RetrogeneDB ID: retro_tbel_1516

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_4952:67229..67612(-)
• Located in intron of: ENSTBEG00000000342

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000002194
• Aliases: None
• Description: None

Sequence

>retro_tbel_1516
CAGAACAACAGAAATAGTTTTTTTCTCCCTCTGCTTAAACTTTGGAAGCGGTACATCCGGGAACTGTGCATTGGTCTCAA
GCCAGACACTCAGCCACAGATGATTCAAGCCAAGTGTTAAAGACAAATCTTCACGGTGCTGTTGTTCTAGTCACAAAATC
CAAATGCCCCTTGTATGTGGACGTTACAGGAGTAATTCTACAGGAAACCAAGCACGTTTTCAAAATTATCACCAAAGACC
ACCTGAAAGTTATCCCCAAGCTAAATTGTGTGTTCACTGTGGAAATGGATGACTTTGTATACTACATTTATGGGAACAAA
TTCTAGTTTCAGTCAAGTGAGTGATCCGCAAAGAATTTTAAAGCAAAGGGCACAGTCGACCTC

Alignment

ORF - retro_tbel_1516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.38 %
• Parental protein coverage: 58.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EQQRYSLFLPLHELWKQYIRDLCNGLKPDTQPQMIQAK-LLKADLHGAIISVTKSKCPSYVGVTGILLQE
          ...R.S.FLPL..LWK.YIR.LC.GLKPDTQPQMIQAK..LK..LHGA...VTKSKCP.YV.VTG..LQE
Retrocopy QNNRNSFFLPLLKLWKRYIRELCIGLKPDTQPQMIQAK<VLKTNLHGAVVLVTKSKCPLYVDVTGVILQE

Parental  TKHVFKIITKEDRLKVIPKLNCVFTVEIDDFVSYIYGSKFQLRSSERSAKKFKAKGTIDL
          TKHVFKIITK.D.LKVIPKLNCVFTVE.DDFV.YIYG.KF...SSE.SAK.FKAKGT.DL
Retrocopy TKHVFKIITK-DHLKVIPKLNCVFTVEMDDFVYYIYGNKF*FQSSE*SAKNFKAKGTVDL

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_1516 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1516 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 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Mustela putorius furo	ENSMPUG00000008041	1 retrocopy	retro_mputfur_1088,
Oryctolagus cuniculus	ENSOCUG00000015974	1 retrocopy	retro_ocun_1367,
Otolemur garnettii	ENSOGAG00000011168	2 retrocopies	retro_ogar_3293, retro_ogar_541,
Sorex araneus	ENSSARG00000004748	1 retrocopy	retro_sara_410,
Tupaia belangeri	ENSTBEG00000002194	6 retrocopies	retro_tbel_1225, retro_tbel_1516 , retro_tbel_2043, retro_tbel_3671, retro_tbel_3821, retro_tbel_89,