RetrogeneDB ID: retro_chof_850

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_155671:1003..1741(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HERPUD2
• Ensembl ID: ENSCHOG00000008035
• Aliases: None
• Description: HERPUD family member 2 [Source:HGNC Symbol;Acc:21915]

Sequence

>retro_chof_850
TTCCCATGTGCAAGGCGAAGAAATGTAGACAGCCAACTTCTTGGGTAAGCAATTCCATCTAGATTCCTAGCAATTCTTGT
TTTCAGCCCATTGCAGATGCTACTGTGGTAACAGATGCATGGCCATCAGTATTATGTATAATATCAAGCTGCAGTTTCAG
TTCAGGCCAAATCATGTGCCAACCGAACTGAACCTGCTGCTTCGTGACTTCTAAATCTGGCACGTATTCTTGGAGAAGAA
CCCCCGTCAGCTCCCAACCCAGTGGCCCAAGGAAATTAACCCACAAATGAGAATGTTCAGTTGAATGCCCAGGGTGGTCC
AATGCCAAATGTAGAAAACTTCAATCAAAACAGGCTAGGCTGGATGTACACATTCTAACGAGCTGCAGTTCCCCTTAGCA
TTGTATCCTTCTATTCTTCTTTTTTTCGGTTTATCATGCTAATGAGAGCCATGCTACCAATTTATTTATACCAAACTGGA
TGGTTTCCTTTTAGGCAAGAAGGAGTTCAGCAGCAGGCTCCCAAAAATGACACAAGTTAACAGTGATGGGAAAACTGTAA
ACAATCTAGAACTTGAAGAAATGGAGCATTTATGGATGATGTGCTTGACAATGAGCATGGGGGAAAAGCAGGTGAAAATG
CCAGTCAACTCAAAGGCCTGACTTAGATGGCTTTACCTTGGTCTTTTATCACCACCTTTATTTCACTTGTACCAGAGGGG
CCTCCCCACGTTGCCAGT

Alignment

ORF - retro_chof_850 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.6 %
• Parental protein coverage: 61.08 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FPYVMQGNIDNQFPEQAIPAGFPVYPAFSPLQMLWWQQMYAHQYYMQYQAAVSAQATSDANPAQLTASQP
          FP.....N.D.Q....AIP..F.....FSPLQML.W.QM..HQYY..YQAAVS.QA.S.AN.....AS..
Retrocopy FPCARRRNVDSQLLG*AIPSRFLAILVFSPLQMLLW*QMHGHQYYV*YQAAVSVQAKSCANRTEPAAS*L

Parental  LNMTHVPGEEPPPAPNLVAQENRPLNENVQMNAQGGPVLNEEDFNRDWLDWMYTFSRAAILLSIVYFYSS
          LN.....GEEPP.APN.VAQ.N.P.NENVQ.NAQGGP..N.E.FN...L.WMYTF.RAA..LSIV.FYSS
Retrocopy LNLARILGEEPPSAPNPVAQGN*PTNENVQLNAQGGPMPNVENFNQNRLGWMYTF*RAAVPLSIVSFYSS

Parental  FSRFIMVMGAMLLVYLHQAGWFPFRQEGGPQHAPNNN-VEVNNDGQNVNNLELEEMERI-MDDGLEDESG
          F.RFIM.M.AML..YL.Q.GWFPFRQE.G.Q.....N...VN.DG..VNNLELEEME...MDD.L..E.G
Retrocopy FFRFIMLMRAMLPIYLYQTGWFPFRQE-GVQQQAPKN>TQVNSDGKTVNNLELEEMEHL<MDDVLDNEHG

Parental  EDAGEDASAIQRPGIMASAWSFITTFFTSLIPEGPPQVAN
          ..AGE.AS.......MA..WSFITTF..SL.PEGPP.VA.
Retrocopy GKAGENASQLKGLT*MALPWSFITTFI-SLVPEGPPHVAS

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_850 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008035	1 retrocopy	retro_chof_850 ,
Tursiops truncatus	ENSTTRG00000007476	1 retrocopy	retro_ttru_1631,