RetrogeneDB ID: retro_chof_301

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_6856:3606..4388(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RRAGD
• Ensembl ID: ENSCHOG00000001038
• Aliases: None
• Description: Ras-related GTP binding D [Source:HGNC Symbol;Acc:19903]

Sequence

>retro_chof_301
GATCCCTCCAGCACTGAGGTGAAGCCAAGAATCTTGCTCATGGGACTGAGGAGAAGTGGCAAGACATCTATTCGGAAAGC
TGTCTTTCACAAAATGTCTCCCAATAAAACCCTGTTCCTGGAGAGCACTAATAAGATATGCCGGGAAGATGTTTCCAACA
GCTCGTTTGTTAATTTTCAGATTTGGGACTTCCCAGGGCAGATTGACTTTTTTGACCCTACATTTGACTGAGATGATCTT
CAGGGGAACAGGAGCACTGATATTTGTCATTGACTCCCAGGACGATTACATGGAAACCCTGGCCAGGCTCCACCTCATGG
TGACCTGCGCCTACAAAATCAACACTGACATCAATTTTGAGGTATTTATTCATAAAGTGGACGGCCTCTCAGTGACCACA
AAATTGAAACCCAAAGAGAGATTCACCAGAGGGCAAATGATGACCTTGCAGATGCTGGACTAGAAAAAATTCACCTCAGC
TTTTATCTGACAAGCATTTATGGTCATTCAATATTTGAAGCTTTTAGCAAAGTGGTTCAAAACTGATTCCATAACTCCCA
ACCCTGAAGAATTTGCTGAACATCTTTATGTCAAATTCTGGAATTGAAAAGGCATTTCTCTTTGATGTTGTTAGCAAAAT
TTATATTGCAACTGATAGTACCCCAGTGGACATGCAAACGTATGAACTCTGCTGTGATATGACAGATGTAGTGATTGACA
TCTCTTGTATTTATGGTCTCAAACAAGATGGAGCAGGAACCTCCTATGACAAGGAATCAACT

Alignment

ORF - retro_chof_301 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.04 %
• Parental protein coverage: 71.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DPFSTEVKPRILLMGLRRSGKSSIQKVVFHKMSPNETLFLESTNKICREDVSNSSFVN-FQIWDFPGQID
          DP.STEVKPRILLMGLRRSGK.SI.K.VFHKMSPN.TLFLESTNKICREDVSNSSFVN.F......G...
Retrocopy DPSSTEVKPRILLMGLRRSGKTSIRKAVFHKMSPNKTLFLESTNKICREDVSNSSFVN>FRFGTSQGRLT

Parental  FFDPTFDYEMIFRGTGALIFVIDSQDDYMEALARLHLTVTRAYKVNTDINFEVFIHKVDGLS-DDHKIET
          F.......EMIFRGTGALIFVIDSQDDYME.LARLHL.VT.AYK.NTDINFEVFIHKVDGLS..DHKIET
Retrocopy FLTLHLT-EMIFRGTGALIFVIDSQDDYMETLARLHLMVTCAYKINTDINFEVFIHKVDGLS<SDHKIET

Parental  QRDIHQRANDDLADAGLEKIHLSFYLTSIYDHSIFEAFSKVVQ-KLIPQLPTLENLLNIFISNSGIEKAF
          QR.IHQRANDDLADAGLEKIHLSFYLTSIY.HSIFEAFSKVVQ.KLIP.LPTL.NLLNIF.SNSGIEKAF
Retrocopy QREIHQRANDDLADAGLEKIHLSFYLTSIYGHSIFEAFSKVVQ<KLIP*LPTLKNLLNIFMSNSGIEKAF

Parental  LFDVVSKIYIATDSTPVDMQTYELCCDMIDVVIDISCIYGLKEDGAGTPYDKEST
          LFDVVSKIYIATDSTPVDMQTYELCCDM.DVVIDISCIYGLK.DGAGT.YDKEST
Retrocopy LFDVVSKIYIATDSTPVDMQTYELCCDMTDVVIDISCIYGLKQDGAGTSYDKEST

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_301 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	ENSBTAG00000018438	1 retrocopy	retro_btau_1643,
Choloepus hoffmanni	ENSCHOG00000001038	1 retrocopy	retro_chof_301 ,
Equus caballus	ENSECAG00000015826	1 retrocopy	retro_ecab_558,