RetrogeneDB ID: retro_chof_1603

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_336511:291..963(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GOLPH3L
• Ensembl ID: ENSCHOG00000013505
• Aliases: None
• Description: golgi phosphoprotein 3-like [Source:HGNC Symbol;Acc:24882]

Sequence

>retro_chof_1603
GGTTACACATCTTTCAGGAATGACTGCATATCATCTGGCCTGTGAGGAGGCATCTTGATAGAGCTGGCCATGAGGGGTGG
AATCTATTTGGAACCTTCCACCATGCATAAGAAGAGACTACCAGATAGAAAGGTACTGCTAAAGTCAGACAGCCCAAAGG
GTGATGTCTTACTGGATGAAACACTCAAGCACATCAAAGCAAAAGAACCCACAGAAACTGTCCAAACGTGGAAAGAGCTC
CTCACTGGTGAGACCTGGAACCCCTTCAATTACAGTACCAGTTGAGGAATGTATGAGAACAAATTGCAAAGAACCTCATA
GAGAAGGGTATTCTAACCACTGGAGAAGCAAAATTTCCTGCTATTTGACATGACTACTCATCCAGTGACCAGTACTACAG
AGAAGCAGCGACTAGTGAAAAAACTTCAAGGTAGTGTACTATAGTGGTGGGTAGATGACTCTCAGCATATGGACAAGCGA
ACTCTGGCACTCGGGATGCTAGCCCACTCCTCCGACATGCTAGAGAATGTCTTCTCCCCACTGGCAGATGAAAAGTGTTA
TGTAGCAATGAATCGAGCCAAGAACCTGGTAGAACTGGACCCTGAAGTGGAGGGCACAAAGCACAGTGCCATAGAGATAA
TCTGGGCTGTGCTGGCAGCTTTCAATAAATCC

Alignment

ORF - retro_chof_1603 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.28 %
• Parental protein coverage: 76.71 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GYTSFWNDCISSGLRGGILIELAMRGRIYLEPPTMRKKRLLDRKVLLKSDSPTGDVLLDETLKHIKATEP
          GYTSF.NDCISSGL.GGILIELAMRG.IYLEP.TM.KKRL.DRKVLLKSDSP.GDVLLDETLKHIKA.EP
Retrocopy GYTSFRNDCISSGL*GGILIELAMRGGIYLEPSTMHKKRLPDRKVLLKSDSPKGDVLLDETLKHIKAKEP

Parental  TETVQTWIELLTGETWNPF-KLQYQLRNVRERIAKNLVEKGILTT-EKQNFLLFDMTTHPVTNTTEKQRL
          TETVQTW.ELLTGETWNPF..LQYQLRNV.E.IAKNL.EKGILTT.EKQNFLLFDMTTHPVT.TTEKQRL
Retrocopy TETVQTWKELLTGETWNPF<QLQYQLRNV*EQIAKNLIEKGILTT>EKQNFLLFDMTTHPVTSTTEKQRL

Parental  VKKLQDSVLERWVNDPQRMDKRTLALLVLAHSSDVLENVFSSLADEKYDVAMNRAKDLVELDPEVEGTKH
          VKKLQ.SVL..WV.D.Q.MDKRTLAL..LAHSSD.LENVFS.LADEK..VAMNRAK.LVELDPEVEGTKH
Retrocopy VKKLQGSVL*WWVDDSQHMDKRTLALGMLAHSSDMLENVFSPLADEKCYVAMNRAKNLVELDPEVEGTKH

Parental  SATEMIWAVLAAFNKS
          SA.E.IWAVLAAFNKS
Retrocopy SAIEIIWAVLAAFNKS

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_1603 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020357	1 retrocopy	retro_btau_1256,
Choloepus hoffmanni	ENSCHOG00000013505	2 retrocopies	retro_chof_1173, retro_chof_1603 ,
Myotis lucifugus	ENSMLUG00000003484	1 retrocopy	retro_mluc_1551,
Rattus norvegicus	ENSRNOG00000047620	1 retrocopy	retro_rnor_2682,