RetrogeneDB ID: retro_ogar_2842

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873671.1:42172..42820(-)
• Located in intron of: ENSOGAG00000012575

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS2
• Ensembl ID: ENSOGAG00000010098
• Aliases: None
• Description: ribosomal protein S2 [Source:HGNC Symbol;Acc:10404]

Sequence

>retro_ogar_2842
ATGGCAGATGACACCAGTGCAACAGGAGGCCTGGAGGCCCCGGGGGCCCTGGAATGAGAGGCCATGGTGGTTTCTATGCA
GGCTTCGGCAGCGGCATTCAGGGCTGGGGTCACAGACATGGTTGGGGCTGAGGCCGCAGAGCTTGTGGAGTCAAGGCCAA
GGCCGAAGAGTGGAAGCCTGTCACCAAGCTGGGCCGCCTGGTCAAGGACATGAAGATGAAATCCCTGGAGGAGATCTATC
TCTTCTCCCTGCCCATTAAGGAATCTGAGATCATTGATTTTTTCTTGGGGGCATCTCTCAAGGATGAGGTTTTGAAGATT
ATGCCAGTGCAAAAGTAGACCTGTGCTGGTCAGTGGATCAGGTTCAATGTGTTTGTTGCCACTGGGGACTACAATGGCCA
TGTCAGTCTGGGTGTTAAGTGGTCCAGGGAAGTAGCCACTGCCATCAAGGGGTCATCATCCTGGCCAAGTTCTCTACTGT
CCCAGAGAGAGGCTACTGGGGGAACAAGACTGGCAAGCCCCAGACTGTTCCTTGCAAGGTAACAGGCCACTGTGGCTCTG
TGCTGGTACGTCTCATCCCTGCTTCTAGAGGAACTGGCCTGTCTCAGCGCCCGTGCCTAAGAAGCTGCTAATGATGTCTG
GGACTGAT

Alignment

ORF - retro_ogar_2842 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.58 %
• Parental protein coverage: 75.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MADDAGAAGG-PGGPGGPGMGGRGGFRGGFGSGIRGRGRGRGRGRGRGRGARGGKAEDKEWMPVTKLGRL
          MADD..A.GG.PGGPGGPGM.G.GGF..GFGSGI.G.G...G.G.GR...A.G.KA...EW.PVTKLGRL
Retrocopy MADDTSATGG<PGGPGGPGMRGHGGFYAGFGSGIQGWGHRHGWG*GRR--ACGVKAKAEEWKPVTKLGRL

Parental  VKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDYNGHVGL
          VKDMK.KSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQK.T.AGQ..RF..FVA.GDYNGHV.L
Retrocopy VKDMKMKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQK*TCAGQWIRFNVFVATGDYNGHVSL

Parental  GVKCSKEVATAIRGA-IILAKLSIVPVRRGYWGNKIGKPHTVPCKVTGRCGSVLVRLIPAPRGTGI-VSA
          GVK.S.EVATAI.G..IILAK.S.VP..RGYWGNK.GKP.TVPCKVTG.CGSVLVRLIPA.RGTG..VSA
Retrocopy GVKWSREVATAIKGS<IILAKFSTVP-ERGYWGNKTGKPQTVPCKVTGHCGSVLVRLIPASRGTGL<VSA

Parental  PVPKKLLMMAGID
          PVPKKLLMM.G.D
Retrocopy PVPKKLLMMSGTD

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_2842 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 9 parental genes, and 139 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002549	1 retrocopy	retro_acar_57,
Felis catus	ENSFCAG00000029191	6 retrocopies	retro_fcat_1245, retro_fcat_1328, retro_fcat_1606, retro_fcat_1610, retro_fcat_1737, retro_fcat_517,
Homo sapiens	ENSG00000140988	47 retrocopies	retro_hsap_1060, retro_hsap_136, retro_hsap_140, retro_hsap_141, retro_hsap_1443, retro_hsap_1444, retro_hsap_1457, retro_hsap_1463, retro_hsap_148, retro_hsap_1648, retro_hsap_1688, retro_hsap_1722, retro_hsap_1812, retro_hsap_1830, retro_hsap_1831, retro_hsap_1838, retro_hsap_1845, retro_hsap_1897, retro_hsap_1953, retro_hsap_1965, retro_hsap_1971, retro_hsap_2124, retro_hsap_2198, retro_hsap_2424, retro_hsap_244, retro_hsap_2483, retro_hsap_2486, retro_hsap_250, retro_hsap_282, retro_hsap_2871, retro_hsap_3035, retro_hsap_3097, retro_hsap_3106, retro_hsap_3182, retro_hsap_3211, retro_hsap_3369, retro_hsap_3464, retro_hsap_3584, retro_hsap_3779, retro_hsap_385, retro_hsap_4094, retro_hsap_4290, retro_hsap_435, retro_hsap_4811, retro_hsap_754, retro_hsap_761, retro_hsap_970,
Macropus eugenii	ENSMEUG00000004508	2 retrocopies	retro_meug_156, retro_meug_2103,
Microcebus murinus	ENSMICG00000012765	28 retrocopies	retro_mmur_1192, retro_mmur_1273, retro_mmur_1283, retro_mmur_1296, retro_mmur_1407, retro_mmur_1417, retro_mmur_1440, retro_mmur_153, retro_mmur_1613, retro_mmur_205, retro_mmur_210, retro_mmur_226, retro_mmur_230, retro_mmur_259, retro_mmur_266, retro_mmur_463, retro_mmur_672, retro_mmur_698, retro_mmur_742, retro_mmur_802, retro_mmur_824, retro_mmur_829, retro_mmur_875, retro_mmur_953, retro_mmur_966, retro_mmur_969, retro_mmur_981, retro_mmur_99,
Monodelphis domestica	ENSMODG00000016077	1 retrocopy	retro_mdom_536,
Otolemur garnettii	ENSOGAG00000010098	19 retrocopies	retro_ogar_1051, retro_ogar_1120, retro_ogar_1205, retro_ogar_1557, retro_ogar_1821, retro_ogar_1835, retro_ogar_1837, retro_ogar_1851, retro_ogar_2101, retro_ogar_2164, retro_ogar_2313, retro_ogar_2648, retro_ogar_2817, retro_ogar_2842 , retro_ogar_2965, retro_ogar_3109, retro_ogar_3177, retro_ogar_3180, retro_ogar_794,
Sarcophilus harrisii	ENSSHAG00000015213	5 retrocopies	retro_shar_186, retro_shar_288, retro_shar_456, retro_shar_525, retro_shar_783,
Tupaia belangeri	ENSTBEG00000006726	30 retrocopies	retro_tbel_1023, retro_tbel_1059, retro_tbel_1105, retro_tbel_1179, retro_tbel_129, retro_tbel_1444, retro_tbel_1545, retro_tbel_1615, retro_tbel_1622, retro_tbel_1786, retro_tbel_1910, retro_tbel_2294, retro_tbel_2749, retro_tbel_2786, retro_tbel_2973, retro_tbel_3179, retro_tbel_3314, retro_tbel_3509, retro_tbel_3523, retro_tbel_3682, retro_tbel_3701, retro_tbel_392, retro_tbel_4373, retro_tbel_463, retro_tbel_4674, retro_tbel_481, retro_tbel_586, retro_tbel_603, retro_tbel_639, retro_tbel_647,