RetrogeneDB ID: retro_tbel_2252

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_10708:34208..34945(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEPT8
• Ensembl ID: ENSTBEG00000002323
• Aliases: None
• Description: septin 8 [Source:HGNC Symbol;Acc:16511]

Sequence

>retro_tbel_2252
AGCATTATACCAGGGATTGCCAAAGCAGATGCGATTTCTGAAGTGGAATTACAGAAGCTTAAGATCAAGCTTATGAGTGA
ACTGGTCAGCAACGCCATCCGGATATACCAGTTCCCGACAGACGGTGGTGCTATTGCCAAAGTCAATGCTGCGATGAACG
GGCATTTGCCCTTTGCGGTTGTAGGAAGTACTGATGAGGTAACAGTCAGCAATGAGACGGCCAAAGCTCGCCAGTACCCT
TGGGGTGTTGTGCAAATGGAGAATGAAACCACTGCGACTCTGTGAAGCTGCAGGAGATGCTCATTTGCACCAACATGGAG
GACCTGCAGGAGCAGACCCATGCAGGGCACTACGAGCTGTACCGGCGCTGCGAACTGGAGGAGATGGGCTTCGCAGACGT
GGGCCCCGAGAACAAGCCCCTCAGCCGTCAGGAGACTTAAGAAGCCAAAAGACATGGATTTCATGGTGAACGGCAGAGGA
AGGGAGAGGAAATGAAGCAGATGCTTGTGCAGCGAGTAAAGGAGAAAGAAGCCATTGTGAAAGAAGCTGAAAGAGAGCTG
CAGACCAAATTTGAGCACCTTAAAGGAGTTCATCAGGAAGAGAGAATGAAGCTTGAAGAAAAGAGAAGATGTTTGGAAGA
ACAAATCGCTTTCTCTAAAAAGAAAGCGACCTCTGAGATATTCCAGAATTAGCCCTATATGGCATCGGGTAAGCTACCTG
AAAAAGGACCACAAGAC

Alignment

ORF - retro_tbel_2252 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.5 %
• Parental protein coverage: 57.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NIIPIIAKADTISKSELHKFKIKIMGELVSNGVQIYQFPTDDEAVAEINAVMNAHLPFAVVGSTEEVKVG
          .IIP.IAKAD.IS..EL.K.KIK.M.ELVSN...IYQFPTD..A.A..NA.MN.HLPFAVVGST.EV.V.
Retrocopy SIIPGIAKADAISEVELQKLKIKLMSELVSNAIRIYQFPTDGGAIAKVNAAMNGHLPFAVVGSTDEVTVS

Parental  NKLVRARQYPWGVVQVENE-NHCDFVKLREMLIRVNMEDLREQTHSRHYELYRRCKLEEMGFQDSDGDSQ
          N....ARQYPWGVVQ.ENE.NHCD.VKL.EMLI..NMEDL.EQTH..HYELYRRC.LEEMGF.D......
Retrocopy NETAKARQYPWGVVQMENE<NHCDSVKLQEMLICTNMEDLQEQTHAGHYELYRRCELEEMGFADVGPENK

Parental  PFSLQETYEAKRKEFLSELQRKEEEMRQMFVNKVKETELELKEKERELHEKFEHLKRVHQEEKRKVEEKR
          P.S.QET.EAKR..F..E.QRK.EEM.QM.V..VKE.E...KE.EREL..KFEHLK.VHQEE..K.EEKR
Retrocopy PLSRQET*EAKRHGFHGERQRKGEEMKQMLVQRVKEKEAIVKEAERELQTKFEHLKGVHQEERMKLEEKR

Parental  RELDEETSAFNRRKAAVEALQSQALHATSQQPLRKDKD
          R.L.E...AF...KA..E..Q.....A....P.....D
Retrocopy RCLEEQI-AFSKKKATSEIFQN*PYMASGKLPEKGPQD

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_2252 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2252 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
Procavia capensis	ENSPCAG00000007178	1 retrocopy	retro_pcap_358,
Tupaia belangeri	ENSTBEG00000002323	2 retrocopies	retro_tbel_2252 , retro_tbel_3268,