RetrogeneDB ID: retro_chof_2175

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_55536:8344..8677(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB14
• Ensembl ID: ENSCHOG00000003669
• Aliases: None
• Description: RAB14, member RAS oncogene family [Source:HGNC Symbol;Acc:16524]

Sequence

>retro_chof_2175
TTAGCAGATGCCAGAATGCTAGCAAGTCAAAACATTGTGATCATCCTCTGTGGAAACAAGAAGGATCTGGATGCAGATCG
TGAAGTTACATTCTTAGAAGCTTCCAGATTCGCTCAAGAAAATGAGCTGACGTTTTTGGAAACAAGTGCACTAACAGGGG
AGAATGTAGAAGAGGCCTTTGTACAGTGTGCAAGAAAAATACTTAACAAAATTGAATCAGGTGAGCTGGATCCAGAAAGA
ATGGGCTCAGGAATTCAGTATGGAGATGCTGCCTTGAGACAGCTGAGGTCACCGCGGCGTGCACAAGCCCAGAGTGCCCA
AGAATGCGGCTGT

Alignment

ORF - retro_chof_2175 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.45 %
• Parental protein coverage: 50.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTDARNLTNPNTVIILIGNKADLEAQRDVTYEEAKQFA-ENGLLFLEASAKTGENVEDAFLEAAKKIYQN
          L.DAR.L...N.VIIL.GNK.DL.A.R.VT..EA..FA.EN.L.FLE.SA.TGENVE.AF...A.KI...
Retrocopy LADARMLASQNIVIILCGNKKDLDADREVTFLEASRFAQENELTFLETSALTGENVEEAFVQCARKILNK

Parental  IQDGSLDLNAAESGVQHKPSAPQGGRLTSEPQPQ-REGCGC
          I..G.LD.....SG.Q....A....R.....Q.Q....CGC
Retrocopy IESGELDPERMGSGIQYGDAALRQLRSPRRAQAQSAQECGC

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_2175 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 10 parental genes, and 16 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,
Cavia porcellus	ENSCPOG00000006688	1 retrocopy	retro_cpor_1081,
Myotis lucifugus	ENSMLUG00000009818	1 retrocopy	retro_mluc_1875,
Oryctolagus cuniculus	ENSOCUG00000013654	1 retrocopy	retro_ocun_1667,
Otolemur garnettii	ENSOGAG00000012973	1 retrocopy	retro_ogar_710,
Pelodiscus sinensis	ENSPSIG00000003919	1 retrocopy	retro_psin_66,
Sarcophilus harrisii	ENSSHAG00000017800	1 retrocopy	retro_shar_80,