RetrogeneDB ID: retro_chof_2292

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_63812:5788..6223(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPATCH11
• Ensembl ID: ENSCHOG00000004377
• Aliases: None
• Description: G patch domain containing 11 [Source:HGNC Symbol;Acc:26768]

Sequence

>retro_chof_2292
CCAAGAAGATACCAGATCTAAGAAGCCCATCGAAGCAAGAAAAGCAGCTGGAGGCTAATTGGAAAAATAGGGAGAAGAGT
TTAAAAGAAGAGAGATGTGACGTTGGTTGAAGAATGCACTAGGTTGTGAAAACAAAGGATTTGCTTTGATCAGAAGATGG
CTTATAAGAGTGGTCAGATTCTTGGCAAGAGTGGAGACGGCATTGTTGAACCAATTCCTCTCAACATCAAAACTGGGAAA
AGTTGTGTTGGTCATGAAGCATTTATTCAAAGCAAACAGAAAACAGAGGAAAAATTAGAAAGCTATAGAAGAAAGATTCA
TATGAAAAACCAAGCCAAAGAAAAAGCTTCAGAACAGTTTTGATTGAGGCTTAAGAAGAAGCAAAACAAAATGAATCTAT
AAGGAGATCTTCAAAGAAACTAGTGAGCCTGTCAA

Alignment

ORF - retro_chof_2292 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.03 %
• Parental protein coverage: 54.65 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PMLRQIREARR-KEEKQLEANLKNRQKSLKEEEEERRDIG-LKNALGCENKGFALL-QKMGYKSGQALGK
          P...QI.EA.R.K.EKQLEAN.KNR.KSLK...EER.D.G.LKNALGCENKGFAL..QKM.YKSGQ.LGK
Retrocopy PRRYQI*EAHR<KQEKQLEANWKNREKSLK---EERCDVG<LKNALGCENKGFALI<QKMAYKSGQILGK

Parental  SGDGIVEPIPLNVKTGKSGIGHEALL--KRKAEEKLESYRRKIHMKNQAEEKATEQFRMRLKTKQDEMKL
          SGDGIVEPIPLN.KTGKS..GHEA....K.K.EEKLESYRRKIHMKNQA.EKA.EQF..RLK.KQ..M.L
Retrocopy SGDGIVEPIPLNIKTGKSCVGHEAFIQSKQKTEEKLESYRRKIHMKNQAKEKASEQF*LRLKKKQNKMNL

Parental  EGDLKRSQRACQ
          .GDL.R...ACQ
Retrocopy *GDLQRN**ACQ

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_2292 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006041	1 retrocopy	retro_cfam_708,
Choloepus hoffmanni	ENSCHOG00000004377	3 retrocopies	retro_chof_1420, retro_chof_2292 , retro_chof_398,
Homo sapiens	ENSG00000152133	1 retrocopy	retro_hsap_2802,
Monodelphis domestica	ENSMODG00000015289	1 retrocopy	retro_mdom_1855,
Nomascus leucogenys	ENSNLEG00000027017	1 retrocopy	retro_nleu_1542,
Pan troglodytes	ENSPTRG00000011832	1 retrocopy	retro_ptro_1899,