RetrogeneDB ID: retro_chof_1515

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_313404:723..1466(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BLZF1
• Ensembl ID: ENSCHOG00000008235
• Aliases: None
• Description: basic leucine zipper nuclear factor 1 [Source:HGNC Symbol;Acc:1065]

Sequence

>retro_chof_1515
TCAGAGGTAAACAGAGGTAAAAAGTTACTGGTGCCTTCTGTTGGGGATGATTTTCAGTACCACTTTGAACATCTAGCCTG
AGAGAAAAATCAGCTTATTTTAGAAAATGAAGCCTTAGGTCTAAACACAGCTCAGCTTTTACGAACAGTTAGAACATGTG
TCAATACAGTGTGATGTATGGCAATGTAAAATTCCTTGCAAGCATGGTTATGGTGGATGAATTAACCAACTCCAGAGCAG
TTTTACAGCATCAAAACCATGATGCACAAATTGCTATACAAGATCTCCTGAGTGAACAAGAACATTTTTGTCTGGAAATG
ATAGCTACCAAGAAATTATTGGAGGAGCTCTTGGTCTCTTTGCAGTGGGGAAGAGAGCACACTTACTACCCTATTGCACA
ACCATACAGCACAGCAGAGCTAGCATTAACAAATCACAAACTGGCAAAAGAAGTGAATTCTCATCTGCTGGGAAATGTTG
GCACTAATAGTCAAAAAAAAAAAAAAAACATACTACCCACAGTTGAATTCTGCAGTGCCCCAGCTGAAAACATGGCTGAA
ATGATTCTATGCATTTTGGATCCAGTTACCTCTACAGAAAACTCACCTTATAGTCCATTTTATGAGTCTTCACCAACCAC
CTTACTCGCTACAAAGAACAATATTTGATGATTTCATCCCTATACTAGATATGAAAATATAGCTTTCAATTACTGCAATC
ACTTCCAGGGAGAACTTGTTGTC

Alignment

ORF - retro_chof_1515 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78. %
• Parental protein coverage: 61.4 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TEVNRELKKLLVASVGDDLQYHFERLAREKNQLILENEALGRNTAQLS-EQLERMSIQGDVWRSK-FLAS
          .EVNR..KKLLV.SVGDD.QYHFE.LA.EKNQLILENEALG.NTAQL..EQLE..SIQ.DVW..K.FLAS
Retrocopy SEVNRG-KKLLVPSVGDDFQYHFEHLA*EKNQLILENEALGLNTAQLL>EQLEHVSIQCDVWQCK>FLAS

Parental  RVMADELTNSRAVLQRQNRDAQIAIQDLLSEREHFRQEMIATKKLLEELLVSLQWGREQTYYPSAQPHST
          .VM.DELTNSRAVLQ.QN.DAQIAIQDLLSE.EHF..EMIATKKLLEELLVSLQWGRE.TYYP.AQP.ST
Retrocopy MVMVDELTNSRAVLQHQNHDAQIAIQDLLSEQEHFCLEMIATKKLLEELLVSLQWGREHTYYPIAQPYST

Parental  AELALTNHKLAKAVNSHLLGNVGTNS---QKKIPSTVEFCNTPAEKMAETILHILDPVTCIERSPDSPFS
          AELALTNHKLAK.VNSHLLGNVGTNS......I..TVEFC..PAE.MAE.IL.ILDPVT..E.SP.SPF.
Retrocopy AELALTNHKLAKEVNSHLLGNVGTNSXXXXXXILPTVEFCSAPAENMAEMILCILDPVTSTENSPYSPFY

Parental  GSSPSILLATKKNIGRFHPYTRYENITFNCCNHCQGELIV
          .SSP..LLATK.NI..FHPYTRYENI.FN.CNH.QGEL.V
Retrocopy ESSPTTLLATKNNI**FHPYTRYENIAFNYCNHFQGELVV

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_1515 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011473	1 retrocopy	retro_amel_627,
Choloepus hoffmanni	ENSCHOG00000008235	1 retrocopy	retro_chof_1515 ,
Echinops telfairi	ENSETEG00000008147	1 retrocopy	retro_etel_53,
Tupaia belangeri	ENSTBEG00000003379	1 retrocopy	retro_tbel_2191,