RetrogeneDB ID: retro_tbel_2874

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_121940:202761..203582(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPDL
• Ensembl ID: ENSTBEG00000002817
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein D-like [Source:HGNC Symbol;Acc:5037]

Sequence

>retro_tbel_2874
GAGAAATTCGCGGAGGGATCCAAGATCAACGCCAGCAAGAATCTGTAGTATGACTGTAAAACGTTTATTGGAGGCTTGAG
CTGGGATACAAGCAAGAAAGATCTGACTGAATATTTGTCTCGGCTTGGGGAATTTGTAGAGTGCACAATTAAAACAGATC
CAGTCACTGGAAGATCAAGAGGATTTGGATTTGCGCTTTTCAAAGATGCTGCTAGTGTTGATAAGGTTTTGGAACTAAAA
GAACACAAACTGGATGGCAAGTTGATAGACCTCCAAAGGGCCAAAGCTTTAAAAGAGAAAGAAGCTCCCAAGAAGATTTT
TGTGGGTGGGCTGAGCCCAGATACTTCAGAAGAACAAATCAGACTATTTCGGAGCCTTTGGAGAGATTGAAAACATTGAA
CTTCCCATGGATACAAAAACGAATGAAAGAAGAGGATTTTGTTTTATCACATACACAGAGGAAGAACCAATAAAGAAATT
ATTAGAAAGCAGATACCATCAAATTGGTTCCAGGAAATGTGAACTCAAGGTTGCACAACCCGAAGGTATATAGGCAACAG
CAAAAACAATAAGGAAGAAGAGGTGCTGCAGCTGGTGGAAGAGGGAGTACTAGGGGTCATGGCAGAGGTCAGGGCCAGAA
CTGGAACCAGGGATTTAATAACTATTTTGATCAAGGAGATGGAAATTATATTAGTGCCTATGGTGGCTATCAAAACTATA
GTGGCTGTGGTGGATATGATTATACTGGGTTTAACTGTGGAAACTGTGGATATGGACAGGGATATCCAGATAGATATCCC
AGTGGCCAATAGAGTACTTAC

Alignment

ORF - retro_tbel_2874 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.91 %
• Parental protein coverage: 69.72 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EEFAEGSKINASKNQQDDGKMFIGGLSWDTSKKDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDA
          E.FAEGSKINASKN...D.K.FIGGLSWDTSKKDLTEYLSR.GE.V.CTIKTDPVTGRSRGFGF.LFKDA
Retrocopy EKFAEGSKINASKNL*YDCKTFIGGLSWDTSKKDLTEYLSRLGEFVECTIKTDPVTGRSRGFGFALFKDA

Parental  ASVDKVLELKEHKLDGKLIDPKRAKALKGKEPPKKVFVGGLSPDTSEEQIKEYFGAFGE-IENIELPMDT
          ASVDKVLELKEHKLDGKLID..RAKALK.KE.PKK.FVGGLSPDTSEEQI................P...
Retrocopy ASVDKVLELKEHKLDGKLIDLQRAKALKEKEAPKKIFVGGLSPDTSEEQIRLFRSLWRD<LKTLNFPWIQ

Parental  KTNERRGF-CFITYTDEEPVKKLLESRYHQIGSGKCEIKVAQ-PKEVYRQQQQQQKGGRGAAAGGRGGTR
          K......F.CFITYT.EEP.KKLLESRYHQIGS.KCE.KVAQ.PK....QQ...Q.G.RGAAAGGRG.TR
Retrocopy KRMKEEDF<CFITYTEEEPIKKLLESRYHQIGSRKCELKVAQ>PKVYRQQQK--Q*GRRGAAAGGRGSTR

Parental  GRGRGQGQNWNQGFNNYYDQGYGNYNSAYGGDQNYSGYGGYDYTGYNYGNYGYGQGYADY--SGQQSTY
          G.GRGQGQNWNQGFNNY.DQG.GNY.SAYGG.QNYSG.GGYDYTG.N.GN.GYGQGY.D...SGQ.STY
Retrocopy GHGRGQGQNWNQGFNNYFDQGDGNYISAYGGYQNYSGCGGYDYTGFNCGNCGYGQGYPDRYPSGQ*STY

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_2874 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2874 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 8 parental genes, and 59 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000003887	7 retrocopies	retro_dnov_1175, retro_dnov_1182, retro_dnov_144, retro_dnov_1603, retro_dnov_31, retro_dnov_723, retro_dnov_930,
Monodelphis domestica	ENSMODG00000011916	6 retrocopies	retro_mdom_1496, retro_mdom_1789, retro_mdom_1951, retro_mdom_2017, retro_mdom_546, retro_mdom_981,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Sarcophilus harrisii	ENSSHAG00000013616	3 retrocopies	retro_shar_297, retro_shar_527, retro_shar_625,
Ictidomys tridecemlineatus	ENSSTOG00000013979	1 retrocopy	retro_itri_1177,
Tupaia belangeri	ENSTBEG00000002327	1 retrocopy	retro_tbel_2698,
Tupaia belangeri	ENSTBEG00000002817	7 retrocopies	retro_tbel_2079, retro_tbel_2283, retro_tbel_2608, retro_tbel_2874 , retro_tbel_3344, retro_tbel_4302, retro_tbel_4405,
Tupaia belangeri	ENSTBEG00000008238	30 retrocopies	retro_tbel_1219, retro_tbel_156, retro_tbel_162, retro_tbel_1643, retro_tbel_1830, retro_tbel_1967, retro_tbel_2192, retro_tbel_2195, retro_tbel_2211, retro_tbel_2330, retro_tbel_261, retro_tbel_2666, retro_tbel_2673, retro_tbel_2703, retro_tbel_276, retro_tbel_2774, retro_tbel_2787, retro_tbel_2970, retro_tbel_3473, retro_tbel_3976, retro_tbel_3995, retro_tbel_4266, retro_tbel_4271, retro_tbel_453, retro_tbel_4653, retro_tbel_4729, retro_tbel_692, retro_tbel_70, retro_tbel_79, retro_tbel_839,