RetrogeneDB ID: retro_chof_181

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_4040:11135..11691(-)
• Located in intron of: ENSCHOG00000007656

Retrocopy information

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

Parental gene information

• Parental gene symbol: KLF3
• Ensembl ID: ENSCHOG00000004256
• Aliases: None
• Description: Kruppel-like factor 3 (basic) [Source:HGNC Symbol;Acc:16516]

Sequence

>retro_chof_181
ATGCTCATGTTTGATCCAGTCACTGTTAAGCAAGAGGCCATGGAGCCTGTCTCAGTGTCATACCCATCTAATTACATGGA
GCTGATGAAACTCAACAAGTATGAGCCACTTAACTCCACACCATTGCCAGACAAGTTCTTTCAGACTTCAGAAGGCCTTT
TGCATAGAATAAAGATGGAGCCAGTGGACCTCACTGTGAACAAGCAGGGTTCAATACCTTCAGGGGAAGATTGCCCTTCC
TTGCTGGAATCCCAGTCATGGCACAGGAGAGCCTTGCCCTGGCTGAGCATGCCCTTTTCTAGTCCCCTGATGAAGAAGCA
CACGCTTCCTCCACCTGTAGTGCAGCCCTTTGGCATGCCGCCGCCCATGACCTAGTGATGGCTGCTACACCCTCCTGGCA
TGGAGTCTGAAGCCCAGGGATACGGCCTGTTGTGCAGCCTGTCCAGTTTATGTACACCAGTCACCTCCAGCAGCTGCTCA
TGGCCTCCTTGTTAGAGATGGAAAATTCAGATAGAACATGCAGGTACCTGTAAATGAATCATATGAGAAGCCTATA

Alignment

ORF - retro_chof_181 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.59 %
• Parental protein coverage: 55.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLMFDPVPVKQEAMDPVSVSYPSNYMEPMKPNKYGVIYSTPLPDKFFQTSEGLSHGIQMEPVDLTVNKRS
          MLMFDPV.VKQEAM.PVSVSYPSNYME.MK.NKY....STPLPDKFFQTSEGL.H.I.MEPVDLTVNK..
Retrocopy MLMFDPVTVKQEAMEPVSVSYPSNYMELMKLNKYEPLNSTPLPDKFFQTSEGLLHRIKMEPVDLTVNKQG

Parental  SPHSAGSSPSSLKFPSSHRRASPGLSMPSSSPPMKKYSPPPPGVQPFGVPLSMP-PVMAAALSRHGIRSP
          S..S....PS.L...S.HRRA.P.LSMP.SSP.MKK...PPP.VQPFG.P..M...VMAA..S.HG..SP
Retrocopy SIPSGEDCPSLLESQSWHRRALPWLSMPFSSPLMKKHTLPPPVVQPFGMPPPMT<LVMAATPSWHGV*SP

Parental  GILPVIQPVVVQPVPFMYTSHLQQPLMVSLSEEMENSNS-SMQVPVIESYEKPI
          G....I.PVV.QPV.FMYTSHLQQ.LM.SL..EMENS....MQVPV.ESYEKPI
Retrocopy G----IRPVV-QPVQFMYTSHLQQLLMASLL-EMENSDR<NMQVPVNESYEKPI

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_181 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017488	1 retrocopy	retro_btau_271,
Choloepus hoffmanni	ENSCHOG00000004256	1 retrocopy	retro_chof_181 ,
Choloepus hoffmanni	ENSCHOG00000009798	1 retrocopy	retro_chof_1208,
Macaca mulatta	ENSMMUG00000003363	1 retrocopy	retro_mmul_2118,
Nomascus leucogenys	ENSNLEG00000017046	1 retrocopy	retro_nleu_2431,
Otolemur garnettii	ENSOGAG00000006524	1 retrocopy	retro_ogar_1686,