RetrogeneDB ID: retro_chof_1896

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_417746:1..910(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NET1
• Ensembl ID: ENSCHOG00000010007
• Aliases: None
• Description: neuroepithelial cell transforming 1 [Source:HGNC Symbol;Acc:14592]

Sequence

>retro_chof_1896
AGAAATAGTGTACTATGGTCAGAGATGTTAGATGTCAATATGAAGGAGTCTTTAACAACCAGAGAAATCAAAAGTTAGAA
GGCAATATATGAAATGTCCCGAGGTGAAAAGGATTTAATTAAGGATCTCAAGCTTGCAAGAAAGGCCTACCATGACCCCA
TGTTAAAGTTGTCTATTATGACAGAAGAAGAGCTCACACATATATTTGGTGATTTGGATGCTTACATACCTTTACATGAA
GATTTGTTGGCAAGAATAGGAGAAGCAACCAAGCCTGATGGAACAGTAGAGCAGATTGGTCATATTCTTGTGAACTGGTT
GCCAGGCTTGAATGCCTACAGAGGCTATTGTAGTAACCAGTTGGCAGCCAAAGCTCTTCTTGATCAAAAGAAACAAGATC
CAACAGTCCAAGACTTCCTCCAGCGATGTCTTGAGTCTCCTTTCAGTCGAAAACTAGATCTTTGGAGCTTCCTAGATATT
CCTCGAAGTCACCTAGTCAAGTACCCTTTACTGTTAAAAGAAATTCTTAGACACACTCCAAAAGACCACCCTGATGTTCA
GCTTCTGGAGGAAGCTGTATTGATAATACAAGGAGTTCTCTCTGATATAAACTTGAAGAAAGGTGAATCAGAATGCCAGT
ATTACATTGACAAACTGGAGTATCTGGATGAAAAGCAGAAGGATCCTAGAATTGAAGCAAGCAAAGTATTACTTTGCCAT
GGGGAATTGAAGAATAAGAGCGGACATAAACTTTACATTTTCCTGTTTCAAGACATCTTGGTTTTGACTCGGCCTGTTAC
ACAGAATGAGCGTCACTCTTACCAAGTTTACCGGCAGCCAATCCCAGTCCAAGAGCTGGTCTTAGAAGACCTGCAGGATG
GAGATGTGAGAATGGGAGGATCCTTTCGA

Alignment

ORF - retro_chof_1896 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.03 %
• Parental protein coverage: 60.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RNSVLWSEMLDVNMKESLTTREIKRQEAIYEMSRGEKDLIEDLKLARKAYHDPMLKLSIMSEEELTHIFG
          RNSVLWSEMLDVNMKESLTTREIK...AIYEMSRGEKDLI.DLKLARKAYHDPMLKLSIM.EEELTHIFG
Retrocopy RNSVLWSEMLDVNMKESLTTREIKS*KAIYEMSRGEKDLIKDLKLARKAYHDPMLKLSIMTEEELTHIFG

Parental  DLDAYIPLHEDLLARIGEATKPDGTVEQIGHILVNWLPGLNAYRGYCSNQLAAKALLDQKKQDPRVQDFL
          DLDAYIPLHEDLLARIGEATKPDGTVEQIGHILVNWLPGLNAYRGYCSNQLAAKALLDQKKQDP.VQDFL
Retrocopy DLDAYIPLHEDLLARIGEATKPDGTVEQIGHILVNWLPGLNAYRGYCSNQLAAKALLDQKKQDPTVQDFL

Parental  QRCLES-FSRKLDLWSFLDIPRSRLVKYPLLLKEILRHTPKDHPDVQLLEEAVLIIQGVLSDINLKKGES
          QRCLES.FSRKLDLWSFLDIPRS.LVKYPLLLKEILRHTPKDHPDVQLLEEAVLIIQGVLSDINLKKGES
Retrocopy QRCLESPFSRKLDLWSFLDIPRSHLVKYPLLLKEILRHTPKDHPDVQLLEEAVLIIQGVLSDINLKKGES

Parental  ECQYYIDKLEYLDEKQKDPRIEASKVLLCHGELKNKSGHKLYIFLFQDILVLTRPVTRNERHSYQVYRQP
          ECQYYIDKLEYLDEKQKDPRIEASKVLLCHGELKNKSGHKLYIFLFQDILVLTRPVT.NERHSYQVYRQP
Retrocopy ECQYYIDKLEYLDEKQKDPRIEASKVLLCHGELKNKSGHKLYIFLFQDILVLTRPVTQNERHSYQVYRQP

Parental  IPVQELVLEDLQDGDVRMGGSFR
          IPVQELVLEDLQDGDVRMGGSFR
Retrocopy IPVQELVLEDLQDGDVRMGGSFR

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_1896 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	ENSCHOG00000010007	1 retrocopy	retro_chof_1896 ,
Monodelphis domestica	ENSMODG00000018500	2 retrocopies	retro_mdom_21, retro_mdom_239,
Mus musculus	ENSMUSG00000021215	1 retrocopy	retro_mmus_1144,