Sequence
atgc intronic sequence ATGC exonic sequence...ccatgattttgaaagcacgtttttcatttcattagtgcagtttccatgacatcatataacgagtctcatcacagaagtggtattacttatttggctgcagGTACAACTTGTGCAACTGTGCTGACTCAGGCAATATTTACAGAAGGCTGCAAGTCTGTAGCTGCTGGTGTAAATGCAATGGATTTACGCAGTGGTATCAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0002g02240.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os05g46290.1 (Oryza sativa), 3'ss of exon 3
ccatgattttgaaagcacgtttttcatttcattagtgcagtttccatgac--atcatataacgagtctca-tcacagaagtggtattacttatttggctgcagGTACAACTTGTGCAACTGTGCTGACTCAGGCAATATTTACAGAAGGCTGCAAGTCTGTAGCTGCTGGTGTAAATGCAATGGATTTACGCAGTGGTATCAA
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-cctcatcgcaaacat-tatcaaccctatgaatagcataattactagcatgaatataatattcagtgtcactcactgcatttctggt-tgtatggggtaacagGTACCACTTGTGCAACTGTACTTACACAGGCTATTCTTACGGAAGGCTGCAAGGCTGTGGCAGCAGGGGTCAATGTTATGGACTTACGTAATGGCATAAA
upper sequence: Vv09s0002g02240.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G01190.1 (Glycine max), 3'ss of exon 3
ccatgattttgaaagcacgtttttcatttcattagtgcagtttccatgacatcata-taacgagtctcatcacagaagt-ggtattacttatttggctgcagGTACAACTTGTGCAACTGTGCTGACTCAGGCAATATTTACAGAAGGCTGCAAGTCTGTAGCTGCTGGTGTAAATGCAATGGATTTACGCAGTGGTATCAA
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-gtggaaaacatagagacgaacacagttatatttgc-ctttatctattcccttttaatactcattcatatcttacaagtcaatgtttcttctctgattccagGTACAACTTGTGCAACTGTTTTGACTCAGGCAATACTCACAGAAGGATGCAAATCGATTGCTGCTGGTGTAAATGTTATGGATTTACGTCATGGAATAAA
upper sequence: Vv09s0002g02240.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G20560.2 (Glycine max), 3'ss of exon 2
ccatgattttgaaagcacgtttttcatttcattagtgcagtttccatgacatcat--ataacgagtctcatcacagaagt-ggtattacttatttggctgcagGTACAACTTGTGCAACTGTGCTGACTCAGGCAATATTTACAGAAGGCTGCAAGTCTGTAGCTGCTGGTGTAAATGCAATGGATTTACGCAGTGGTATCAA
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--aggaaaacatagggacgaactcagttatatttgc-ctttatctattccctttttaatactcattcatatcttacaagtcactgtttcttctctgattccagGTACAACTTGTGCAACTGTTTTGACTCAGGCAATACTCACAGAAGGATGTAAATCGATTGCTGCTGGCATAAATGTTATGGACTTACGTAATGGAATAAA
upper sequence: Vv09s0002g02240.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G13860.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------ccatgattttgaaagcacgtttttcatttcattagtgcagttt--ccatgacatcatataacgagtctcatcacagaagtggtattacttatttggctgcagGTACAACTTGTGCAACTGTGCTGACTCAGGCAATATTTACAGAAGGCTGCAAGTCTGTAGCTGCTGGTGTAAATGCAATGGATTTACGCAGTGGTATCAA
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gtaatattttctcttttgagttcataatcatggataagtttttattgaaaacatacggtgaagagataatagta-aagtcttaatttctgcttgccttcctttcgtta--tatagGTACCACTTGTGCCACTGTTTTGACTCAGGCGATACTCATCGAAGGCTGCAAGTCGGTGGCTGCAGGTGTAAATGTGATGGATTTGCGTGTTGGAATTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgacatcatataacgagtctcatcacagaagtggtattacttatttggctgcagGTACAACTTGTGCAACTGTGCTGACTCAGGCAATATTTACAGAAGGCTGCAAGTCTGTAGCTGCTGGTGTAAATGCAATGGATTTACGCAGTGGTATCAA
atataac putative branch site (score: 3)
cttattt putative PPT
tattacttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccatgattttgaaagcacgtttttcatttcattagtgcagtttccatgacatcatataacgagtctcatcacagaagtggtattacttatttggctgcagGTACAACTTGTGCAACTGTGCTGACTCAGGCAATATTTACAGAAGGCTGCAAGTCTGTAGCTGCTGGTGTAAATGCAATGGATTTACGCAGTGGTATCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
ccatgat
- - - - - gaaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatcac