGQNIYNACCTLRIDFFKLTNP*L*KYNNDKSR

Parental  DFTRL-DLPTGDG-QP-SLEPPMAAA-FGAPGII
          DF..L...PTGDG.QP..L.P..AAA.FGAPGII
Retrocopy DFPSL*TFPTGDG>QPFPLNPLLAAA>FGAPGII

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_1487 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 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,