RetrogeneDB ID: retro_chof_1252

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_237070:1147..1691(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPK
• Ensembl ID: ENSCHOG00000013993
• Aliases: None
• Description: centromere protein K [Source:HGNC Symbol;Acc:29479]

Sequence

>retro_chof_1252
ATGGAAGAATGTCAGAATAATGTATTGCTGGTTGGAGCTGAGATCCTCACTGAATCAAATGATCAGCTACCATTATCAAT
TGTGCAAGCAAAAGGTTTGACTGCTGAACTCAGTCAGTGGCAGAAAAAAACTCCTGAAATAATTCTACTGAGTCAATATT
TTCAGGTTTCATGAGGAAAAGAAGAGTACCAAATATTGACACATGATCTTGAAATGGTACCATCTACTCTTCAATCAAAG
AATGAAAAATTAAAGGAAGACTTGAAAGGGAGCAACACTGGCTAGAGAACAAAAACAGATACTGGAATCTCTTAATGTAC
TGCACAAGGAACTAAAAAATGAAGTTGAACCATTTTCTGAATCAAGAATTTAATGGACTGAAAACTAAAATTCTTAGTAT
AAGAGAATATAAGAAGAAATGCTTAATTACCTTGGGTTAGTATCTAAAAGACCATTTTCCTCTGCCTGATGAAAGTGCTA
AAAAGAAAAAGAAAGACATTCAAGAACCAACAGCACAGCTGATAACACTTATGAAATTTTACAG

Alignment

ORF - retro_chof_1252 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.49 %
• Parental protein coverage: 84.33 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEECQNKLLLVGTEALTESNAQLSLLIMQAKCLTAELSQWQKETPEIIPLNQDVLVTLGKEEFQKLTHDL
          MEECQN..LLVG.E.LTESN.QL.L.I.QAK.LTAELSQWQK.TPEII.L.Q...V..GKEE.Q.LTHDL
Retrocopy MEECQNNVLLVGAEILTESNDQLPLSIVQAKGLTAELSQWQKKTPEIILLSQYFQVS*GKEEYQILTHDL

Parental  EMVLSTLQSKNEKLQEDL-EREQQWLDEQKQILESLNVLHNELKNQVEPFSESRIFNGLKTKMLRIREYK
          EMV.STLQSKNEKL.EDL.EREQ.WL.........L.......K.....F.....FNGLKTK.L.IREYK
Retrocopy EMVPSTLQSKNEKLKEDL<EREQHWLENKNRYWNLLMYCTRN*KMKLNHFLNQE-FNGLKTKILSIREYK

Parental  EKLLISLGEFLEDHFPLPDESAKKKKKNIQEPTVQLITL-HEILE
          .K.LI.LG..L.DHFPLPDESAKKKKK.IQEPT.QLITL..EIL.
Retrocopy KKCLITLG*YLKDHFPLPDESAKKKKKDIQEPTAQLITL<YEILQ

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_1252 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	ENSCHOG00000013993	1 retrocopy	retro_chof_1252 ,
Dipodomys ordii	ENSDORG00000007357	1 retrocopy	retro_dord_787,
Equus caballus	ENSECAG00000019165	1 retrocopy	retro_ecab_181,
Erinaceus europaeus	ENSEEUG00000005831	1 retrocopy	retro_eeur_81,
Monodelphis domestica	ENSMODG00000019645	1 retrocopy	retro_mdom_1446,
Oryctolagus cuniculus	ENSOCUG00000011568	2 retrocopies	retro_ocun_1199, retro_ocun_74,
Tursiops truncatus	ENSTTRG00000006527	1 retrocopy	retro_ttru_1310,