RetrogeneDB ID: retro_chof_2647

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_93947:5396..6124(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DUSP11
• Ensembl ID: ENSCHOG00000012041
• Aliases: None
• Description: dual specificity phosphatase 11 (RNA/RNP complex 1-interacting) [Source:HGNC Symbol;Acc:3066]

Sequence

>retro_chof_2647
ATTAGCAAAAGGTGGAAAAACTATCTCTCAGTTGGACAATGGATGCCTGGGAGTCATTTCATTGCTTTCAATGTTACTTT
GAAAAAGAACTTTTAAGGGAATATTGCACTAGAAGAATGTTTTTTCCCTTTGGATATTTCCAACAAAATCCAACAACAAA
ATGAAGAACTTACACCAATTATTCTTTTAACTTATACAGAACGCTCTTAGAAACCATATGATTTATCAGAAACAATTCCT
TACTTAAAGCTTCTTACAGTTGGGCATAAGGTGCCTGATGATGGCACTATTTTAAAACTCAAGTGTGCTGTTAATTGGTT
TTTGAGAGAAAATGAAGATAATGACAAACTTATTGGGATCCAGTGTACCCATGGCTTAAACAGGACTTGCTATCTCATTT
GCAGGTATTTGGTTGATGTTGAAGGCATGAAGCCAGATGATGCAATTGAATTTTTCAGTAGGTGCTGGAAACACTGCATA
GAAAGACAAAACACACTGAAGACCTTTATAATGATCCTGTCAGGAGGTATGGGATTTCTGGTGTATCCATTTCAAGTGGT
TTTGAAAAATCAACACAAATCCTGGAACCAGTCAATAAGTCTGTTAACCAAGGAACTTGGTATACTTTTTATCAGACCCA
CAGTTACCAACACCTTCCCAGCATTTCCACTCCAACACCCAAGATTTGCACACCCAGTCAGAAAATTTTCTCAGAAGAGA
ACATTTAC

Alignment

ORF - retro_chof_2647 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.13 %
• Parental protein coverage: 74.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IPERWKTCLPVAQRMPGTHFIAFKVPLKKSFEGNLAPEECF--LDVFNKIGQN--EFGLITDLTYTERYN
          I..RWK..L.V.Q.MPG.HFIAF.V.LKK.F.GN.A.EECF..LD..NKI.Q...E...I..LTYTER..
Retrocopy ISKRWKNYLSVGQWMPGSHFIAFNVTLKKNF*GNIALEECFFPLDISNKIQQQNEELTPIILLTYTERS*

Parental  KPEDFPETIPYLKF-TVGHRVPDDDTILQFKYAVNG--RENKDNDKLIGVHCTHGLNRTGYLICRYLIDV
          KP.D..ETIPYLK..TVGH.VPDD.TIL..K.AVN...REN.DNDKLIG..CTHGLNRT.YLICRYL.DV
Retrocopy KPYDLSETIPYLKLLTVGHKVPDDGTILKLKCAVNWFLRENEDNDKLIGIQCTHGLNRTCYLICRYLVDV

Parental  EGMRPDDAIELFNRCRGHCLERQN-YIEDLQNGPVRKYGGSGVSRSSGFEESTQILESVNKSVNRGPQYN
          EGM.PDDAIE.F.RC..HC.ERQN...EDL.N.PVR.YG.SGVS.SSGFE.STQILE.VNKSVN.G..Y.
Retrocopy EGMKPDDAIEFFSRCWKHCIERQN<HTEDLYNDPVRRYGISGVSISSGFEKSTQILEPVNKSVNQGTWYT

Parental  LYRTQGY-PVPSRHFHFNSRDLQ-QSVRKFSQ-NQNIY
          .Y.T..Y.P.PS.HFH.N..DL....VRKFSQ...NIY
Retrocopy FYQTHSY<PTPSQHFHSNTQDLH<HPVRKFSQ<EENIY

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_2647 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 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012041	2 retrocopies	retro_chof_2647 , retro_chof_932,
Echinops telfairi	ENSETEG00000005304	1 retrocopy	retro_etel_487,
Macropus eugenii	ENSMEUG00000009370	1 retrocopy	retro_meug_1073,
Tupaia belangeri	ENSTBEG00000014600	1 retrocopy	retro_tbel_1984,
Tursiops truncatus	ENSTTRG00000015444	5 retrocopies	retro_ttru_1220, retro_ttru_1512, retro_ttru_1627, retro_ttru_1746, retro_ttru_1877,