RetrogeneDB ID: retro_chof_1208

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_225364:1388..2275(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000003350
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KLF5
• Ensembl ID: ENSCHOG00000009798
• Aliases: None
• Description: Kruppel-like factor 5 (intestinal) [Source:HGNC Symbol;Acc:6349]

Sequence

>retro_chof_1208
TCAGAACCTGTTACCATTTTCAGCCACCAGAGTGAAACGACTGCCCCTCCTCCGGTCCAGACCCAGGCCCTTCCCGAGTT
CACCAGCATATTCAGCTCACACCAGACCGCAGCTCCAGAGGTGAACAATATTTTCATCAAACAAGAATTTCCTACACCAG
ATCTTCATCTTTCTGTCCCTTCCCAGCAGGGCCATTTGTACCAGCTATTGAATACACCGGATCTAGATATGCCCAGTTCT
ACAAATCAGACAACAGTAATGGACACTCTTAATGTTTCTATGTCAGACGCCATGGCAGGCCTTAACACACTCACCTCTGC
TGTACCAAAGACTGCAATGAAACAATTTCAGGGCATGCCCCCCTGCACATACACAATGCCAAGTCAGTTTCTTCCACAAC
AGGCCACTTACTTTTCCCCATCACCACCAAGCTCAGAGCCTGGAAGTCCAGATAGACAAGCAGAGAGATACTCCAGAATT
TAACCCCACCTCCATCCTATGCTGCTACGATCGCTTCTAAACTGGCAATACACAATCCAAATTTACCTGCTACCCTGCCA
GTTAATTCGCAAAACATCCAACCTGTTAGATACAATAGAAGAAGTAACCCTGATTTGGAGAAGAGACGCATCCACTACTG
CGATTACCCTGGCTGCACAAAAGTTTATACAAAGTCTTCTCATTTAAAAGCTCACCTGAGGACTCATACTGGTGAGAAGC
CGTACAAATGCACCTGGGAAAGCTGCGACTGGAGGTTCGCGCGGTCGGACGAGCTGACCCGCCACTACTGGAAGCACACG
GGCGCCAAGCCGTTCCAGTGCTCCGTGTGCAACCGCAGCTTCTCCCGCTCCGACCACCTGGCCCTGCACATGAAGAGGCA
CCAGAAC

Alignment

ORF - retro_chof_1208 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.94 %
• Parental protein coverage: 64.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TEPVTIFSHQSETTAPPPAQTQALPEFTSIFSSHQTAAPEVNNIFIKQELPTPDLHLSVPSQQGHLYQLL
          .EPVTIFSHQSETTAPPP.QTQALPEFTSIFSSHQTAAPEVNNIFIKQE.PTPDLHLSVPSQQGHLYQLL
Retrocopy SEPVTIFSHQSETTAPPPVQTQALPEFTSIFSSHQTAAPEVNNIFIKQEFPTPDLHLSVPSQQGHLYQLL

Parental  NTPDLDMPSSTNQTTVMDTLNVSMSDAMAGLNTLTSAVPQTAMKQFQGMPPCTYTMPSQFLPQQATYFSP
          NTPDLDMPSSTNQTTVMDTLNVSMSDAMAGLNTLTSAVP.TAMKQFQGMPPCTYTMPSQFLPQQATYFSP
Retrocopy NTPDLDMPSSTNQTTVMDTLNVSMSDAMAGLNTLTSAVPKTAMKQFQGMPPCTYTMPSQFLPQQATYFSP

Parental  SPPSLEPGSPDRQAEILQNLTP-PP-SYAATIASKLAIHNPNLPATLPVNSQNIQPVRYNRRSNPDLEKR
          SPPS.EPGSPDRQAE......P.PP.SYAATIASKLAIHNPNLPATLPVNSQNIQPVRYNRRSNPDLEKR
Retrocopy SPPSSEPGSPDRQAERYSRI*P<PPPSYAATIASKLAIHNPNLPATLPVNSQNIQPVRYNRRSNPDLEKR

Parental  RIHYCDYPGCTKVYTKSSHLKAHL-THTGEKPYKCTWEGCDWRFARSDELTRHYRKHTGAKPFQCAVCSR
          RIHYCDYPGCTKVYTKSSHLKAHL.THTGEKPYKCTWE.CDWRFARSDELTRHY.KHTGAKPFQC.VC.R
Retrocopy RIHYCDYPGCTKVYTKSSHLKAHLRTHTGEKPYKCTWESCDWRFARSDELTRHYWKHTGAKPFQCSVCNR

Parental  SFSRSDHLALHMKRHQN
          SFSRSDHLALHMKRHQN
Retrocopy SFSRSDHLALHMKRHQN

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_1208 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.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004256	1 retrocopy	retro_chof_181,
Choloepus hoffmanni	ENSCHOG00000009798	1 retrocopy	retro_chof_1208 ,
Callithrix jacchus	ENSCJAG00000021146	1 retrocopy	retro_cjac_3188,
Nomascus leucogenys	ENSNLEG00000016120	1 retrocopy	retro_nleu_65,
Pan troglodytes	ENSPTRG00000039565	2 retrocopies	retro_ptro_111, retro_ptro_2968,