Sequence
atgc intronic sequence ATGC exonic sequence...attaataaatacatgaaatgaaaaaaaataaaaaatcaaacatatatccatggtaattgatttcattgttttttaaaatgtataattttcctgttcctagGGTGATAGTATCCTAGCGGATTCCGGCACAGAGCAGCTGGAGTTTATTGCCCTTTCTCAAAGGACTGGTGATCCAAAGTATCAGAAAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0054g00370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 6
-attaataaatacatgaaatgaaaaaaaataaa-aaatcaaacatatatccatggtaattgatttcattgttttttaaaatgtataattttcctgttcct--agGGTGATAGTATCCTAGCGGATTCCGGCACAGAGCAGCTGGAGTTTATTGCCCTTTCTCAAAGGACTGGTGATCCAAAGTATCAGAAAAAG
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catcaataattgc-tcaatggattgtttataaatgcatttgacctgaaactattttctct---ctctttggatggtgaaccatgtacattgtgtgtttctgcagGGTGATAGTATCCTTGCTGATTCTGGCACGGAGCAACTTGAATTTATAGCTTTGTCACAGAGGACTGGTGATCCCAAGTATCAACAAAAG
upper sequence: Vv09s0054g00370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 6
-attaataaatac-atgaaatgaaaaaaaataaaaaatcaaacatatatccatggta-attgatttcattgttttttaaaatgtataattttcctgttcctagGGTGATAGTATCCTAGCGGATTCCGGCACAGAGCAGCTGGAGTTTATTGCCCTTTCTCAAAGGACTGGTGATCCAAAGTATCAGAAAAAG
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gagtaccaagtgtgatcaggtttagatatgtttcagtttcattgaggacatgtgctgtgtcagttttactgattgctacacttttt---ttttgttttactagGGAGACAGTATTCTCGCAGACTCCGGCACTGAGCAGCTCGAGTTTATTGCCCTTTCCCAAAGGACAGGGGACCCAAAATATCAGCAGAAG
upper sequence: Vv09s0054g00370.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 6
----attaataaatacatga--aatg-aaaaaaaataaaaaatcaaacatatatccatggtaattgatttcattgttttttaaaatgtataattttcctgttcctagGGTGATAGTATCCTAGCGGATTCCGGCACAGAGCAGCTGGAGTTTATTGCCCTTTCTCAAAGGACTGGTGATCCAAAGTATCAGAAAAAG
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tttcactagcaagctcatgtttaatgtggaatgggtaccatctgatctatttacatatgtctttcggtttagttgattgtt------tacttctttcttgttt-tagGGAGACAGTATTCTTGCAGATTCTGGTACTGAGCAGCTTGAATTTATTGCCCTTTCCCAGAGGACAGGGGACCCAAAATATCAGCAAAAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|46917940|gb|CN547269.1|CN547269EST: ACATTATTAACTTGGCACATGGAAATGCACATAACCCTGGATGGACTGGA GGTGACAGTATCCTAGCGGATTCCGGCACAGAGCAGCTGGAGTTTATTGCC
genomic: ACATTATTAACTTGGCACATGGAAATGCACATAACCCTGGATGGACTGGAgtaagtgtct ... ctgttcctagGGTGATAGTATCCTAGCGGATTCCGGCACAGAGCAGCTGGAGTTTATTGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atccatggtaattgatttcattgttttttaaaatgtataattttcctgttcctagGGTGATAGTATCCTAGCGGATTCCGGCACAGAGCAGCTGGAGTTTATTGCCCTTTCTCAAAGGACTGGTGATCCAAAGTATCAGAAAAAG
aattgat putative branch site (score: 4)
ttttcctgttcct putative PPT
taattgatttcattgt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attaataaatacatgaaatgaaaaaaaataaaaaatcaaacatatatccatggtaattgatttcattgttttttaaaatgtataattttcctgttcctagGGTGATAGTATCCTAGCGGATTCCGGCACAGAGCAGCTGGAGTTTATTGCCCTTTCTCAAAGGACTGGTGATCCAAAGTATCAGAAAAAG
- -aataaat
- - - - - -catgaaa
- - - - - - - - - - aaaaaaa
- - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - caaacat
- - - - - - - - - - - - - - - - - - - - - - - -ccatggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaatgt