RetrogeneDB ID: retro_tbel_570

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_2447:661698..662195(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTBP2
• Ensembl ID: ENSTBEG00000010797
• Aliases: None
• Description: polypyrimidine tract binding protein 2 [Source:HGNC Symbol;Acc:17662]

Sequence

>retro_tbel_570
CAGGCTTTCTTAGAAATGGCTTCTGAGGAAGCTGTTGTTACTATGGTGAATTATTACACTCCCGTTACTCCTCACCTTCG
AAGCCAGCCTGTTTATATTCCGTATTCTAATCACAGAGAACTTAAGACTGACAATCTTCCTAATCAAGGTAGAGCCCAAG
CTGCACTGCAGGCTGTCAGTGCTGTCCAGTCAGGAAGCTTGGCCCCTTCCTGGAGCTCCTTCCAATGAAGACCCAGTCCT
ACCTGGGCAGAGCCCCGTACTTCGAATAATTATTGAAAACCTCTTTTATCCTGTTACTCTGGAAGTTCTTCATCAGATAT
TTTCTAAATTTGGCACAGTCCTGAAGATTATCACCTTTACAAAAAGTAATCAGTTTCAAAGCATTGCTTCAGTATGCTGA
CCCAGTGAATGCACATCTTGCCAAAATGGTAATTATCATGTTTTCATCTTTCAATTGTTCATTGAAAACTGAAGAAAGTA
TTCATGTCTCCTCTAAT

Alignment

ORF - retro_tbel_570 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.09 %
• Parental protein coverage: 55.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKELKTDNTLNQ-RAQAVLQAVTAVQTANT-PL
          QAFLE.A.EEA..TMVNYY..VTPHLR.QP.YI.YSNH.ELKTDN..NQ.RAQA.LQAV.AVQ.....PL
Retrocopy QAFLEMASEEAVVTMVNYYTPVTPHLRSQPVYIPYSNHRELKTDNLPNQGRAQAALQAVSAVQSGSL>PL

Parental  SGTTVSESAVTPAQSPVLRIIIDNMYYPVTLDVLHQIFSKFGAVLKIITFTKNNQFQ-ALLQYGDPVNAQ
          .G....E..V.P.QSPVLRIII.N..YPVTL.VLHQIFSKFG.VLKIITFTK.NQFQ.ALLQY.DPVNA.
Retrocopy PGAPSNEDPVLPGQSPVLRIIIENLFYPVTLEVLHQIFSKFGTVLKIITFTKSNQFQ>ALLQYADPVNAH

Parental  QAKLALDGQNIYNACCTLRIDFSKLVNLN
          .AK.........N..C.L....S..V..N
Retrocopy LAKMVIIMFSSFN--CSLKTEESIHVSSN

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_570 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_570 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona savignyi	ENSCSAVG00000007421	1 retrocopy	retro_csav_17,
Tupaia belangeri	ENSTBEG00000010797	1 retrocopy	retro_tbel_570 ,
Tupaia belangeri	ENSTBEG00000016563	1 retrocopy	retro_tbel_1340,