RetrogeneDB ID: retro_tbel_3851

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_23623:846..1277(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GINM1
• Ensembl ID: ENSTBEG00000009606
• Aliases: None
• Description: glycoprotein integral membrane 1 [Source:HGNC Symbol;Acc:21074]

Sequence

>retro_tbel_3851
GATGTTACTGAAATTGATATTTTAGTTAAGAACCAAGGGATACGCAGACATTCAAACTACACTCTTCCTTTGGGAGAAGC
TTGCTGTACTTTATTTTCCAAGACAATGCATTTTATTTACTCTTCTCAAAATCTTCAGAAAAGGCAGTGTAGTCATTGCA
GACCACCAGTCTGTACCTCACCAGCAGGTGGAAACCACTGTAGCTGAAGAAGCCTTACCTGGCAAATGACATGAAACTCC
TCTCAGGGCAAAACCTCCATCTTCAATAAGGTAATGTGTCGGTGGGTGGCAAAGTTCAGAAAAGATCTGTGTAGTTTCTG
GAGCAGTACTTTTCCAGGATCCTTGATGTTTTTGAAAGTCATGGTGGTTGAAATTACAGGACAGCTGTGGTAGCAGCCAT
CTTAAAGGTGTTCGTCCCAGTTTCTCAGTAC

Alignment

ORF - retro_tbel_3851 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.13 %
• Parental protein coverage: 50.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DVTELDILVKNQGILRHSNYTLPLEE-SMLYSISRDND-ILFTLPNLSKKESVSSSSLQTTSQYLIRNVE
          DVTE.DILVKNQGI.RHSNYTLPL.E.S.LY.I..DN..ILFTL.....K.SV.....Q.........VE
Retrocopy DVTEIDILVKNQGIRRHSNYTLPLGE<SLLYFIFQDNA<ILFTLLKIFRKGSVVIADHQSVPH---QQVE

Parental  TTVDEDALPGKLPETPLRAEPPSSY-KVMCQWMEKFRKDLCRFWSSIFPVCFMFLKVVVVGITG-AAVII
          TTV.E.ALPGK..ETPLRA.PPSS..KVMC.W..KFRKDLC.FWSS.FP...MFLKV.VV.ITG..AV..
Retrocopy TTVAEEALPGK*HETPLRAKPPSSI<KVMCRWVAKFRKDLCSFWSSTFPGSLMFLKVMVVEITG<TAVVA

Parental  TILKVLVPVSQY
          .ILKV.VPVSQY
Retrocopy AILKVFVPVSQY

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_3851 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3851 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000016822	1 retrocopy	retro_mdom_1159,
Tupaia belangeri	ENSTBEG00000009606	2 retrocopies	retro_tbel_119, retro_tbel_3851 ,