RetrogeneDB ID: retro_chof_1339

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_268021:610..1583(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BUB3
• Ensembl ID: ENSCHOG00000010213
• Aliases: None
• Description: BUB3 mitotic checkpoint protein [Source:HGNC Symbol;Acc:1151]

Sequence

>retro_chof_1339
ATGACCAGCTCTAATGAGTTCAAGCTGAACCAGCCACCTGAGGATGGCATCTCTTCAGTGAAGTTCAGCCCCAACACCTC
CCAGTTCCTGTTGGTCTCCTCCTGGGACACATTCATGTGCCTGTATGATGTGTCCGCCAACTCCATGCGACTCAAGTACC
AGCACACCAGCGCGGTTCTGTACTGCGCGTTCTACAATCCAACACTTGCCTGGAGTGGGGGATTAGATCATTGATTGAAA
ATGCATGATTTGAACACTGATCAAGAAAATCTAGTTGGAACCCATGATGCCCCTATCAGATGTGTTGAATACTGTCCGGA
AGTGAATGTGATGGTTACTGGAAGCTGGGATCAGACAGTTAAATTGTGGGATCCCAGAACTCCTTGTAATGCCAGAACCT
TCTCTCAGCCTGAAAAGGTATACACTCTCTTGGTGTCTGGAGACCGGTTGATCGTGGGGACGGCGGGCCGCAGAGTGTTG
GTCTGGGACTTAGGGAACATGGGCTATATGCAGCAGTGCCGAGAGTCCAGCCTCAAGCACCAGACCTGCTGCATACAGGC
CTTCCCAAACAAGCAGGGTTACGTGTTAGGCTCTATTGAAGGCGGGTGGTGGTTGCGTACTTGGACCCAAGCCCTGAAGT
ACAGAGGAAGAAGTATACCTTCAAATGTCACAGACTAAAGGAAAATAATATTGAGCAGATTTACTCAGTCAATGCCATTT
TGTTTCATAACATCCACAATATATTTGCCACAGGTGGTTCTGATGGGTTTGTAAATATTTGGGATCCCTTTAACAAAATG
TGGCTGTGCCAGTTCCATCGGTATCCCACTAGCATCGCTTCACTTGCCTTCAGCAATGACGGGACTACACTTCAATAGCA
TCATCATGTATGTATGAAATGGATGACACTGAACATCCTGAAGATGGTATCTTCATTCGCCAATTGACAGTTGCAGAAAC
AAAACCCAAGTCC

Alignment

ORF - retro_chof_1339 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.99 %
• Parental protein coverage: 99.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTGSNEFKLNQPPEDGISSVKFSPNTSQFLLVSSWDTSVRLYDVPANSMRLKYQHTGAVLDCAFYDPTHA
          MT.SNEFKLNQPPEDGISSVKFSPNTSQFLLVSSWDT...LYDV.ANSMRLKYQHT.AVL.CAFY.PT.A
Retrocopy MTSSNEFKLNQPPEDGISSVKFSPNTSQFLLVSSWDTFMCLYDVSANSMRLKYQHTSAVLYCAFYNPTLA

Parental  WSGGLDHQLKMHDLNTDQENLVGTHDAPIRCVEYCPEVNVMVTGSWDQTVKLWDPRTPCNAGTFSQPEKV
          WSGGLDH.LKMHDLNTDQENLVGTHDAPIRCVEYCPEVNVMVTGSWDQTVKLWDPRTPCNA.TFSQPEKV
Retrocopy WSGGLDH*LKMHDLNTDQENLVGTHDAPIRCVEYCPEVNVMVTGSWDQTVKLWDPRTPCNARTFSQPEKV

Parental  YTLSVSGDRLIVGTAGRRVLVWDLRNMGYVQQRRESSLKYQTRCIRAFPNKQGYVLSSIEG-RVAVEYLD
          YTL.VSGDRLIVGTAGRRVLVWDL.NMGY.QQ.RESSLK.QT.CI.AFPNKQGYVL.SIEG.RV.V.YLD
Retrocopy YTLLVSGDRLIVGTAGRRVLVWDLGNMGYMQQCRESSLKHQTCCIQAFPNKQGYVLGSIEG<RVVVAYLD

Parental  PSPEVQKKKYAFKCHRLKENNIEQIYPVNAISIHNIHNTFAAGGSDGFVNIWDPFNKKRLCQFHRYPTSI
          PSPEVQ.KKY.FKCHRLKENNIEQIY.VNAI..HNIHN.FA.GGSDGFVNIWDPFNK..LCQFHRYPTSI
Retrocopy PSPEVQRKKYTFKCHRLKENNIEQIYSVNAILFHNIHNIFATGGSDGFVNIWDPFNKMWLCQFHRYPTSI

Parental  ASLAFSNDGTTL-AIASSYMYEMDDTEHPEDGIFIRQVTDAETKPKS
          ASLAFSNDGTTL..IASS.MYEMDDTEHPEDGIFIRQ.T.AETKPKS
Retrocopy ASLAFSNDGTTL<SIASSCMYEMDDTEHPEDGIFIRQLTVAETKPKS

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_1339 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
Choloepus hoffmanni	ENSCHOG00000010213	1 retrocopy	retro_chof_1339 ,
Macaca mulatta	ENSMMUG00000003092	1 retrocopy	retro_mmul_1729,
Sarcophilus harrisii	ENSSHAG00000010372	1 retrocopy	retro_shar_358,