RetrogeneDB ID: retro_chof_1963

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_434675:464..841(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4E2
• Ensembl ID: ENSCHOG00000013109
• Aliases: None
• Description: eukaryotic translation initiation factor 4E family member 2 [Source:HGNC Symbol;Acc:3293]

Sequence

>retro_chof_1963
ATAAACAACAAGTTCGATGCCTTGAAAGATGATGGCAGTGGGGACCATGATCAGAATGAAGAAAACAGCACACAGAAAGA
TGGTGAGAAGGAAAAAATGGAACAAGACAAGAGTCAGAGCAGCAGCAGCAAGAGGAAGGCTCTTGTCCCAGGACCAGCAG
AGCATCCTCTGCAGTACAACTACACTTTCTGGTACTCCAGGAGGACCCCCGGCCATCCCACCAGCTCACAGATCTATAAA
CAGAATACAAGCAGATCAGCACCCTTGCCTCTGTGGAGCAGTTCTGGAGGTTTTACTGCCACATAGTGTGTCCTGGGGAC
CTGATAGGGCACAGTGACTTCCATCTCTTCTAAGAAGGCATTAAGCCCACGTGGGAA

Alignment

ORF - retro_chof_1963 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.25 %
• Parental protein coverage: 51.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNNKFDALKDDDSGDHDQNEENSTQKDGEKEKTERDKSQSSS-KRKAVVPGPAEHPLQYNYTFWYSRRTP
          .NNKFDALKDD.SGDHDQNEENSTQKDGEKEK.E.DKSQSSS.KRKA.VPGPAEHPLQYNYTFWYSRRTP
Retrocopy INNKFDALKDDGSGDHDQNEENSTQKDGEKEKMEQDKSQSSSSKRKALVPGPAEHPLQYNYTFWYSRRTP

Parental  GRPTSSQSYEQN-IKQIGTFASVEQFWRFYSHMVRPGDLTGHSDFHLFKEGVKPMWE
          G.PTSSQ.Y.QN..KQI.T.ASVEQFWRFY.H.V.PGDL.GHSDFHLF.EG.KP.WE
Retrocopy GHPTSSQIYKQN<YKQISTLASVEQFWRFYCHIVCPGDLIGHSDFHLF*EGIKPTWE

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_1963 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 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016456	1 retrocopy	retro_amel_1304,
Canis familiaris	ENSCAFG00000011328	1 retrocopy	retro_cfam_183,
Choloepus hoffmanni	ENSCHOG00000009450	9 retrocopies	retro_chof_1177, retro_chof_1219, retro_chof_124, retro_chof_1319, retro_chof_1551, retro_chof_200, retro_chof_604, retro_chof_918, retro_chof_992,
Choloepus hoffmanni	ENSCHOG00000013109	3 retrocopies	retro_chof_1963 , retro_chof_369, retro_chof_567,
Callithrix jacchus	ENSCJAG00000013786	2 retrocopies	retro_cjac_1061, retro_cjac_2717,
Echinops telfairi	ENSETEG00000007930	1 retrocopy	retro_etel_1385,
Microcebus murinus	ENSMICG00000015082	2 retrocopies	retro_mmur_806, retro_mmur_975,
Myotis lucifugus	ENSMLUG00000011269	1 retrocopy	retro_mluc_60,
Mustela putorius furo	ENSMPUG00000005206	2 retrocopies	retro_mputfur_110, retro_mputfur_1554,
Otolemur garnettii	ENSOGAG00000009155	1 retrocopy	retro_ogar_104,
Sarcophilus harrisii	ENSSHAG00000013108	1 retrocopy	retro_shar_101,