RetrogeneDB ID: retro_chof_405

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_104424:1558..2317(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAF1D
• Ensembl ID: ENSCHOG00000013436
• Aliases: None
• Description: TATA box binding protein (TBP)-associated factor, RNA polymerase I, D, 41kDa [Source:HGNC Symbol;Acc:28759]

Sequence

>retro_chof_405
GATACCTCATCGTCTGGTAGCAGCTTATTTAAAACTCAATAGGTTCCTTCCTTATCTAAGCAGAGGCAAGAAAACCCTGT
TAGGAAATTTGATTTACAAGAAAATGTTCAAGCTAGAGATTCATCAAGTGATTGCTCTTTGGAATCAATACCACTGACTT
TAAAAGCTATTTTTGAAAGATCCAAGTATAAGAAACATATAGAGAGGAAATAAAAACCAACAAGAAGACTAAAGGGGAGA
CCAAAAGGAAGGAGAAACACCAGAAATTCATGAATAGGCAAAAAACAACTTAAAGAAGAGGACCCAGGTTCTCATTTTTA
GAATCAGAGAATGGAAGAAACCATTACCTTGGAAGAAAATTTTAACCTCTGAGCAAAACTATTGCAAGAGGATTTTTCAA
CTACATTGGAAACTGAAGTATGAATACTACCTCAAGGAATCCTTGAAACAAATGCATGTTGGTGAAGATTTAGAAAAAGA
AGATCATGATAGTTGTCGATACAAATACGTGGATGATGATGGATCCATTTCTCCTATTGAAGAGTCAGTGGCAGAGGATG
AAGATACAGTGCATCTTGAACACGGTGATGCATGTGATATCAAATTGGTGGAGGATAATTATTTCATAATAAGTTCAGAA
TTGCCAAAGAAGAAGAATGCTTATTTAGAGCAAGAGAAAATAGTAAAGAAAAGGATTTATCGAGAAAAAGAAATTCAAAG
GCAAAAACATTGGACAAAAAGAATGACATGAAATGGAGT

Alignment

ORF - retro_chof_405 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.76 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DSSSSGSSLFKTQRVPSLPKRREGNPVRKFDLQENAQAGESSSDSSSEPIPRTLKAIFERFKKKKRKKRK
          D.SSSGSSLFKTQ.VPSL.K.R..NPVRKFDLQEN.QA..SSSD.S.E.IP.TLKAIFER.K.KK...RK
Retrocopy DTSSSGSSLFKTQ*VPSLSKQRQENPVRKFDLQENVQARDSSSDCSLESIPLTLKAIFERSKYKKHIERK

Parental  YKRTGRPKGRPKGRRNTRSSQIGKKQFKDRRPGFSFLES-ENGKQLPWKKILNFEQ-AVARGFFNYIE-K
          .K.T.R.KGRPKGRRNTR.S.IGKKQ.K...PG..F....E..K.LPWKKIL..EQ...ARGFFNYI..K
Retrocopy *KPTRRLKGRPKGRRNTRNS*IGKKQLKEEDPGSHF*NQ>EWKKPLPWKKILTSEQ>TIARGFFNYIG<K

Parental  LKYEYHLKESLKQMNVGEDLEKEDLDSRRYKYLDDDGSISPIEESVAEDEDTMHLEHGDECDIKLVEDNY
          LKYEY.LKESLKQM.VGEDLEKED.DS.RYKY.DDDGSISPIEESVAEDEDT.HLEHGD.CDIKLVEDNY
Retrocopy LKYEYYLKESLKQMHVGEDLEKEDHDSCRYKYVDDDGSISPIEESVAEDEDTVHLEHGDACDIKLVEDNY

Parental  FIISSKLP-RRNAYLEQ-GDDSEETALLRKRNSKAK--NKVQVLKWS
          FIISS.LP...NAYLEQ....S.E..L.RKRNSKAK...K....KWS
Retrocopy FIISSELPKKKNAYLEQ<RENSKEKDLSRKRNSKAKTLDKKNDMKWS

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_405 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013436	1 retrocopy	retro_chof_405 ,
Myotis lucifugus	ENSMLUG00000011431	1 retrocopy	retro_mluc_2033,
Monodelphis domestica	ENSMODG00000008546	1 retrocopy	retro_mdom_1216,
Oryctolagus cuniculus	ENSOCUG00000001096	2 retrocopies	retro_ocun_101, retro_ocun_23,
Otolemur garnettii	ENSOGAG00000002521	1 retrocopy	retro_ogar_1139,
Sarcophilus harrisii	ENSSHAG00000005874	1 retrocopy	retro_shar_566,
Tarsius syrichta	ENSTSYG00000014258	1 retrocopy	retro_tsyr_1107,