RetrogeneDB ID: retro_ogar_1981

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873579.1:409669..410264(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000026473
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SAR1A
• Ensembl ID: ENSOGAG00000005040
• Aliases: None
• Description: SAR1 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:10534]

Sequence

>retro_ogar_1981
ATGTCCTTCATCTTTGAATGGATCTACAATGGCTTCAGAAGTGTGCTCCAGTGCCTAAGATTCTACAAAAAATCTGGAAA
ACTTGTATTCTTGGGTTTGGACAATGCAGGCAAAACCACTCTTCTTCACATGCTCAAAGATGACAGATTGGGCCAACAAC
GTTCCAACACTGCATCCGACATCAGACGAGCTGACAATTGCTGGCATGACTATTACAACTTTCAATCTTGTTGGGCATGA
GCAAGCACATTGGGTTTGGAAAAATTATCTCCCGGCAGTTAAAGGGATTGTCTTCCTGGTGGACTGTGCAGATCATTCTT
GCCTCATGGAATCCAAAGTTGAGCTTAATGCTTTAATGACTGATGAAACAATATCCAATGTGCCAATCCTTATCTTGGGT
AACAAAATTGACAGAACAGATGCAATCAGTGAAGAAAAACTCTGTGAGATTTTTGGGCTTAATGGACAGACCACAGGAAA
GGGGAATGTGACCCTGAAGGAGCTGAATGCCCGCCCCCTGGAAGTGTTCATGTGCAGCGTGCTCAAGAGGCGAGGTTACG
GCGAGGGTTTCCGCTGGCTCTCCCAGTATATTGAC

Alignment

ORF - retro_ogar_1981 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.45 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSFIFEWIYNGFSSVLQFLGLYKKSGKLVFLGLDNAGKTTLLHMLKDDRLGQ-HVPTLHPTSEELTIAGM
          MSFIFEWIYNGF.SVLQ.L..YKKSGKLVFLGLDNAGKTTLLHMLKDDRLGQ..VPTLHPTS.ELTIAGM
Retrocopy MSFIFEWIYNGFRSVLQCLRFYKKSGKLVFLGLDNAGKTTLLHMLKDDRLGQ>NVPTLHPTSDELTIAGM

Parental  TFTTFDLGGHEQARRVWKNYLPAINGIVFLVDCADHSRLMESKVELNALMTDETISNVPILILGNKIDRT
          T.TTF.L.GHEQA..VWKNYLPA..GIVFLVDCADHS.LMESKVELNALMTDETISNVPILILGNKIDRT
Retrocopy TITTFNLVGHEQAHWVWKNYLPAVKGIVFLVDCADHSCLMESKVELNALMTDETISNVPILILGNKIDRT

Parental  DAISEEKLREIFGLYGQTTGKGNVTLKELNARPMEVFMCSVLKRQGYGEGFRWLSQYID
          DAISEEKL.EIFGL.GQTTGKGNVTLKELNARP.EVFMCSVLKR.GYGEGFRWLSQYID
Retrocopy DAISEEKLCEIFGLNGQTTGKGNVTLKELNARPLEVFMCSVLKRRGYGEGFRWLSQYID

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_1981 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 13 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016353	5 retrocopies	retro_cjac_1006, retro_cjac_2242, retro_cjac_2305, retro_cjac_4081, retro_cjac_957,
Homo sapiens	ENSG00000079332	4 retrocopies	retro_hsap_2976, retro_hsap_3568, retro_hsap_4714, retro_hsap_639,
Gorilla gorilla	ENSGGOG00000024879	3 retrocopies	retro_ggor_144, retro_ggor_2408, retro_ggor_2929,
Myotis lucifugus	ENSMLUG00000006626	2 retrocopies	retro_mluc_1317, retro_mluc_1996,
Nomascus leucogenys	ENSNLEG00000011243	4 retrocopies	retro_nleu_1987, retro_nleu_2231, retro_nleu_2311, retro_nleu_2759,
Otolemur garnettii	ENSOGAG00000005040	3 retrocopies	retro_ogar_1447, retro_ogar_1981 , retro_ogar_2467,
Otolemur garnettii	ENSOGAG00000013347	1 retrocopy	retro_ogar_2472,
Pongo abelii	ENSPPYG00000002374	4 retrocopies	retro_pabe_2468, retro_pabe_2940, retro_pabe_3661, retro_pabe_565,
Pan troglodytes	ENSPTRG00000002584	4 retrocopies	retro_ptro_2011, retro_ptro_2423, retro_ptro_3133, retro_ptro_465,
Ictidomys tridecemlineatus	ENSSTOG00000012780	2 retrocopies	retro_itri_1191, retro_itri_590,
Tupaia belangeri	ENSTBEG00000008657	5 retrocopies	retro_tbel_1060, retro_tbel_14, retro_tbel_2319, retro_tbel_2366, retro_tbel_2846,
Tarsius syrichta	ENSTSYG00000005955	2 retrocopies	retro_tsyr_1204, retro_tsyr_2099,
Vicugna pacos	ENSVPAG00000002631	2 retrocopies	retro_vpac_5, retro_vpac_77,