Sequence
atgc intronic sequence ATGC exonic sequence...gctttcttctgttacaccccatcccaccaaaaaaaaaaaaaaaggaaagcttcaaagtttatgattaccaaatttaactcattggaacaaattgctgcagCGTTTTGGAAGTGGTTCTGTGCCAACTCACCTTATTGGAGCTGCATTACTCAGAGGAGAGTGGGAAACTGCTGTGAGCTTGATTCTGGATCCAAGAGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0030g01850.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g43374.1 (Oryza sativa), 3'ss of exon 5
gctttcttctgttacaccccatcccaccaaaaaaaaaaaaaaaggaaagcttcaaagtttatgattaccaaatttaactcattggaacaaattgctgcagCGTTTTGGAAGTGGTTCTGTGCCAACTCACCTTATTGGAGCTGCATTACTCAGAGGAGAGTGGGAAACTGCTGTGAGCTTGATTCTGGATCCAAGAGAAG
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gtatgaagccagaaccttttcgttatgcttcaaaacctaactggtacgtgtttacttttgaagctcatcaagttcatcttttttg------ttggt-tagCGTTTTGGAAGTGGTTCAGTACCTACTCACCTTGTTGGAGCTGCTTTGCTTAGAGGAGAGTGGAGAAGTTCTGTAAATTTGATTCTTGATCCAAGGGAAG
upper sequence: Vv14s0030g01850.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G173137_T01 (Zea mays), 3'ss of exon 8
gctttcttctgttacaccccatcccaccaaaaaaaaaaaaaaaggaaagcttcaaagtttatgattaccaaatttaactcattggaacaaattgctgcagCGTTTTGGAAGTGGTTCTGTGCCAACTCACCTTATTGGAGCTGCATTACTCAGAGGAGAGTGGGAAACTGCTGTGAGCTTGATTCTGGATCCAAGAGAAG
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--------------------gtattatgtcctcaagtttaaaactattgccctgttatttctga--agctcatcgattttatgttttcatctggtt--agCGGTTTGGAAGTGGTTCAATACCAACACATCTTGTTGGGGCTGCTTTGCTTAGAGGAGAGTGGAAGGTTGCTGTAAACTTGATTCTTGATCCAAGGGAAG
upper sequence: Vv14s0030g01850.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G427822_T01 (Zea mays), 3'ss of exon 7
gctttcttctgttacaccccatcccaccaaaaaaaaaaaaaaaggaaagcttcaaagtttatgattaccaaatttaactcattggaacaaattgctgcagCGTTTTGGAAGTGGTTCTGTGCCAACTCACCTTATTGGAGCTGCATTACTCAGAGGAGAGTGGGAAACTGCTGTGAGCTTGATTCTGGATCCAAGAGAAG
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---------------gtattatatcctcaagtttaaaactattgccctgtt--atttctgaagctcatcgattttatcttttc--atctggtt-----agCAGTTTGGAAGTGGTTCAATACCAACACATCTTGTTGGGGCTGCTTTGCTTAGAGGAGAGTGGAAGGTTGCTGTAAACTTGATTCTTGATCCAAGGGAAG
upper sequence: Vv14s0030g01850.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G43270.1 (Glycine max), 3'ss of exon 9
gctttcttctgttacaccccatcccaccaaaaaaaaaaaaaaaggaaagcttcaaagtttatgattaccaaattt--aactcattggaacaaattgctgcagCGTTTTGGAAGTGGTTCTGTGCCAACTCACCTTATTGGAGCTGCATTACTCAGAGGAGAGTGGGAAACTGCTGTGAGCTTGATTCTGGATCCAAGAGAAG
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gttcatttctattagactg-attattttaagacttaattttatttttcattt-atgctttacaagcaactaatttgtatgtgaatgtgctcactgtgctcagCGTTTTGGAAGTGGTTCTTTGCCAACTCACCTTATTGGAGCTGCATTACTCCGAGGGGAATGGAAACTTGCTGTAGACATGATCCTCGATCCAAGAGATG
upper sequence: Vv14s0030g01850.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G40600.1 (Glycine max), 3'ss of exon 9
gctttcttctgttacaccccatcccaccaaaaaaaaaaaaaaaggaaagcttcaaagtttatgattaccaaatttaactcattgg-aacaaattgctg------cagCGTTTTGGAAGTGGTTCTGTGCCAACTCACCTTATTGGAGCTGCATTACTCAGAGGAGAGTGGGAAACTGCTGTGAGCTTGATTCTGGATCCAAGAGAAG
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-----cttgagagtgaatcaggcctaattcatttctaatagactgattattttaacattttt--ttttcatttttgctttatgagcaactaatttgtatgtgctcagCGTTTTGGAAGTGGTTCTTTGCCAACTCACCTTATTGGAGCTGCATTACTCCAAGGGGAATGGAAACTTGCTGTAGACATGATCCTTGATCCAAGAGATG
upper sequence: Vv14s0030g01850.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G04820.1 (Arabidopsis thaliana), 3'ss of exon 9
----------------------------------------------------gctttcttctgtta---caccccatcccaccaaaaaaaaaaaaaaaggaaagcttcaaagtttatgattaccaaatttaactcattgga---acaaat-tgctgcagCGTTTTGGAAGTGGTTCTGTGCCAACTCACCTTATTGGAGCTGCATTACTCAGAGGAGAGTGGGAAACTGCTGTGAGCTTGATTCTGGATCCAAGAGAAG
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gtactattctcttgtcgagttgtaatgatatatatgttattttctctttttagtttttagtagctaattcaacttacacttttgcattgtggtatcgagtagtacttgaatattatcaaatagaaatattttcttatgaattttgtaattgtgtgacagCGTTTTGGAAGTGGTTCAGTACCAACCCACCATGTAGGAGCTGCACTATTGAAAGGAGAGTGGAAAGATGCTGTAGACATGATTCTTGATCCAAGAGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagcttcaaagtttatgattaccaaatttaactcattggaacaaattgctgcagCGTTTTGGAAGTGGTTCTGTGCCAACTCACCTTATTGGAGCTGCATTACTCAGAGGAGAGTGGGAAACTGCTGTGAGCTTGATTCTGGATCCAAGAGAAG
atttaac putative branch site (score: 3)
aaagtttatgatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gctttcttctgttacaccccatcccaccaaaaaaaaaaaaaaaggaaagcttcaaagtttatgattaccaaatttaactcattggaacaaattgctgcagCGTTTTGGAAGTGGTTCTGTGCCAACTCACCTTATTGGAGCTGCATTACTCAGAGGAGAGTGGGAAACTGCTGTGAGCTTGATTCTGGATCCAAGAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - -cttctgt
- - - - - - - - - ccatccc
- - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - -ggaaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaacaa