RetrogeneDB ID: retro_chof_900

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_165120:3448..4050(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB2B
• Ensembl ID: ENSCHOG00000000710
• Aliases: None
• Description: RAB2B, member RAS oncogene family [Source:HGNC Symbol;Acc:20246]

Sequence

>retro_chof_900
ATGACTTATGCTTATCTCTTCAAGTACATCATCATTGGAGACACAGGTGTGGGCAAACCATGTCTCTTTCTGCAGTTTAC
TGACAAACAGTTCCAGCCTGTTCACAACCTCACAATTGGTGTGGAGTTTGGTGCCCATATGGTCAACATTGATGGAAGAC
AAATCAAACTGCAAATCTGAGATACGGCTGGACAAGAATCCTTCCATTCTATCACCCATTCCTACTACAGGGGAGCAGCT
GGAGCACTGCTGGTGTACGACATTACAAGGCGTGAAACCTTCAGTCACCTCACCTCATGGTTAGAGGATGCCCGGTAACG
CTCCAGCTCCAATATGGTTATCATGTTGATTGGGAATAAGAGTGACCTAGAGTCCTGCAGGTATGTAAAGAGAGAAGAAG
GATAGGCCTTCTTCAAGAGGAGCTTGGACTTATATTCATGGAGACTTCAGCCAAAACAGCTTCCAATGTTGAAGAGGCCT
TCATTAACACAGCCAAAGAAATATATAGGAAGATCCAGCAGGGTTTATTTGATGTTCACAACGAGGCAAATGGTGTCAAG
ATTGGGCCCCAGCAGCCAATTTCAACATCCGTGGGACCCTGC

Alignment

ORF - retro_chof_900 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTYAYLFKYIIIGDTGVGKSCLLLQFTDKRLQPAHDLTIGVEFGARMVNIDGKQIKLQIWDTAGQESFRS
          MTYAYLFKYIIIGDTGVGK.CL.LQFTDK..QP.H.LTIGVEFGA.MVNIDG.QIKLQI.DTAGQESF.S
Retrocopy MTYAYLFKYIIIGDTGVGKPCLFLQFTDKQFQPVHNLTIGVEFGAHMVNIDGRQIKLQI*DTAGQESFHS

Parental  ITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSSSNMVIMLIGNKSDLESRRDVKREEGEAF-AQ
          IT.SYYRGAAGALLVYDITRRETF.HLTSWLEDAR..SSSNMVIMLIGNKSDLES.R.VKREEG.AF..Q
Retrocopy ITHSYYRGAAGALLVYDITRRETFSHLTSWLEDAR*RSSSNMVIMLIGNKSDLESCRYVKREEG*AF<LQ

Parental  EH-GLIFMETSAKTASNVEEAFINTAKEIYRKIQQGLFDVHNEGFSVPQQNSRDLGYNSGCC
          E..GLIFMETSAKTASNVEEAFINTAKEIYRKIQQGLFDVHNE...V............G.C
Retrocopy EELGLIFMETSAKTASNVEEAFINTAKEIYRKIQQGLFDVHNEANGVKIGPQQPISTSVGPC

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_900 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.

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000044207	1 retrocopy	retro_btau_991,
Canis familiaris	ENSCAFG00000005641	1 retrocopy	retro_cfam_1510,
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,
Cavia porcellus	ENSCPOG00000026575	1 retrocopy	retro_cpor_839,
Macropus eugenii	ENSMEUG00000010489	2 retrocopies	retro_meug_2160, retro_meug_91,
Myotis lucifugus	ENSMLUG00000001902	3 retrocopies	retro_mluc_1243, retro_mluc_1251, retro_mluc_2103,
Sorex araneus	ENSSARG00000004969	1 retrocopy	retro_sara_97,
Ictidomys tridecemlineatus	ENSSTOG00000001886	1 retrocopy	retro_itri_468,