RetrogeneDB ID: retro_chof_2293

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_63884:4662..4997(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF1
• Ensembl ID: ENSCHOG00000008378
• Aliases: None
• Description: eukaryotic translation initiation factor 1 [Source:HGNC Symbol;Acc:3249]

Sequence

>retro_chof_2293
ATGTCCACTATCCAGAACCTCCAATCTTTTGATCCCTTTGCTGATGCAACTAAGGGTGACAACTTACTCCTGGCGAGGGC
TGAGGACTACATTCATATAAAAATCCACCAATGAAATGGCAGAAAGACATTGACTACTGTTCAGGGCATTGCAGATGATT
ATGACAAAAAGAAACTTGTGAAAGCTTTCAAAAGTAATCTGCCTGTAATGGAACTGTGATTGAACATCCTGAACACAGAG
AGGTTATTCAGCTTCAAGGTGACCAAAGAAAAAACATTTGCCAGTTTCTCTTGGAGGTTGACCTTGTTGAGGTGGAACAG
CTTAAGGTTCATGGA

Alignment

ORF - retro_chof_2293 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.88 %
• Parental protein coverage: 99.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSAIQNLHSFDPFADASKDDDLLPAGTEDYIHIRNQQRNGRKTLTTVQGIADDYDKKKLVKAFKKKF-AC
          MS.IQNL.SFDPFADA.K.D.LL.A..EDYIHI...Q.NGRKTLTTVQGIADDYDKKKLVKAFK....AC
Retrocopy MSTIQNLQSFDPFADATKGDNLLLARAEDYIHIKIHQ*NGRKTLTTVQGIADDYDKKKLVKAFKSNL<AC

Parental  NGTVIEHPEYGEVIQLQGDQRKNICQFLVEIGLAKDDQLKVHG
          NGTVIEHPE..EVIQLQGDQRKNICQFL.E..L....QLKVHG
Retrocopy NGTVIEHPEHREVIQLQGDQRKNICQFLLEVDLVEVEQLKVHG

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_2293 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 6 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008378	7 retrocopies	retro_chof_1435, retro_chof_170, retro_chof_2236, retro_chof_2293 , retro_chof_2625, retro_chof_320, retro_chof_708,
Dipodomys ordii	ENSDORG00000013853	4 retrocopies	retro_dord_349, retro_dord_350, retro_dord_663, retro_dord_753,
Rattus norvegicus	ENSRNOG00000032769	1 retrocopy	retro_rnor_520,
Rattus norvegicus	ENSRNOG00000033765	15 retrocopies	retro_rnor_1088, retro_rnor_1347, retro_rnor_1518, retro_rnor_1744, retro_rnor_1971, retro_rnor_2067, retro_rnor_2171, retro_rnor_2203, retro_rnor_2532, retro_rnor_2548, retro_rnor_2579, retro_rnor_45, retro_rnor_532, retro_rnor_571, retro_rnor_65,
Sorex araneus	ENSSARG00000006287	1 retrocopy	retro_sara_36,
Sarcophilus harrisii	ENSSHAG00000005729	1 retrocopy	retro_shar_42,