RetrogeneDB ID: retro_ogar_2668

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873646.1:2260776..2261255(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000034790
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TPT1
• Ensembl ID: ENSOGAG00000012523
• Aliases: None
• Description: tumor protein, translationally-controlled 1 [Source:HGNC Symbol;Acc:12022]

Sequence

>retro_ogar_2668
ATTATCTACTGGGACCTCATCAGCCATGATGAGATGTTCTCTGACATTTACAAGATCTGAGAGATTGCAGGTGGCCTATG
CCTAGAGGTGGAGGGAAGATGGTCAGTAGGACAGAGGGTAACATTGATGACTCACTCATTGGTGGAAATGCTTCTGCTGA
AGGACTTGAGGGTGAAGGTACCAAAAGCACAGTTATCATTGGTGTTGATATTGTCGTGAACCATCACTTGCAGGAAACCA
GCTTCACAAAAGAAGCCTACAAGAAGCACATCAAAAATTACATGAAGTCAATCAAAGGCAAACTTGAAGAACAGAGACCA
GAAAGAATTAAACCTTTTATGACAGGGGATGCAGAACAAATCAAGCACATCCTGGCTAATTTCAAAAACTACCAGTTCTT
TATTGGTGAAAACATGAATGCAGATGGCATGGTTGCTCTCCTGGACTATCGTGAGGATGGTGTGACCACATATATGATT

Alignment

ORF - retro_ogar_2668 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.68 %
• Parental protein coverage: 93.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IIYRDLISHDEMFSDIYKIREIADGLCLEVE-GKMVSRTEGNIDDSLIGGNASAEGPEGEGTESTVVTGV
          IIY.DLISHDEMFSDIYKI.EIA.GLCLEVE.GKMVSRTEGNIDDSLIGGNASAEG.EGEGT.STV..GV
Retrocopy IIYWDLISHDEMFSDIYKI*EIAGGLCLEVE<GKMVSRTEGNIDDSLIGGNASAEGLEGEGTKSTVIIGV

Parental  DIVMNHHLQETSFTKEAYKKYIKDYMKSIKGKLEEQRPERVKPFMTGAAEQIKHILANFKNYQFFIGENM
          DIV.NHHLQETSFTKEAYKK.IK.YMKSIKGKLEEQRPER.KPFMTG.AEQIKHILANFKNYQFFIGENM
Retrocopy DIVVNHHLQETSFTKEAYKKHIKNYMKSIKGKLEEQRPERIKPFMTGDAEQIKHILANFKNYQFFIGENM

Parental  NPDGMVALLDYREDGVTPYMI
          N.DGMVALLDYREDGVT.YMI
Retrocopy NADGMVALLDYREDGVTTYMI

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_2668 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 12 parental genes, and 98 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006531	2 retrocopies	retro_acar_156, retro_acar_58,
Bos taurus	ENSBTAG00000010156	2 retrocopies	retro_btau_21, retro_btau_235,
Callithrix jacchus	ENSCJAG00000019229	2 retrocopies	retro_cjac_1786, retro_cjac_314,
Dasypus novemcinctus	ENSDNOG00000000653	22 retrocopies	retro_dnov_1071, retro_dnov_1202, retro_dnov_1349, retro_dnov_1705, retro_dnov_2082, retro_dnov_2283, retro_dnov_2305, retro_dnov_237, retro_dnov_2412, retro_dnov_2531, retro_dnov_2687, retro_dnov_276, retro_dnov_342, retro_dnov_397, retro_dnov_417, retro_dnov_453, retro_dnov_71, retro_dnov_847, retro_dnov_870, retro_dnov_909, retro_dnov_934, retro_dnov_981,
Latimeria chalumnae	ENSLACG00000004306	2 retrocopies	retro_lcha_24, retro_lcha_34,
Loxodonta africana	ENSLAFG00000021740	7 retrocopies	retro_lafr_1008, retro_lafr_1195, retro_lafr_1211, retro_lafr_1247, retro_lafr_347, retro_lafr_484, retro_lafr_883,
Monodelphis domestica	ENSMODG00000014940	2 retrocopies	retro_mdom_128, retro_mdom_9,
Nomascus leucogenys	ENSNLEG00000002108	8 retrocopies	retro_nleu_1262, retro_nleu_1281, retro_nleu_1637, retro_nleu_2127, retro_nleu_2539, retro_nleu_2540, retro_nleu_368, retro_nleu_9,
Otolemur garnettii	ENSOGAG00000012523	20 retrocopies	retro_ogar_1141, retro_ogar_1249, retro_ogar_1538, retro_ogar_1682, retro_ogar_1754, retro_ogar_2193, retro_ogar_2225, retro_ogar_2298, retro_ogar_2331, retro_ogar_2594, retro_ogar_2668 , retro_ogar_2819, retro_ogar_2893, retro_ogar_2944, retro_ogar_344, retro_ogar_350, retro_ogar_3503, retro_ogar_622, retro_ogar_746, retro_ogar_906,
Sarcophilus harrisii	ENSSHAG00000001545	1 retrocopy	retro_shar_227,
Tupaia belangeri	ENSTBEG00000013539	25 retrocopies	retro_tbel_1009, retro_tbel_1556, retro_tbel_1634, retro_tbel_1724, retro_tbel_1725, retro_tbel_2086, retro_tbel_2100, retro_tbel_2265, retro_tbel_2278, retro_tbel_2464, retro_tbel_2550, retro_tbel_2767, retro_tbel_3238, retro_tbel_3354, retro_tbel_3403, retro_tbel_3410, retro_tbel_3592, retro_tbel_3888, retro_tbel_4226, retro_tbel_4400, retro_tbel_4526, retro_tbel_459, retro_tbel_4641, retro_tbel_4733, retro_tbel_830,
Vicugna pacos	ENSVPAG00000008472	5 retrocopies	retro_vpac_1, retro_vpac_101, retro_vpac_159, retro_vpac_539, retro_vpac_552,