RetrogeneDB ID: retro_tbel_1416

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4633:84763..85538(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRIM68
• Ensembl ID: ENSTBEG00000012986
• Aliases: None
• Description: tripartite motif containing 68 [Source:HGNC Symbol;Acc:21161]

Sequence

>retro_tbel_1416
GAGCAGGAGGTGGGGGAAACCATGCAGAAATTGAAGTCAAATCATGACAAACTCATCCAGCATAGCCAGGTCCTATGGAG
AATGATTGCAGAGTTGAAAGAGTGAGCTCAGAAGCCCATCTACTCGATGCTACAGGGTATTCGGGAAGTTGTAAACAGAG
GCAAGTCTTGGAGCCTGCAGTGGCCAGAACCAGTCTCTTTGGAACTGAAGACAAATTGCCACGTGTTGGGACTGAGAGAG
AGCCTGAAGATGTATACAGCTGATGTACACCTGAATTTGGATACTGCTTATTCCTGCCTTATTGTGTCCCAGGACAGAAA
ATGTGTGCACTACAGAGACACTAAGCAAAAATGGTCAGACCATCTGGAGAGATTTTATTGTTGTAATATTGTCCTGGGCA
GCCAATGCATCTCCTCGGGCCAGCACTACTGGGAGATGGAGGTGGGAGACAGGTCTGAGTGGGTCCTGGGAGTGTGTAAG
GAAAATGCAGGTCAGAAAGAGGTGGTCTACTTATCCCCCCACTATGGCTTCTGGGTGATAAGGTCGAGGAAGGGAAATGA
GTACTGGGCAAGCACTGATGAATACCCTCTCCTGTCCTTGTCAGTCCCCTCTACGCCAGGCAGGGATTTTCCAGCATTAC
AAGGTCCATGATAACTCATTCTACAATGTGGCTGATGGCAGCTCCCACATTTTTACTTTCCTACACTATCTCTTCCCTGG
GCACCTCCTGCCCTATTTCAGCCCTTGCTATGGCATCAGGGCCAACAACATTGCT

Alignment

ORF - retro_tbel_1416 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.52 %
• Parental protein coverage: 63.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EQEVEETMQKLKLNHDQLIQQSRVLWRMIEELEERAQRPVRWMLQGIQEVINRGKSWSLQQPE-VSLELK
          EQEV.ETMQKLK.NHD.LIQ.S.VLWRMI.EL.E.AQ.P...MLQGI.EV.NRGKSWSLQ.PE.VSLELK
Retrocopy EQEVGETMQKLKSNHDKLIQHSQVLWRMIAELKE*AQKPIYSMLQGIREVVNRGKSWSLQWPEPVSLELK

Parental  TDCRVLGLRETLKMYXXDVCLDPDTAYSRLIVSEDRKCVHYGDTKQKLPDNPERFYRYNIVLGSQCISSG
          T.C.VLGLRE.LKMY..DV.L..DTAYS.LIVS.DRKCVHY.DTKQK..D..ERFY..NIVLGSQCISSG
Retrocopy TNCHVLGLRESLKMYTADVHLNLDTAYSCLIVSQDRKCVHYRDTKQKWSDHLERFYCCNIVLGSQCISSG

Parental  RHYWEVEVGDRSEWGLGVCKEDVDRKEVVYLSPHYGFWVIRLRNGSEYQAGTDEYSLLSLSVPP-RRVGV
          .HYWE.EVGDRSEW.LGVCKE....KEVVYLSPHYGFWVIR.R.G.EY.A.TDEY.LLSLSVP..R..G.
Retrocopy QHYWEMEVGDRSEWVLGVCKENAGQKEVVYLSPHYGFWVIRSRKGNEYWASTDEYPLLSLSVPS>RQAGI

Parental  FLDYEAHDISFYNVTDGGSHIFTFPRYPFPRPLLPYFSPCYSIGANNTA
          F..Y..HD.SFYNV.DG.SHIFTF..Y.FP..LLPYFSPCY.I.ANN.A
Retrocopy FQHYKVHDNSFYNVADGSSHIFTFLHYLFPGHLLPYFSPCYGIRANNIA

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_1416 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1416 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000022682	1 retrocopy	retro_mmul_1708,
Tupaia belangeri	ENSTBEG00000012986	1 retrocopy	retro_tbel_1416 ,