RetrogeneDB ID: retro_tbel_4346

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_77824:4118..4870(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GAPDHS
• Ensembl ID: ENSTBEG00000008617
• Aliases: None
• Description: glyceraldehyde-3-phosphate dehydrogenase, spermatogenic [Source:HGNC Symbol;Acc:24864]

Sequence

>retro_tbel_4346
AAGATTAGATGGGGTGATGCTGATGCTGAGTATGTTGTGGGAGTCTACTGTCTTCATCACCATGGAGAAAGCTGTGGCTC
ACTTGAAGGGTGGGGCCAAAAGGGTCATCATCTCTGCCCCTTCTGCTGATGCCCTCATGTTTGTGATGGGCATGAACCAC
AAGAAGTATGACAACTCCCTGAAGATCATCAGCAATGCCTCCTGCACCACCAACTGCTTGCCTCCAGGCCAAGGTCATCC
ACAAAAGCTTTGGCATCGTGGAGGGGCTCACGACCACAGTCTGTGCCATCACTGCCACCTAGAAGATTGTGGACGGCCTC
TCAGAGAAACTGTGGCGTGATGGCCATGGGGCTGCCCAGAATATCATTCCAGCATCTACCGGGGCTGCCAAGGCTGTGGA
CAAAGTCATCCTGGAACTGAACGGGAAGCTCACCAGCGTGGTCTTCCATGTCCCCACCCCCAATGTGTCAGTTGTGGATC
TGACTTGCTGCCGGGAAAAAACTGCCAAATACAATGGCATCAAGAAGGTAGTGTAGCAGGCATTGCAGGGCTCCCTGAAG
AGCATCCTAGGCTACTTCTAGAACCAGGTCATCTCCTGTGACTTTAACAGTGATAAGCACTCTTCCACCTTCGATGCTGG
GGCTGGCATTGCCTTCAATGACCATTTTGTCAAGCTCATTTCCTGGTATGATAATGAATTTGGCTACAGCAACAGAGTGG
TGGACCTCATGGTCCACATAGCCTCCAAGGAG

Alignment

ORF - retro_tbel_4346 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.86 %
• Parental protein coverage: 98.06 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EIPWKSVGSPYVV-ESTGVYLSLEAASEHISAGAQRVVICAPSPDAPMFVMGVNENDYNPGFMNIVSNAS
          .I.W......YVV.EST.V....E.A..H...GA.RV.I.APS.DA.MFVMG.N...Y......I.....
Retrocopy KIRWGDADAEYVV>EST-VFITMEKAVAHLKGGAKRVIISAPSADALMFVMGMNHKKYDNSLKIISNASC

Parental  CT-TNCLAPLVKVIHERFGIVEGLMTTVHSYTATQKTVDGPSKKAWRDGRGAHQNIIPASTGAASAVGKV
          .T.T.CL....KVIH..FGIVEGL.TTV...TAT.K.VDG.S.K.WRDG.GA.QNIIPASTGAA.AV.KV
Retrocopy TT>TACLQ--AKVIHKSFGIVEGLTTTVCAITAT*KIVDGLSEKLWRDGHGAAQNIIPASTGAAKAVDKV

Parental  IPELKGKLTGMAFRVPTPDVSVVDLTCRLAQPTPYSAIKEAVKAAAKGPLAGILAYTEDQVVSTDFVGDT
          I.EL.GKLT...F.VPTP.VSVVDLTC.......Y..IK..V..A..G.L..IL.Y...QV.S.DF..D.
Retrocopy ILELNGKLTSVVFHVPTPNVSVVDLTCCREKTAKYNGIKKVV*QALQGSLKSILGYF*NQVISCDFNSDK

Parental  HSSIFDAKAGIALNDNFVKVISWYDNEYGYSHRVVDLIRYMFSRD
          HSS.FDA.AGIA.ND.FVK.ISWYDNE.GYS.RVVDL.....S..
Retrocopy HSSTFDAGAGIAFNDHFVKLISWYDNEFGYSNRVVDLMVHIASKE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_4346 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4346 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 6 parental genes, and 72 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000061099	2 retrocopies	retro_mmus_3024, retro_mmus_528,
Otolemur garnettii	ENSOGAG00000009491	25 retrocopies	retro_ogar_1269, retro_ogar_1332, retro_ogar_1460, retro_ogar_1472, retro_ogar_1798, retro_ogar_1968, retro_ogar_2074, retro_ogar_2266, retro_ogar_2376, retro_ogar_2446, retro_ogar_2469, retro_ogar_2631, retro_ogar_2647, retro_ogar_2884, retro_ogar_2957, retro_ogar_315, retro_ogar_3197, retro_ogar_3262, retro_ogar_3517, retro_ogar_355, retro_ogar_468, retro_ogar_582, retro_ogar_632, retro_ogar_658, retro_ogar_785,
Petromyzon marinus	ENSPMAG00000009321	1 retrocopy	retro_pmar_9,
Pan troglodytes	ENSPTRG00000010848	1 retrocopy	retro_ptro_2211,
Tupaia belangeri	ENSTBEG00000001510	27 retrocopies	retro_tbel_1055, retro_tbel_1149, retro_tbel_1315, retro_tbel_1359, retro_tbel_1519, retro_tbel_1684, retro_tbel_232, retro_tbel_2380, retro_tbel_2442, retro_tbel_2731, retro_tbel_2992, retro_tbel_3109, retro_tbel_3205, retro_tbel_3418, retro_tbel_3463, retro_tbel_3826, retro_tbel_3829, retro_tbel_393, retro_tbel_4036, retro_tbel_4094, retro_tbel_4310, retro_tbel_4377, retro_tbel_441, retro_tbel_4560, retro_tbel_4635, retro_tbel_4706, retro_tbel_480,
Tupaia belangeri	ENSTBEG00000008617	16 retrocopies	retro_tbel_1017, retro_tbel_1193, retro_tbel_124, retro_tbel_1650, retro_tbel_1685, retro_tbel_2010, retro_tbel_2486, retro_tbel_249, retro_tbel_2793, retro_tbel_2832, retro_tbel_2873, retro_tbel_2929, retro_tbel_3117, retro_tbel_425, retro_tbel_4292, retro_tbel_4346 ,