RetrogeneDB ID: retro_tbel_644

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_2650:114061..114677(+)
• Located in intron of: ENSTBEG00000014934

Retrocopy information

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

Parental gene information

• Parental gene symbol: GDI2
• Ensembl ID: ENSTBEG00000011523
• Aliases: None
• Description: GDP dissociation inhibitor 2 [Source:HGNC Symbol;Acc:4227]

Sequence

>retro_tbel_644
CCACCAGCATCCATGGGAAAAGGGAGAGACTGGAAGGTTGAGTTAATTCCCAAGTTACTATGGCTGATGGTCAGCTACTT
AAGATAGTGTTTTATACAGAGGTTACTCATTATCTGCATTTCAAAGTGACTGAAGGGAGCTTTGTTTATAAGAGAGGAAG
AATCTGTAAGGTTCCTTCCACCGAAGCAGACTCCCTGGCATCTACCTTGATGGGACTTTTTGAAAAACATCGCTTCAGAA
AATTCCTAGTGAATGTTGCCAATTTTGATGAAAAAGATTGTAGAACTTTGAGGGCATTCATCCAAAGAAAACTTCAATGT
GAGATATGAACAAGAAATTTGATTTGGGACAAGACATGATAGATTTTACTGGTCATGCTCTTGCACTTTAGAGAACTGAT
GAATACTTAGACCAACCATGTTGTGAAACCATCATTAAGATTAAACTTTACAGTGAGACCTTGGCAAGATATGGCAAAAG
CTCATACCTTTACCCACTCGCTGGCCTTGGAGAACTTCCACAAGGATTTGCAAGGCTAAATGCTATTTATGGAAGTACCT
ACATGCTGAATGAACCAGTTGAAGAAACTGTTGTGCAGAACGTAAAACCTGAAGGA

Alignment

ORF - retro_tbel_644 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.85 %
• Parental protein coverage: 50.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PPASMGRGRDWNVDL-PKFL-MANGQLVKMLLYTEVTRYLDFKVTEGSFVYKGGKIYKVPSTEAEALASS
          PPASMG.GRDW.V.L.PK.L.MA.GQL.K...YTEVT.YL.FKVTEGSFVYK.G.I.KVPSTEA..LAS.
Retrocopy PPASMGKGRDWKVELIPKLL<MADGQLLKIVFYTEVTHYLHFKVTEGSFVYKRGRICKVPSTEADSLAST

Parental  LMGLFEKRRFRKFLVYVANFDEKDSRT-FEGIDPKKTSMRDVYKKFDLGQDVIDFTGHALALYRTDDYLD
          LMGLFEK.RFRKFLV.VANFDEKD.RT.FEGI.PKKTSM.D..KKFDLGQD.IDFTGHALAL.RTD.YLD
Retrocopy LMGLFEKHRFRKFLVNVANFDEKDCRT<FEGIHPKKTSM*DMNKKFDLGQDMIDFTGHALAL*RTDEYLD

Parental  QPCCETINRIKLYSESLARYGKSPYLYPLYGLGELPQGFARLSAIYGGTYMLNKPIEEIIVQNGKVIG
          QPCCETI..IKLYSE.LARYGKS.YLYPL.GLGELPQGFARL.AIYG.TYMLN.P.EE..VQN.K..G
Retrocopy QPCCETIIKIKLYSETLARYGKSSYLYPLAGLGELPQGFARLNAIYGSTYMLNEPVEETVVQNVKPEG

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_644 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_644 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005316	1 retrocopy	retro_btau_1208,
Canis familiaris	ENSCAFG00000005223	2 retrocopies	retro_cfam_2196, retro_cfam_886,
Callithrix jacchus	ENSCJAG00000020512	2 retrocopies	retro_cjac_1168, retro_cjac_3115,
Cavia porcellus	ENSCPOG00000013449	1 retrocopy	retro_cpor_696,
Gorilla gorilla	ENSGGOG00000003623	1 retrocopy	retro_ggor_2590,
Mus musculus	ENSMUSG00000021218	2 retrocopies	retro_mmus_2971, retro_mmus_360,
Oryctolagus cuniculus	ENSOCUG00000005367	1 retrocopy	retro_ocun_69,
Ictidomys tridecemlineatus	ENSSTOG00000006449	1 retrocopy	retro_itri_757,
Tupaia belangeri	ENSTBEG00000011523	1 retrocopy	retro_tbel_644 ,
Tupaia belangeri	ENSTBEG00000012540	4 retrocopies	retro_tbel_1832, retro_tbel_2262, retro_tbel_2457, retro_tbel_3930,