Sequence
atgc intronic sequence ATGC exonic sequence...ccaaatggagcctgaaaaaagaaagaaaagagaaaaacttgcttgatagtgcctaagaatatggtgaatgcctttctaacttctggacatgggtgtgcagATCAAACAAGCCTAATGGACAGCCTAAGTGGCTTCTTTCTTTTATTCCAGATTATCCGTTGCTCAACTTCATGCTCACGACTGCCATCTATATCTTA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os05g50510.1 (Oryza sativa), 3'ss of exon 13
-ccaaatggagcctgaaaaaagaaagaaaagagaaaaacttgcttgatagtgcctaagaatatggtgaatgcctttctaacttctggacatgggtgtgcagATCAAACAAGCCTAATGGACAGCCTAAGTGGCTTCTTTCTTTTATTCCAGATTATCCGTTGCTCAACTTCATGCTCACGACTGCCATCTATATCTTA
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tatgaaatacgtctaggatttgttggcattgtccactctattgtgtccagtgtttttaattttaagaactggaaccacgg-tgctgattcttattttacagGTCTAGCACGCCAAATGGGCAGCCAAAATGGCTCCTATCTTTTGTACCAGATTATCCATTGCTTAACTTCATGCTTACTACAGCAATCTATCTTCTT
upper sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G458538_T01 (Zea mays), 3'ss of exon 8
-------------------------------------------------------------------------------------------------ccaaatggagcctgaaaaaagaaagaaaagagaaaaacttgcttgatagtgcctaagaatatggtgaatgcctttctaacttctggacatgggtg---tgcagATCAAACAAGCCTAATGGACAGCCTAAGTGGCTTCTTTCTTTTATTCCAGATTATCCGTTGCTCAACTTCATGCTCACGACTGCCATCTATATCTTA
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gtatgactcttgagttacctctacgtttttccctaattattgaaggtgcttccagttcactaaccttgtggtaatagcatgttggtagaagatcaactccaatgtttcttctcatatagcagtagtttattcaactgaactaaaaatgctgctcaa-atg-tctttgcttcgccacattgtgaccaagcttcttttgcagGTCTAGCATGCCAAATGGACAACCAAAGTGGCTTCTTTGTTTCATACCAGATTATCCTATGCTTAACTTCATGCTTACTACAGCGATCTATCTTCTT
upper sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA05G25780.2 (Glycine max), 3'ss of exon 14
----ccaaatggagcctgaaaaaagaaagaaaagagaaaaacttgcttgatagtgcctaagaatatggtgaatgc-ctttctaacttctggacatgggtgtgcagATCAAACAAGCCTAATGGACAGCCTAAGTGGCTTCTTTCTTTTATTCCAGATTATCCGTTGCTCAACTTCATGCTCACGACTGCCATCTATATCTTA---
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gatcaagaacaaacattggaaaagattataatggaacgaaactcg--taaacgaacttcaactcagtaagagtgtacttgataatttcc---tctttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTTGTA
upper sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 14
----ccaaatggagcctgaaaaaagaaagaaaagagaaaaacttgcttgatagtgcctaagaatatggtgaatgcctttctaacttctggacatgggtgtgcagATCAAACAAGCCTAATGGACAGCCTAAGTGGCTTCTTTCTTTTATTCCAGATTATCCGTTGCTCAACTTCATGCTCACGACTGCCATCTATATCTTA
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gatcaagaacaaagataggaaaagattataatgaaacgaaacgtgcgaacgaacttcgactaagtaagagtgtac-ttgataatttcc---tctttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTT
upper sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 14
----ccaaatggagcctgaaaaaagaaagaaaagagaaaaacttgcttgatagtgcctaagaatatggtgaatgc-ctttctaacttctggacatgggtgtgcagATCAAACAAGCCTAATGGACAGCCTAAGTGGCTTCTTTCTTTTATTCCAGATTATCCGTTGCTCAACTTCATGCTCACGACTGCCATCTATATCTTA
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gatcaagaacaaacattggaaaagattataatggaacgaaactcg--taaacgaacttcaactcagtaagagtgtacttgataatttcc---tctttgcatacagGTCTAACATGCCAAACGGACAGCCCAAGTGGCTTCTTTCTCTTATCCCGGAGTATCCTATGCTCAACTTCATGCTAACAACTGCTATATACGTCTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atagtgcctaagaatatggtgaatgcctttctaacttctggacatgggtgtgcagATCAAACAAGCCTAATGGACAGCCTAAGTGGCTTCTTTCTTTTATTCCAGATTATCCGTTGCTCAACTTCATGCTCACGACTGCCATCTATATCTTA
ttctaac putative branch site (score: 1)
taagaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccaaatggagcctgaaaaaagaaagaaaagagaaaaacttgcttgatagtgcctaagaatatggtgaatgcctttctaacttctggacatgggtgtgcagATCAAACAAGCCTAATGGACAGCCTAAGTGGCTTCTTTCTTTTATTCCAGATTATCCGTTGCTCAACTTCATGCTCACGACTGCCATCTATATCTTA
ccaaatg
- - - - - - -gaaaaaa
- - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - agaaaaa
- - - - - - - - - - - - - - - - - - - -tgcttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - aagaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgaatg