RetrogeneDB ID: retro_tbel_3700

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_148848:4955..5694(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000001671
• Aliases: None
• Description: None

Sequence

>retro_tbel_3700
GAGCGCATCTCCATCTATATTAGTCTGGCTGGTATCCAGATCAATAGTGCCTGTTGGGAGCTCTAATATTGCCTGGAACA
TGGCTTCCAACCTGATGGCCAGAAGTCAAGTGGCAAGACCACTGGGGAAGGATAAAACTCCTTCAACACCTTATTCAGTG
AGACTGACACTGACAAGCCTATGCCCAGGGCAATATTTATAGACCTGGAACCCACAGTCATTGATGAAGTTCACATTGGC
AACTACCACCACCTTTTTCACTCTAAGTAGCTCATCACAAGCAATGAAGATGCTGCCAATAACTAGGTCCATGGGCAATA
GACCACTGACAAGGAGATCATTGACCTCGTTTTGGATTGAATTCACAAGATGGCTGATCAGTGCACAGATCGGCAGGGTT
TCTTGGTTTTCCACAGCTTTGGGGGGGTAATTGGTTCTGTGTTTACCTTCTTACTGATGGAATGGCTCTTGGTGGATTAT
GGCAAGAAGTCCAAGCTTAATTCTCTATCTATCCAGTCCTCAGATTTTCACAGCTGTAGTTGAGCACTACAATGCTTTCC
TCACCACCAACACCACCCTGGAACACTCTGACTGTGACTTCATGGTAGACAATGAGGCCAGCTATGACATCTGTCATAGA
AACCTTGACATTTAACTCCCAACCAATACTAATCTTAACTGCCTTATAAATCAGATTGTGTCCTCCATCACTGCTTCCTT
CTGATTTGATGGAGCTCTA

Alignment

ORF - retro_tbel_3700 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.68 %
• Parental protein coverage: 54.67 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ECISIHVGQAGVQIGNACWEL-YCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLE
          E.ISI....AG.QI..ACWEL.YCLEHG.QPDGQ..S.KT.G.G..SFNT.FSET...K..PRA.F.DLE
Retrocopy ERISIYISLAGIQINSACWEL*YCLEHGFQPDGQKSSGKTTGEG*NSFNTLFSETDTDKPMPRAIFIDLE

Parental  PTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSF
          PTVIDEV..G.Y..LFH...LIT..EDAANN...G..T..KEIIDLVLD.I.K.ADQCT..QGFLVFHSF
Retrocopy PTVIDEVHIGNYHHLFHSK*LITSNEDAANN*VHGQ*TTDKEIIDLVLD*IHKMADQCTDRQGFLVFHSF

Parental  GGGTGSGFTSLLMERLSVDYGKKSKLE-FSIYP-APQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAI
          GG..GS.FT.LLME.L.VDYGKKSKL..FSIYP..PQ..TAVVE.YN..LTT.TTLEHSDC.FMVDNEA.
Retrocopy GGVIGSVFTFLLMEWLLVDYGKKSKLN<FSIYP<SPQIFTAVVEHYNAFLTTNTTLEHSDCDFMVDNEAS

Parental  YDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGAL
          YDIC.RNLDI..PT.TNLN.LI.QIVSSITAS..FDGAL
Retrocopy YDICHRNLDI*LPTNTNLNCLINQIVSSITASF*FDGAL

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_3700 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3700 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 13 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006872	4 retrocopies	retro_amel_1162, retro_amel_1367, retro_amel_1387, retro_amel_1895,
Canis familiaris	ENSCAFG00000008640	8 retrocopies	retro_cfam_1481, retro_cfam_1751, retro_cfam_1895, retro_cfam_1917, retro_cfam_1979, retro_cfam_2000, retro_cfam_463, retro_cfam_926,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Cavia porcellus	ENSCPOG00000013016	1 retrocopy	retro_cpor_96,
Felis catus	ENSFCAG00000027011	1 retrocopy	retro_fcat_588,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Loxodonta africana	ENSLAFG00000010021	1 retrocopy	retro_lafr_326,
Microcebus murinus	ENSMICG00000017551	3 retrocopies	retro_mmur_144, retro_mmur_705, retro_mmur_885,
Myotis lucifugus	ENSMLUG00000002622	4 retrocopies	retro_mluc_154, retro_mluc_186, retro_mluc_234, retro_mluc_270,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Tupaia belangeri	ENSTBEG00000001671	1 retrocopy	retro_tbel_3700 ,
Tarsius syrichta	ENSTSYG00000013266	7 retrocopies	retro_tsyr_1014, retro_tsyr_1278, retro_tsyr_1281, retro_tsyr_1679, retro_tsyr_1834, retro_tsyr_243, retro_tsyr_6,
Tursiops truncatus	ENSTTRG00000004794	1 retrocopy	retro_ttru_407,