RetrogeneDB ID: retro_chof_464

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_112227:2619..3459(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSL1
• Ensembl ID: ENSCHOG00000001862
• Aliases: None
• Description: NSL1, MIS12 kinetochore complex component [Source:HGNC Symbol;Acc:24548]

Sequence

>retro_chof_464
ATGGCGGGAAATTCTAAACCGCTGGTCCTCGTCCCTCCGCTGAACAGGGAGATAGTGGCGGGTAGAGATGACCTGGCCTC
GGTCCCCAGTGTGCCCGGAGAGGACTTCAGGGTGCGCTGCACCTCTAAGCGGGCTGTGACAGAAATGCTAGAGCTGTGCG
GTCGCTTCGTGCAAAGGCTCTGGGATGCGTTAGCAGAGGAGATTTGGGAACCTGCGCGGCGAGATGCGCAGTGGACTTCT
GAATCAGCTATGCACGAGAATATGATCAGCGTTAATGGGCAACCATGGCAGGAAGCTTCAGATAATGGTTTTATGGATTC
TGACATCAAAGTACTTGAAGATCAGTTTGATGAAATCATAGTAGATGTAGCCATGAAACGTAAGCAGTATCCCAGAAAGA
TCCTTGAATGTGTCATCAAAACCATAAAGGCAAAACAAGAAATTCTGAAGCAGTACCAACCTGTTGTACATCCATTGGAC
CTAAAATTTAACCCTGATCCATCCTCTCATATGGAAAATTTGAAATGCAGAGAGGAAACAATAGCTAAGGAGATCAGTGG
AACCATGAAGTCCTTGTCTGTGTTAATTGAACAAGCAGACGGATTTCCCCAAGTTTTAAAGATGCAGCCTACTATCCAGC
TCGGAAGAGTCCGTCAAGAAGTCTTTTCCAGTTGTTACAAGAAACCGGATGTTAAACCTGAGAACTTTATAACACAACTA
GAAACCACACCAACAGAGACTGCTGCCACGAAAACCGCTGACATAGTATTGAAAAGAAAGAGAACTAAAGATTGCCCCCA
GAGAAAATGGTATCCATTGCGGCCGAAAAGAATTGATCTT

Alignment

ORF - retro_chof_464 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.07 %
• Parental protein coverage: 99.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGGSEPVVIVPPLT-ELVTGRR-LVSVPGVPGEDFRVRCTSKRAVTEMLELCGCIVQGLGDALPEEIRE
          MAG.S.P.V.VPPL..E.V.GR..L.SVP.VPGEDFRVRCTSKRAVTEMLELCG..VQ.L.DAL.EEI.E
Retrocopy MAGNSKPLVLVPPLNREIVAGRDDLASVPSVPGEDFRVRCTSKRAVTEMLELCGRFVQRLWDALAEEIWE

Parental  HALRDAQWTFESAMHEN-ISINGQAWQEASDNGFMDSDIKVLEDQFDEIIVDVAMKRKQYPRKILECVIK
          .A.RDAQWT.ESAMHEN.IS.NGQ.WQEASDNGFMDSDIKVLEDQFDEIIVDVAMKRKQYPRKILECVIK
Retrocopy PARRDAQWTSESAMHENMISVNGQPWQEASDNGFMDSDIKVLEDQFDEIIVDVAMKRKQYPRKILECVIK

Parental  TIKAKQEILKQYQPVVHPLDLKFDPDPASHIENLECRGETITKEISEAMRSLPVLIEAA-GFSQVLKMQP
          TIKAKQEILKQYQPVVHPLDLKF.PDP.SH.ENL.CR.ETI.KEIS..M.SL.VLIE.A.GF.QVLKMQP
Retrocopy TIKAKQEILKQYQPVVHPLDLKFNPDPSSHMENLKCREETIAKEISGTMKSLSVLIEQADGFPQVLKMQP

Parental  IIQLQRVHQEAFSSCYRKPDVKSENFITQIETTPMETPARKTTVIVLKRKRTKDCPQKKWSPLQPKRINL
          .IQL.RV.QE.FSSCY.KPDVK.ENFITQ.ETTP.ET.A.KT..IVLKRKRTKDCPQ.KW.PL.PKRI.L
Retrocopy TIQLGRVRQEVFSSCYKKPDVKPENFITQLETTPTETAATKTADIVLKRKRTKDCPQRKWYPLRPKRIDL

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_464 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001862	1 retrocopy	retro_chof_464 ,
Rattus norvegicus	ENSRNOG00000042286	1 retrocopy	retro_rnor_2027,
Tarsius syrichta	ENSTSYG00000003900	1 retrocopy	retro_tsyr_202,
Tursiops truncatus	ENSTTRG00000016584	1 retrocopy	retro_ttru_564,