RetrogeneDB ID: retro_ogar_3263

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873758.1:110186..110663(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CASP3
• Ensembl ID: ENSOGAG00000005985
• Aliases: None
• Description: caspase 3, apoptosis-related cysteine peptidase [Source:HGNC Symbol;Acc:1504]

Sequence

>retro_ogar_3263
TTGAGCTATGGTGAAGAAGGAATAATTTGGGGGACAATGGACCTGTTGACCTGAAAAAAATAACAAGTTTCTTCAGAGGG
GATGATTGTAGAAGTCTAACTAGAAAACCCAAACTTTTCATTATTCAGGCCTGCTGAGGTACAGAACTGGACTGTGGCAT
TGAGACAGATAGTGGTGCTGAGGATGACATGGCATGTCAGAAAATACTGATGGAGGCTGACTTCCTGTATGCTAACTCCA
CACAGCCTGGTTACTATTCCTGGCGAAACTCAAAGAATAGCTCCTGGATGGTTCCAGTCGCTTTGCACCATGCTGAAACC
GTATGCTCACAAGCTCAAGTTTATGCACATTCTCACCCAGGTGAACCCAAAGGCAGCAACAGAATTTAAATCCTTTTCCT
TTGACTCTACTTTTCATGCAAAGAAACAGATTCCATGTATTGTGTCCATACTCACAAAAGACCTGTATTTTTATCAC

Alignment

ORF - retro_ogar_3263 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.09 %
• Parental protein coverage: 57.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LSHGEEGIIFGT-NGPVDLKKITSFFRGDYCRSLTGKPKLFIIQACRGTELDCGIETDSGTEDDMACQKI
          LS.GEEGII.GT.NGPVDLKKITSFFRGD.CRSLT.KPKLFIIQAC.GTELDCGIETDSG.EDDMACQKI
Retrocopy LSYGEEGIIWGT<NGPVDLKKITSFFRGDDCRSLTRKPKLFIIQAC*GTELDCGIETDSGAEDDMACQKI

Parental  PVEADFLYAYSTAPGYYSWRNSKDGSWFI-QSLCAMLKLYAHKLEFMHILTRVNRKVATEFESFSFDSTF
          ..EADFLYA.ST.PGYYSWRNSK..SW...QSLC.MLK.YAHKL.FMHILT.VN.K.ATEF.SFSFDSTF
Retrocopy LMEADFLYANSTQPGYYSWRNSKNSSWMV>QSLCTMLKPYAHKLKFMHILTQVNPKAATEFKSFSFDSTF

Parental  HAKKQIPCIVSMLTKDLYFYH
          HAKKQIPCIVS.LTKDLYFYH
Retrocopy HAKKQIPCIVSILTKDLYFYH

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_3263 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000012511	2 retrocopies	retro_cpor_1203, retro_cpor_1450,
Dasypus novemcinctus	ENSDNOG00000013931	1 retrocopy	retro_dnov_1013,
Microcebus murinus	ENSMICG00000004809	2 retrocopies	retro_mmur_1389, retro_mmur_691,
Macaca mulatta	ENSMMUG00000012053	1 retrocopy	retro_mmul_114,
Otolemur garnettii	ENSOGAG00000005985	2 retrocopies	retro_ogar_1756, retro_ogar_3263 ,
Rattus norvegicus	ENSRNOG00000010475	1 retrocopy	retro_rnor_2747,
Sarcophilus harrisii	ENSSHAG00000009178	1 retrocopy	retro_shar_404,
Ictidomys tridecemlineatus	ENSSTOG00000003865	2 retrocopies	retro_itri_172, retro_itri_586,