RetrogeneDB ID: retro_tbel_996

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3536:1240836..1241479(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YBX3
• Ensembl ID: ENSTBEG00000012570
• Aliases: None
• Description: Y box binding protein 3 [Source:HGNC Symbol;Acc:2428]

Sequence

>retro_tbel_996
GCCAACATAACTGGCCCAGATGGAGTTTTATAGAAGACAGTCCATACACTGCTGATCGGCGCCACTGTAGATATGGCTTC
TATGGCAGACGCCAGTGAATCTCCTGGTAATTACACTTGGGAGAAGGAAGGGAGCAGCAGCAGTGAAGGATTTGACTCCC
CTGCCACAGACAGGCAGTTCTCTGGGGCCCAGAATCAGCTGCGTCGCCCCTAGTATCACCCTCAGTACCAGCAGTGGCAG
TTTCCGCCTTACCACACAGGACAGACATTCGGCCATTGCTCACGGGCCTTTCCCCACCCCAGTAGATTACAAGCTGGAGA
GACTGGAGAGATGAAGGATGGAGTCCCAGAGGGAGCTCAGCTTCAGGGATGGGTTCATCAGAATCCAACTTATTGCCCAT
GGTACCATAGGGGACCTCTTTGCCTATGACCTGCCCCAGCTATGGGAGAGGCTGAAGACAGAGAATCAACAAACAGCCAA
TGGTCCAAACCAACCATCTGTTCGCCGGGGATACCTGTGTCCCTACAACTACCGGCACCGTCCCCATCCTCTTAATGCTC
CCTCACAAAGTGGCAAAGAGACCAAAGCAGGTGAAGCACCAACTGAGAACCCTGTTCCAGCCACTGAGCAGAGCAGCACT
GAG

Alignment

ORF - retro_tbel_996 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.4 %
• Parental protein coverage: 60.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ANVTGPDGVP-VEGSRYAADRRRYRRGYYGRRR-GPPRNYAGEEEEEGSGSSEGFDPPATDGQFSGARNQ
          AN.TGPDGV...E.S.Y.ADRR..R.G.YGRR....P.NY..E.E..GS.SSEGFD.PATD.QFSGA.NQ
Retrocopy ANITGPDGVL<IEDSPYTADRRHCRYGFYGRRQ>ESPGNYTWEKE--GSSSSEGFDSPATDRQFSGAQNQ

Parental  LRRPQYRPQYRQRRFPPYHVGQTFDRRSRVFPHPSRMQAGEIGEMKDGVPEGAQLQGQVHRNPTYRPRYR
          LRRP.Y.PQY.Q..FPPYH.GQTF...SR.FPHPSR.QAGE.GEMKDGVPEGAQLQG.VH.NPTY.P.Y.
Retrocopy LRRP*YHPQYQQWQFPPYHTGQTFGHCSRAFPHPSRLQAGETGEMKDGVPEGAQLQGWVHQNPTYCPWYH

Parental  SRGPPRPRPAPAVGEAEDKEN-QQAANGPNQPSVRRGYRRPYNYRRRPRPPNAPSQDGKETKAGEAPTEN
          .RGP....PAPA.GEAED.E..Q.A.NGPNQPSVRRGY..PYNYR.RP.P.NAPSQ.GKETKAGEAPTEN
Retrocopy -RGPLCL*PAPAMGEAEDRES>QTA-NGPNQPSVRRGYLCPYNYRHRPHPLNAPSQSGKETKAGEAPTEN

Parental  PAPATEQSSAE
          P.PATEQSS.E
Retrocopy PVPATEQSSTE

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_996 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_996 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000060138	1 retrocopy	retro_hsap_1674,
Pongo abelii	ENSPPYG00000004279	1 retrocopy	retro_pabe_1420,
Tupaia belangeri	ENSTBEG00000012570	1 retrocopy	retro_tbel_996 ,
Tupaia belangeri	ENSTBEG00000015642	9 retrocopies	retro_tbel_1183, retro_tbel_1955, retro_tbel_2347, retro_tbel_2694, retro_tbel_2702, retro_tbel_2961, retro_tbel_3590, retro_tbel_4037, retro_tbel_4478,