RetrogeneDB ID: retro_ogar_1160

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873537.1:17329657..17329975(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL36A-HNRNPH2
• Ensembl ID: ENSOGAG00000004551
• Aliases: None
• Description: RPL36A-HNRNPH2 readthrough [Source:HGNC Symbol;Acc:48349]

Sequence

>retro_ogar_1160
GCCAATAGTGCTCCTACAAACATAGGGAACGTTACTAAAATCCACCAGACTTTATGTGAAAGTTGTGGCAAATACCAACT
CCACATAATGACAAAATACAAGAAGAACAAAGGTTTTCTGTATCCCCAGAGAAAGAAGCATTATGACAAAAAATCAGAGT
AGCTATGGTGGGGCAGTCTAAGACTATTTTCTGAGGGGGGGGGATAAAACTATAAAAAAGATTGTTCTGAGGTTCGAATA
CATTGAGATCAACTGTAGATCTAGAGAATGCTGGCTATTAGGAGATGCAAGCATTCTGAACTGGGAGGACATAAAAAG

Alignment

ORF - retro_ogar_1160 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.48 %
• Parental protein coverage: 93.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ADSARANMVNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRK-QSGYGGQTKPIF-RKKAK
          A.SA..N..NV.K...T.C..CGK.Q.H..T.YKK.K..LY.Q.K..YD.K.QS.YGG.....F.....K
Retrocopy ANSAPTNIGNVTKIHQTLCESCGKYQLHIMTKYKKNKGFLYPQRKKHYDKK>QSSYGGAV*DYFLXXXXK

Parental  TTKKIVLRLECVEPNCRSK-RMLAIKRCKHFELGGDKK
          T.KKIVLR.E..E.NCRS..RMLAI.RCKH.ELGG.KK
Retrocopy TIKKIVLRFEYIEINCRSR<RMLAIRRCKHSELGGHKK

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_1160 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 11 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008503	1 retrocopy	retro_acar_98,
Ailuropoda melanoleuca	ENSAMEG00000009384	1 retrocopy	retro_amel_85,
Callithrix jacchus	ENSCJAG00000004864	4 retrocopies	retro_cjac_304, retro_cjac_353, retro_cjac_55, retro_cjac_72,
Equus caballus	ENSECAG00000015464	9 retrocopies	retro_ecab_129, retro_ecab_131, retro_ecab_204, retro_ecab_219, retro_ecab_265, retro_ecab_268, retro_ecab_294, retro_ecab_543, retro_ecab_646,
Homo sapiens	ENSG00000257529	1 retrocopy	retro_hsap_1353,
Monodelphis domestica	ENSMODG00000025578	2 retrocopies	retro_mdom_1878, retro_mdom_971,
Nomascus leucogenys	ENSNLEG00000007540	27 retrocopies	retro_nleu_1003, retro_nleu_1243, retro_nleu_1291, retro_nleu_153, retro_nleu_157, retro_nleu_1632, retro_nleu_178, retro_nleu_1833, retro_nleu_1903, retro_nleu_1959, retro_nleu_2145, retro_nleu_2345, retro_nleu_2381, retro_nleu_2699, retro_nleu_2965, retro_nleu_2995, retro_nleu_2996, retro_nleu_3027, retro_nleu_3028, retro_nleu_3059, retro_nleu_3111, retro_nleu_385, retro_nleu_453, retro_nleu_644, retro_nleu_805, retro_nleu_842, retro_nleu_991,
Otolemur garnettii	ENSOGAG00000004551	6 retrocopies	retro_ogar_1160 , retro_ogar_1681, retro_ogar_2390, retro_ogar_2519, retro_ogar_294, retro_ogar_470,
Pteropus vampyrus	ENSPVAG00000001569	1 retrocopy	retro_pvam_17,
Rattus norvegicus	ENSRNOG00000011494	1 retrocopy	retro_rnor_259,
Sarcophilus harrisii	ENSSHAG00000013479	1 retrocopy	retro_shar_467,