RetrogeneDB ID: retro_tbel_3324

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_137319:42330..42856(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000011678
• Aliases: None
• Description: None

Sequence

>retro_tbel_3324
GAAAAGATTTATAAATTCAATGAGGACATGCCCTGCAGTGTGGCAGGCATAACCTCTGATGCCAGCATCCTGACTAATGA
ACTGAGGTTTGTTGCTCAAAGGTATTTATTATAGTATCAGGAGTGAATTCCTTATAGCAGCTGGCTACAGCACTATGTGA
GATCAAACAAGCTTATACACAGTTTGGAGGAAAACATCCCTTGGGGGTTTCTTCACTAGGCATTAGCTGGGACAAGCACT
ATGGCTTTCAGCTCTATCAGAGTGGTCCCAGTGGAAATAATGGGGGTTGGAAAGTCACATGCATTGGAAATAACAGTGCT
GCAGCCTTGTCAATGCTGAAACCAGATGACAAAGGACGAGAAAGGACTTTGGAATCAGAACTTGCATTAGCTATCAAAGT
ACTAAATAAGACCATGGATGTTAGTAAACTACCTGCCGAAAAGTGGAAATTGCCACACTGGCAAGAGAGCAAGGAAAGAT
GGTGATCAGAGTTCTCAAACCAAAGGAAGTGAAGCACTTGATCAAA

Alignment

ORF - retro_tbel_3324 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.65 %
• Parental protein coverage: 67.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCE-QLVTALCDIKQAYTQFGGKRPFG
          EKIYK.NEDM.CSVAGITSDA..LTNELR..AQRYLL.YQE.IP...QL.TALC.IKQAYTQFGGK.P.G
Retrocopy EKIYKFNEDMPCSVAGITSDASILTNELRFVAQRYLL*YQE*IPYS<QLATALCEIKQAYTQFGGKHPLG

Parental  VSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYKEGEMTLKSALALAIKVLNKTM
          VS.L.I.WDKHYGFQLYQS.PSGN.GGWK.TCIGNNSAAA.SMLK.D.K..E.TL.S.LALAIKVLNKTM
Retrocopy VSSLGISWDKHYGFQLYQSGPSGNNGGWKVTCIGNNSAAALSMLKPDDKGRERTLESELALAIKVLNKTM

Parental  DVSKLSAE-KVEIATLTRENGKTVIRVLRQKEVEQLIK
          DVSKL.AE.KVEIATL.RE.GK.VIRVL..KEV..LIK
Retrocopy DVSKLPAE<KVEIATLAREQGKMVIRVLKPKEVKHLIK

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_3324 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3324 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010369	1 retrocopy	retro_cjac_58,
Myotis lucifugus	ENSMLUG00000027860	1 retrocopy	retro_mluc_1404,
Mus musculus	ENSMUSG00000032301	2 retrocopies	retro_mmus_1035, retro_mmus_1707,
Pteropus vampyrus	ENSPVAG00000009182	2 retrocopies	retro_pvam_1229, retro_pvam_824,
Tupaia belangeri	ENSTBEG00000011678	5 retrocopies	retro_tbel_1746, retro_tbel_2953, retro_tbel_3324 , retro_tbel_4164, retro_tbel_614,
Tarsius syrichta	ENSTSYG00000011745	1 retrocopy	retro_tsyr_21,