RetrogeneDB ID: retro_ogar_1710

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873562.1:11434273..11434651(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPCS3
• Ensembl ID: ENSOGAG00000003825
• Aliases: None
• Description: signal peptidase complex subunit 3 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:26212]

Sequence

>retro_ogar_1710
GCCTTCTCGCTGAGCATGCTGGCAGCATTCACTGTTAGCCGCTTCATCACCACTGCCTTCCAAGACAGGAGTGATCGGCT
GCACATGCTGCAGATCATGCTATAACATGTAGACTTCACCGGGCCTGGAGAAAGGAGTGGTCTGGGATTCATTGCATTTG
ATATAACTGCTGATCTGGAGAATATATTTGAGTGGAATGTTAAGCAATTGTTTATTTATCAGCAGAATATTCAGGAAAAA
AATGATCTAACCCAAGTTGTCTTATGGGACAAGATTATTCTGAGAGGTGATAATCTGAAGCTGCTGCTGAAAAATGCAAA
AACACTTTTTCTTTGACAATGAAATGGTCTCAAGGAAAACAGGAATGTCACTTTGACA

Alignment

ORF - retro_ogar_1710 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.92 %
• Parental protein coverage: 73.89 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AFSLSVMAALTFGCFITTAFKDRSVPVRLHVSRIMLKNVEDFTGPRERSDLGFITFDITADLENIFDWNV
          AFSLS..AA.T...FITTAF.DRS...RLH...IML..V.DFTGP.ERS.LGFI.FDITADLENIF.WNV
Retrocopy AFSLSMLAAFTVSRFITTAFQDRSD--RLHMLQIML*HV-DFTGPGERSGLGFIAFDITADLENIFEWNV

Parental  KQLFLYLSAEYSTKNNALNQVVLWDKIVLRGDNPKLLLKDMKTKYFFFDDGNGLKGNRNVTLT
          KQLF.Y.........N.L.QVVLWDKI.LRGDN.KLLLK..KT...F....NGLK.NRNVTLT
Retrocopy KQLFIY--QQNIQEKNDLTQVVLWDKIILRGDNLKLLLKNAKT--LFL*Q*NGLKENRNVTLT

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_1710 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000029741	1 retrocopy	retro_ocun_119,
Otolemur garnettii	ENSOGAG00000003825	1 retrocopy	retro_ogar_1710 ,
Pongo abelii	ENSPPYG00000015218	1 retrocopy	retro_pabe_138,
Sarcophilus harrisii	ENSSHAG00000015012	1 retrocopy	retro_shar_481,
Ictidomys tridecemlineatus	ENSSTOG00000013678	1 retrocopy	retro_itri_57,