RetrogeneDB ID: retro_tbel_2788

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_119112:281635..282112(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DERL2
• Ensembl ID: ENSTBEG00000009213
• Aliases: None
• Description: derlin 2 [Source:HGNC Symbol;Acc:17943]

Sequence

>retro_tbel_2788
TTCACCACCGCCACTGTGCTCTTTTCCTAGTTCAGCAGTTGGAATTTATCAGGCCTATTCAGTTGTACTTCACATCTGAA
TTAATCTTTAAACATTCTCAAATATGGAGGTTAATCACCAAGTTCTTATTTTTTGGGTCAGTTGGATTCAATTTCTTATT
TAATATGATTTTTCTTAACCATTACTGTTAAATGCTAGAAGAAGGCTCTTTCCATGGTCAAACTGCAGTCTTTGTATTTA
TGTTCCTTTTTGGTAGATTCTTAGTGACTCTTTTTGGTTTCTTCCAGAGCTCATTTCTGATGAGGCGTTTACAATAATGC
TCATCTACCTGTGGGGCCCTAGGAACTCATATGTCTCATGGACTTCTTCCATGGACTTCAACTTCCAGGCCCCCTTTCTG
TTTGGGCATTCATGGCATTATCCTTGTTGTTGGGTAACTCAATCATTGTGGACCTCTTGGGTATTGCAGTTAGACAC

Alignment

ORF - retro_tbel_2788 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.29 %
• Parental protein coverage: 77.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YTTACVLTT-AAVQLELITPFQLYFNPELIFKHFQIWRLITNFLFFGPVGFNFLFNMIFLYRYCRMLEEG
          .TTA.VL......QLE.I.P.QLYF..ELIFKH.QIWRLIT.FLFFG.VGFNFLFNMIFL..YC.MLEEG
Retrocopy FTTATVLFS<LVQQLEFIRPIQLYFTSELIFKHSQIWRLITKFLFFGSVGFNFLFNMIFLNHYC*MLEEG

Parental  SFRGRTADFVFMFLFGGFLMTLFGLFVSLVFL-GQAFTIMLVYVWSRRNPYVRMNFFGLLNFQAPFL-PW
          SF.G.TA.FVFMFLFG.FL.TLFG.F....FL...AFTIML.Y.W..RN.YV........NFQAPFL..W
Retrocopy SFHGQTAVFVFMFLFGRFLVTLFG-FFQSSFL<DEAFTIMLIYLWGPRNSYVSWTSSMDFNFQAPFL<VW

Parental  VLMGFSLLLGNSIIVDLLGIAVGH
          ..M..SLLLGNSIIVDLLGIAV.H
Retrocopy AFMALSLLLGNSIIVDLLGIAVRH

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_2788 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2788 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 4 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011304	3 retrocopies	retro_cjac_1540, retro_cjac_3886, retro_cjac_3980,
Oryctolagus cuniculus	ENSOCUG00000004811	2 retrocopies	retro_ocun_1561, retro_ocun_1908,
Tupaia belangeri	ENSTBEG00000009213	1 retrocopy	retro_tbel_2788 ,
Tarsius syrichta	ENSTSYG00000000394	4 retrocopies	retro_tsyr_1148, retro_tsyr_1538, retro_tsyr_2049, retro_tsyr_537,