RetrogeneDB ID: retro_chof_1420

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_287352:364..875(-)
• 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_1420
GGCAAAATTGGAGATGGCATTGTTGAACCGATTCCTCTCATTGTCAAAACTGGGAAAGGTGGCATTGGTCATGAAGCCTT
ATTAAAACGGAAAGCAGAGGAAAAATTAGAAAGCTACAGAAGAAAGATTCGTATGAATTACCAGGCCGAAGAATAAGCTG
CAAAACAATTTTGAATGAGACTTAAGAATAAGCAAGGTGAAATGAAGCTAGGAGATCTTAAGAGAAGCCAGTGAGCCTGT
CAACAATTGGATACTCAGAAGAATAGTCAGGTTTCCAGAGAGACATGGTTCTGGTTGAGGCCTGAACAGGAGAATGAAGA
AGAGGAAGAGTTGGAAAAAAGAACAGAACGAAGATGAATATGTGAATGGAGATTTAAGTGTACTGGAAAAATTACAAATT
ATTGACTAGTTATTTAAGAGAAGAACATCTGCATTGTATTTAGTGTGGAACAGCCTATGAAGATAAAAATTTAACTTCAA
ATTCCTAGGACCAACTTCTGTACATCATGAC

Alignment

ORF - retro_chof_1420 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.41 %
• Parental protein coverage: 64.31 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GKSGDGIVEPIPLNVKTGKSGIGHEALLKRKAEEKLESYRRKIHMKNQAEEKATEQFRMRLKTKQDEMKL
          GK.GDGIVEPIPL.VKTGK.GIGHEALLKRKAEEKLESYRRKI.M..QAEE.A..QF.MRLK.KQ.EMKL
Retrocopy GKIGDGIVEPIPLIVKTGKGGIGHEALLKRKAEEKLESYRRKIRMNYQAEE*AAKQF*MRLKNKQGEMKL

Parental  EGDLKRSQRACQQLDTHKNVQVPREAWYWLRPEQENEEEEESEEK-EQDEDEQESEDLSVLEKLQI-LTS
          .GDLKRSQ.ACQQLDT.KN.QV.RE.W.WLRPEQENEE.EE..EK.EQ.EDE....DLSVLEKLQI.LTS
Retrocopy -GDLKRSQ*ACQQLDTQKNSQVSRETWFWLRPEQENEE-EEELEK>EQNEDEYVNGDLSVLEKLQI>LTS

Parental  YLREEHLYCIWCGTAYEDKEDLTSNC-PGPTSAAHD
          YLREEHL.CI.CGTAYEDK..LTSN...GPTS..HD
Retrocopy YLREEHLHCI*CGTAYEDK-NLTSNS<LGPTSVHHD

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_1420 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,