RetrogeneDB ID: retro_chof_1706

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_363122:0..625(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SKA3
• Ensembl ID: ENSCHOG00000003518
• Aliases: None
• Description: spindle and kinetochore associated complex subunit 3 [Source:HGNC Symbol;Acc:20262]

Sequence

>retro_chof_1706
ACCTACCAATCACCAACTAAAGTACTAAAAACTCCAAAATGTGCACTAAAGATGGATGATTTTGAGTGCATAACTCCTAA
ATTAGAACACTTTGGTATTTCTGAATATACTATGTGTTTAAATGAAGATTATACAATGGGGCTCAAAAATGTGAGCATAA
TAAAAGCGAGGAAGACATAGAAAGGAAAGCAATGACCAATGATCATTTCTTAACCACTCCTGGCCCCATAATCCAGCAGT
TGGGAAAATATGATGCTGAGTATACAAATTCACCCTTGGCCCCTACATTCTATACTCCTGGTTTGAAAATTCCTTCTACA
AAGAGCAGTACAGCTTTGGAATCTACAAATTATCCATTATCAAAAAAAATAGTTCATCAAATGATTTGGAAATGAAAGAT
TGTACTTCATTAGTTTTAAATTCAGAGAAGTGCTTTGAAGATCTTGTGAATCCCTTTTCTCCTAAAATTTCTTCTTATGA
GAATCTGCTCAGAACACCTACACCTCCAGAAGTAACTACAATTCCAGAAGATATTATCCAGATTTTGTCAAAATACAATT
CAAACCTAGCTACCCCTGTAGCAGTGAAAGCAGTGTCACCCAGCAAAGTCTTTCTTGCTAAATAT

Alignment

ORF - retro_chof_1706 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91. %
• Parental protein coverage: 50.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TKQSPTKVLKTPKCALKMDDFECITPKLEHFGISEYTMCLNEDYTMGLKNV-KHNKSEEAIERKAMTSDH
          T.QSPTKVLKTPKCALKMDDFECITPKLEHFGISEYTMCLNEDYTMGLKNV..HNKSEE.IERKAMT.DH
Retrocopy TYQSPTKVLKTPKCALKMDDFECITPKLEHFGISEYTMCLNEDYTMGLKNV<EHNKSEEDIERKAMTNDH

Parental  FLTTPGPIIQQLGKNDAEYTNSPLAPTFCTPGLKIPSTKNNTALESTNYPLSKTN-SSSNDLEMKDCTSL
          FLTTPGPIIQQLGK.DAEYTNSPLAPTF.TPGLKIPSTK..TALESTNYPL.....SSSNDLEMKDCTSL
Retrocopy FLTTPGPIIQQLGKYDAEYTNSPLAPTFYTPGLKIPSTKSSTALESTNYPLXXXX<SSSNDLEMKDCTSL

Parental  VLNSEKCFEDLLDPFSPKISSYENLLKTPTPPEVTTIPEDIIQILSKYNSNLATPVAVKAVPPSKVFLTK
          VLNSEKCFEDL..PFSPKISSYENLL.TPTPPEVTTIPEDIIQILSKYNSNLATPVAVKAV.PSKVFL.K
Retrocopy VLNSEKCFEDLVNPFSPKISSYENLLRTPTPPEVTTIPEDIIQILSKYNSNLATPVAVKAVSPSKVFLAK

Parental  Y
          Y
Retrocopy Y

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_1706 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003314	1 retrocopy	retro_btau_796,
Choloepus hoffmanni	ENSCHOG00000003518	1 retrocopy	retro_chof_1706 ,
Tursiops truncatus	ENSTTRG00000016915	1 retrocopy	retro_ttru_25,