Sequence
atgc intronic sequence ATGC exonic sequence...ttaataaatacatgaaatggaaaaaaaaaaaaaatcaaacatatatccatggtaattgatttcattgttttttaaaatgtataattttccttgttcctagGGTGACAGTATCCTAGCCGATTCCGGCACAGAGCAGCTGGAGTTTATTGCCCTTTCTCAAAGGACTGGTGATCCAAAGTATCAGAAAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0054g00230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 6
--ttaataaatacatgaaatggaaaaaaaaaaaaaatcaaacatatatccatggtaattgatttcattgttttttaaaatgtata-attttccttgttcctagGGTGACAGTATCCTAGCCGATTCCGGCACAGAGCAGCTGGAGTTTATTGCCCTTTCTCAAAGGACTGGTGATCCAAAGTATCAGAAAAAG
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catcaataattgctcaatggattgtttataaatgcatttgacctgaaactattttctct---ctctttggatggtgaaccatgtacattgtgtgtttctgcagGGTGATAGTATCCTTGCTGATTCTGGCACGGAGCAACTTGAATTTATAGCTTTGTCACAGAGGACTGGTGATCCCAAGTATCAACAAAAG
upper sequence: Vv09s0054g00230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 6
--ttaataaatac-atgaaatggaaaaaaaaaaaaaatcaaacatatatccatggta-attgatttcattgttttttaaaatgtataattttccttgttcctagGGTGACAGTATCCTAGCCGATTCCGGCACAGAGCAGCTGGAGTTTATTGCCCTTTCTCAAAGGACTGGTGATCCAAAGTATCAGAAAAAG
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gagtaccaagtgtgatcaggtttagatatgtttcagtttcattgaggacatgtgctgtgtcagttttactgattgctacacttt----ttttttgttttactagGGAGACAGTATTCTCGCAGACTCCGGCACTGAGCAGCTCGAGTTTATTGCCCTTTCCCAAAGGACAGGGGACCCAAAATATCAGCAGAAG
upper sequence: Vv09s0054g00230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 6
-----ttaataaatacatgaa-atggaaaaaaaaaaaaaatcaaacatatatccatggtaattgatttcattgttttttaaaatgtataattttccttgttcctagGGTGACAGTATCCTAGCCGATTCCGGCACAGAGCAGCTGGAGTTTATTGCCCTTTCTCAAAGGACTGGTGATCCAAAGTATCAGAAAAAG
|| || |||| | | || | ||| | ||| | ||| || |||| |||| | | ||| || || | | | ||||| |||||||| || || ||||| || || |||||||| || |||||||||||||| || ||||| || || ||||| |||||| |||||
tttcactagcaagctcatgtttaatgtggaatgggtaccatctgatctatttacat----atgtctttcg--gtttagttgattgtttacttctttcttgttttagGGAGACAGTATTCTTGCAGATTCTGGTACTGAGCAGCTTGAATTTATTGCCCTTTCCCAGAGGACAGGGGACCCAAAATATCAGCAAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccatggtaattgatttcattgttttttaaaatgtataattttccttgttcctagGGTGACAGTATCCTAGCCGATTCCGGCACAGAGCAGCTGGAGTTTATTGCCCTTTCTCAAAGGACTGGTGATCCAAAGTATCAGAAAAAG
aattgat putative branch site (score: 4)
ttttccttgttcct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaataaatacatgaaatggaaaaaaaaaaaaaatcaaacatatatccatggtaattgatttcattgttttttaaaatgtataattttccttgttcctagGGTGACAGTATCCTAGCCGATTCCGGCACAGAGCAGCTGGAGTTTATTGCCCTTTCTCAAAGGACTGGTGATCCAAAGTATCAGAAAAAG
- aataaat
- - - - - catgaaa
- - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - -caaacat
- - - - - - - - - - - - - - - - - - - - - - - ccatggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaatgt