RetrogeneDB ID: retro_chof_1935

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_426608:1..773(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LZTFL1
• Ensembl ID: ENSCHOG00000003899
• Aliases: None
• Description: leucine zipper transcription factor-like 1 [Source:HGNC Symbol;Acc:6741]

Sequence

>retro_chof_1935
AGGCTGGTGGAGGAGACTTCACCATCAATGAAGACTCCAAAGTCTGAGTGGGTTACAGGCTGTGGTTCATCGCAAGGTGG
ATTCTGAGCTCATCAACACCACATACACTGATGTGATGTGCTACTTCTGTGGCAGCTTTTTTTCACAAGCTGAGAAGTGA
TACCTAAAGCTACAGACAGATATCTCTGAACTTGAAAACAGAGAATTTTTAGAACAAGTTGCAGAATTTGAAAAAGCAGA
ATTTACATCTTCAAATAAAAAGCCTATCATAAATATCGTAAAACCAAAATTTGTTCTACTTAATAAAGGCTGTACAGCAA
AACTCCTAAACAAGGAAATTTCAAGACTTCAAGAAGAGATTGAGAAATTGAAGTCAAGGCTAAAGACCATGGAAATACAG
GCTACAAATGCATTAGATGACAAGTCAAAACTAGAAAGAGCACTGCAAGATTTACAACTCAATCAAGGAAATGAGAAGGA
TTTTATAAACGCTGAAGACTTAAGTGGCTTGGAAAATACAGTTGCTGCTTTAAAGAGTGACTTCCAGAAGACACTTAATG
ACAAGAAAGAAAACCAGAAGTCCCTGGAGAACAATTTAGCAACAGCCAAGCATGACCTGCTCAGGGTCCAGGAGCAGCTG
AGTTTGGCTGAAAAGGAATTAGAGAGGAAATTCCAACAAAAAGCAGCTTATTGAAACATTAAAGAGATTCTTACAAAGAA
TGACCAAATCAAAGACTGAAGGAAAATACTGGCAAAACATGAACCTGAAGAT

Alignment

ORF - retro_chof_1935 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.61 %
• Parental protein coverage: 85.91 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RLVEET-FTIDEVSEV-LSGLQAVVHSEVESELINTAYTNVL--LLRQLFSQAEKWYLNLQTDISELENR
          RLVEET.FTI.E.S.V.LSGLQAVVH..V.SELINT.YT.V........FSQAEK.YL.LQTDISELENR
Retrocopy RLVEET<FTINEDSKV<LSGLQAVVHRKVDSELINTTYTDVMCYFCGSFFSQAEK*YLKLQTDISELENR

Parental  ELLEQVAEFEKAEFTSSNKKPIIDIIKPKLAPLNEGGTAELLNKEI-RLQEENERLKSRLKTMEIQATNA
          E.LEQVAEFEKAEFTSSNKKPII.I.KPK...LN.G.TA.LLNKEI.RLQEE.E.LKSRLKTMEIQATNA
Retrocopy EFLEQVAEFEKAEFTSSNKKPIINIVKPKFVLLNKGCTAKLLNKEISRLQEEIEKLKSRLKTMEIQATNA

Parental  LDEKSKLERALQDLQLNQGNEKDFIKAEDLSELENTVAALKNEFQKTLNDKTENQKSLEENLATAKHDLL
          LD.KSKLERALQDLQLNQGNEKDFI.AEDLS.LENTVAALK..FQKTLNDK.ENQKSLE.NLATAKHDLL
Retrocopy LDDKSKLERALQDLQLNQGNEKDFINAEDLSGLENTVAALKSDFQKTLNDKKENQKSLENNLATAKHDLL

Parental  RVQEQLSLAEKELEKKFQQTAAYRNMKEILAKKNDQIKDLRKRLAKYEPED
          RVQEQLSLAEKELE.KFQQ.AAY.N.KEIL..KNDQIKD.RK.LAK.EPED
Retrocopy RVQEQLSLAEKELERKFQQKAAY*NIKEILT-KNDQIKD*RKILAKHEPED

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_1935 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003899	1 retrocopy	retro_chof_1935 ,
Echinops telfairi	ENSETEG00000013761	1 retrocopy	retro_etel_1726,
Loxodonta africana	ENSLAFG00000010237	1 retrocopy	retro_lafr_155,
Mus musculus	ENSMUSG00000025245	3 retrocopies	retro_mmus_1834, retro_mmus_3266, retro_mmus_3276,
Procavia capensis	ENSPCAG00000009783	1 retrocopy	retro_pcap_313,