RetrogeneDB ID: retro_chof_787

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_148072:3866..4781(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CEP41
• Ensembl ID: ENSCHOG00000003340
• Aliases: None
• Description: centrosomal protein 41kDa [Source:HGNC Symbol;Acc:12370]

Sequence

>retro_chof_787
TTTTCGAGACTAAAAGTTACAACTTTTGCCCAGCTGGTCATCCAAGTTGCTTCTCTATCCAATCAAACACTGGAAGTCAC
AGCTGAGGAGATTCAAAGACTGGAAGACAATGATTCTACAACTTCAGACCCTGATGCTGAACTCACTGCCAGGACCAATG
GGAAGGGGAGCCCCGGTGAGGAGTTGCCTAGTCCTGTCCAGTTCATAAACAGGGCAGGAGCTGGGGACTCCAGTCGCTCA
GCGCTTTAGAGCGTCATCAGTGGTGTTGGAGAGCTGGATCTAGACAAAGGGCTAGTGAAGAAAGCAGAGCCCAACACCAA
AGACAAACCTTAACCTAACTGCTCCTTCCTGCTGCTAGATGTACAAGATAGAGATTCTTACCAGCAATGCCACACTGTTG
GAGCTTACAGTTATCCAATCGCAACTCTGTCTAGAACAATGAACCCTTATTCAAACAATATTCTGGAATATAAAAATGCC
CATGGCAAGATCATCATTCTGTACGATGATGACGAAAGACTGGCCAGCCAGGCCACCACCACCATGTGTGAGCGGGGATT
TGAGAACCTCTTCATGCTCTCTGGAGGTCTAAAAGTCTTAGCTCAGAAATTCTCAGAAGGACTGATCACTGGTTCCCTGC
CAGCCTCTTGTCAGCAGGCCCTTCCTCCTGGTTCTGCTCGGAAGCAGTCCAGCCCCAGAGTGCCACCCTCACCAGCTGAG
ACTAAATGGAGATTTACCCCAGAAGACTTAAAAAAGATAGAATATTACCTGCAAGAGGATCAGGGTCCTGCAGAAGATCC
TAGTCGACTGAACCAAGCTAACTCCTCTGGAAGACATTCCAAGGGTGGAAGAGACTCGAAGGTTCCTGGTGCCCGCAGCG
GGCAGAGCATGTCTGCTGGGGGTCCCGCCAGCCAC

Alignment

ORF - retro_chof_787 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.87 %
• Parental protein coverage: 81.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FKRLKVTTFAQLVIQVASLSDQTLEVTAEEIQRLEDNDSTTSDPDAELTARTNGKGSPGEEPPSPVQFIN
          F.RLKVTTFAQLVIQVASLS.QTLEVTAEEIQRLEDNDSTTSDPDAELTARTNGKGSPGEE.PSPVQFIN
Retrocopy FSRLKVTTFAQLVIQVASLSNQTLEVTAEEIQRLEDNDSTTSDPDAELTARTNGKGSPGEELPSPVQFIN

Parental  RAGAGDSSRSTLQSVISGVGELDLDKRLVKKAEPNTKDRPYPDCPFLLLDVRDRDSYQQCHIVGAYSYPI
          RAGAGDSSRS.L.SVISGVGELDLDK.LVKKAEPNTKD.P.P.C.FLLLDV.DRDSYQQCH.VGAYSYPI
Retrocopy RAGAGDSSRSAL*SVISGVGELDLDKGLVKKAEPNTKDKP*PNCSFLLLDVQDRDSYQQCHTVGAYSYPI

Parental  ATLSRTMNPYSNDILEYKNAHGKIIILYDDDERLASQAATTMCERGFENLFMLSGGLKVLAQKFPEGLIT
          ATLSRTMNPYSN.ILEYKNAHGKIIILYDDDERLASQA.TTMCERGFENLFMLSGGLKVLAQKF.EGLIT
Retrocopy ATLSRTMNPYSNNILEYKNAHGKIIILYDDDERLASQATTTMCERGFENLFMLSGGLKVLAQKFSEGLIT

Parental  GSLPASCQQALPPGSARKRSSPRVPPSPAETKWRFTPEDLKKIEYYLQEDQGPAENPSRLNQANSSGRDS
          GSLPASCQQALPPGSARK.SSPRVPPSPAETKWRFTPEDLKKIEYYLQEDQGPAE.PSRLNQANSSGR.S
Retrocopy GSLPASCQQALPPGSARKQSSPRVPPSPAETKWRFTPEDLKKIEYYLQEDQGPAEDPSRLNQANSSGRHS

Parental  KVPGARGGQSMPAGGPASHPNPRSH
          K............G...S...P.SH
Retrocopy KGGRDSKVPGARSGQSMSAGGPASH

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_787 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003340	2 retrocopies	retro_chof_1532, retro_chof_787 ,