RetrogeneDB ID: retro_chof_562

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_122062:1170..1599(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCL2
• Ensembl ID: ENSCHOG00000012692
• Aliases: None
• Description: phosducin-like 2 [Source:HGNC Symbol;Acc:29524]

Sequence

>retro_chof_562
AGAACTTATGAAGATATGACTTTGGAAGAGCTAGAGGATAATGAAGATGAATTGAAGGAGGATGAACATGCTATTGAGAT
GTACAGGCAGCAAAGACAGGCTGATTGGAAAGACAGTATACTAAAGAATAAATTTGGAGAAGTTCTAGAGATCTCAGGAA
AGGATTGTGTCCAAGAAGTTACCAAAGCTGATGAGGTACAATGGGTAATCTTGCACCTTTACAAACAAGGGATTCCCCTC
TGCACCCTGATAAATCAACAATACAGTGAACTTGCAAGGAAGTTTCCTGATGTCAAATTTATCAAAGCCATTTCAATGTC
CTGCATACCCAATTATCCTGATAGGAATCTGCCCACAATATTTGTGTACCTTGAAGGTGATATCAGGGCTCAATTTATTG
GTCCTTTAGTGTTTGGTGGCATGAACCTG

Alignment

ORF - retro_chof_562 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.08 %
• Parental protein coverage: 97.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KPYEKMSLAQLKEAEDEFDEEDMRAIEVYREKRLQEWKALKERQKFGELREISGNQYVKEVTNAEKDVWV
          ..YE.M.L..L...EDE...ED..AIE.YR..R...WK......KFGE..EISG...V.EVT.A....WV
Retrocopy RTYEDMTLEELEDNEDEL-KEDEHAIEMYRQQRQADWKDSILKNKFGEVLEISGKDCVQEVTKADEVQWV

Parental  IILLYRSSIPMCLLVNQHLSLLARKFPETKFVKAIVNSCIQHYHDNCLPTIFVYKNGQIEGKFIGIIECG
          I..LY...IP.C.L.NQ..S.LARKFP..KF.KAI..SCI..Y.D..LPTIFVY..G.I...FIG....G
Retrocopy ILHLYKQGIPLCTLINQQYSELARKFPDVKFIKAISMSCIPNYPDRNLPTIFVYLEGDIRAQFIGPLVFG

Parental  GINL
          G.NL
Retrocopy GMNL

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_562 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 5 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012692	3 retrocopies	retro_chof_1554, retro_chof_562 , retro_chof_737,
Echinops telfairi	ENSETEG00000000666	1 retrocopy	retro_etel_1568,
Gorilla gorilla	ENSGGOG00000007908	1 retrocopy	retro_ggor_2890,
Monodelphis domestica	ENSMODG00000020680	2 retrocopies	retro_mdom_1048, retro_mdom_993,
Pan troglodytes	ENSPTRG00000016073	7 retrocopies	retro_ptro_148, retro_ptro_1810, retro_ptro_1865, retro_ptro_2402, retro_ptro_2690, retro_ptro_2784, retro_ptro_675,