RetrogeneDB ID: retro_chof_1582

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_330921:296..950(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000002774
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB11B
• Ensembl ID: ENSCHOG00000013525
• Aliases: None
• Description: RAB11B, member RAS oncogene family [Source:HGNC Symbol;Acc:9761]

Sequence

>retro_chof_1582
ATGGGGACCCAGGACAACGAGTACTACTACTATTCAAAGTAGTGCTCACTGGGGACTCGGGCATGGGGAAGAGCAACCTG
CTCTCATGTGTCACCCGCAGTGAGTTCAATCTGGAGAGCAAGAGCATCATCAGTGTGGAGTTCGCCAACTGCAGCATCCA
GGTGGACAGCAAGACCATCAAGGCGCAGATGTGGGACATGGCTGGCCAGGAGTGCTAACTGTGCCATCACCTCCGTGTAC
TACTGTGGCAAAGTGGGCATGCTGCTGGTGCATGACATCGCCAAGCACCTGACATATGAGAACACGGAGCACTGGCTGAA
GGATCTGCAGGACTATGCAGACGGCAACATCGTCATCATGCTGGTGGGCAACAAAAGCGACCTGCACCACCTGCAGGCTG
TGTCCACTGATGAGGCCCATGCCATCGCCGAAAAATACAACTTGTCCTTCATTGAGACCTCAGCCTTGGATTCCACCAAT
GTAGAGGAAGCTTGCAAGAACATCCTTACAGAGATCTACCACATTGTGTTACAGAAGCAGATCACCGATAGCGCCGCCCA
TGACGAGTCCCCCAGCAACAACGTGGTGGACATTAGCGTGCCACCCACCACTGACAGACAGAAACCCAACAAGCTGCAGT
GCTGCCAGAACCTG

Alignment

ORF - retro_chof_1582 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGTRDDEYDY-LFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDGKTIKAQIWDTAG
          MGT.D.EY.Y.LFKVVL.GDSG.GKSNLLS..TR.EFNLESKS.I.VEFA..SIQVD.KTIKAQ.WD.AG
Retrocopy MGTQDNEYYY<LFKVVLTGDSGMGKSNLLSCVTRSEFNLESKSIISVEFANCSIQVDSKTIKAQMWDMAG

Parental  -QERYRAITSAYYRGAVGALL--DIAKLLMYENA-CWLKDM-DHAYSLLNILLEVDMSDLFTLLE-ATDL
          ......AITS.YY.G.VG.LL..DIAK.L.YEN...WLKD..D.A.....I.L....SDL..L....TD.
Retrocopy >RSANCAITSVYYCGKVGMLLVHDIAKHLTYENTEHWLKDLQDYADGNIVIMLVGNKSDLHHLQAVSTDE

Parental  ERCXXXKNNLSFIETSALDSTNVEEAFKNILTEIYRIVSQKQIADRAAHDESPGNNVVDISVPPTTDGQK
          ......K.NLSFIETSALDSTNVEEA.KNILTEIY.IV.QKQI.D.AAHDESP.NNVVDISVPPTTD.QK
Retrocopy AHAIAEKYNLSFIETSALDSTNVEEACKNILTEIYHIVLQKQITDSAAHDESPSNNVVDISVPPTTDRQK

Parental  PNKLQCCQNL
          PNKLQCCQNL
Retrocopy PNKLQCCQNL

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_1582 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 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000710	3 retrocopies	retro_chof_2314, retro_chof_706, retro_chof_900,
Choloepus hoffmanni	ENSCHOG00000003669	1 retrocopy	retro_chof_2175,
Choloepus hoffmanni	ENSCHOG00000013525	1 retrocopy	retro_chof_1582 ,
Choloepus hoffmanni	ENSCHOG00000013866	5 retrocopies	retro_chof_1017, retro_chof_1761, retro_chof_2377, retro_chof_64, retro_chof_703,
Callithrix jacchus	ENSCJAG00000010778	2 retrocopies	retro_cjac_3866, retro_cjac_3917,
Erinaceus europaeus	ENSEEUG00000009165	2 retrocopies	retro_eeur_284, retro_eeur_565,
Mus musculus	ENSMUSG00000077450	1 retrocopy	retro_mmus_1846,
Otolemur garnettii	ENSOGAG00000003227	1 retrocopy	retro_ogar_2405,
Petromyzon marinus	ENSPMAG00000009335	1 retrocopy	retro_pmar_25,
Pteropus vampyrus	ENSPVAG00000009645	1 retrocopy	retro_pvam_64,
Tupaia belangeri	ENSTBEG00000000667	1 retrocopy	retro_tbel_4634,