Sequence
atgc intronic sequence ATGC exonic sequence...nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaaaaaaaaaaaaaaaaaaagatatagtgctgttataatgactcctgcaacttctggcagGTATGTGCATGGGGATGTAAAGCCTGAGAACTTTTTGCTTGGTCCTCCAGGAACTAATGAGGAGAAAAAACTGTTTCTTGTTGACCTTGGATTAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 6
-nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaaaaaaaaaaaaaaaaaaagatatagtgctgttataatgactcctgcaacttctggcagGTATGTGCATGGGGATGTAAAGCCTGAGAACTTTTTGCTTGGTCCTCCAGGAACTAATGAGGAGAAAAAACTGTTTCTTGTTGACCTTGGATTAG
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gtatttgtttttttctctgatcctctcttggcagtgaagcctaatagttttttgcatgttgcattttgaaatatagc--taactctt---atttatgttagGTATGTTCATGGTGATGTAAAACCTGAGAATTTTTTGCTTGGAACCCCAGGAACCCTGGAAGAGAAAAAACTTTTTCTTGTTGACCTTGGATTAG
upper sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 6
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaaaaaaaaaaaaaaaaaaagatatagtgctgttataatgactcctgcaacttctggcagGTATGTGCATGGGGATGTAAAGCCTGAGAACTTTTTGCTTGGTCCTCCAGGAACTAATGAGGAGAAAAAACTGTTTCTTGTTGACCTTGGATTAG
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gtaactcgacctgctcttcagatgttccgtaagagtgtttcacatggcgtctctgaa---gttttagc-------taataaattttgt---ttatgacagGTACGTCCATGGTGATGTGAAACCTGAGAACTTTTTGCTTGGTCCTCCAGATACCCCTGAAGGGAAGAAACTTTTTCTTGTTGATCTTGGACTAG
upper sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 6
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaaaaaaaaaaaaaaaaaaagatatagtgctgttataatgactcctgcaacttctggcagGTATGTGCATGGGGATGTAAAGCCTGAGAACTTTTTGCTTGGTCCTCCAGGAACTAATGAGGAGAAAAAACTGTTTCTTGTTGACCTTGGATTAG
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gtgatctgctttctgttgttgagatggaactttttttcttatatggttgttttaaaagtggat------ctcataagatg-cgtatatgac-----acagGTATGTCCATGGTGATGTGAAGCCTGAGAACTTCTTGCTTGGTCCTCCTGGTACCCCAGAGGAGAAGAAGCTTTTTCTTGTTGACCTTGGATTGG
upper sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 6
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaaaaaaaaaaaaaaaaaaagatatagtgctgttataatgactcctgcaacttctggcagGTATGTGCATGGGGATGTAAAGCCTGAGAACTTTTTGCTTGGTCCTCCAGGAACTAATGAGGAGAAAAAACTGTTTCTTGTTGACCTTGGATTAG
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--gtacctgatgtagtctagtcaaaggatagtaatatattttgtatactgtgtatagaatgata----gctaaagaaat--ctcttgt---ttatgatagGTACGTCCATGGAGATGTGAAGCCTGAAAATTTTTTGCTTGGACCTCCAGGCACCCTACAAGAGAAGAAACTTTTTCTCGTTGACCTTGGTTTAG
upper sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 6
-nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaaaaaaaaaaaaaaaaaaagatatagtgctgttataatgactcctgcaacttctggcagGTATGTGCATGGGGATGTAAAGCCTGAGAACTTTTTGCTTGGTCCTCCAGGAACTAATGAGGAGAAAAAACTGTTTCTTGTTGACCTTGGATTAG
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gtaattttctaatatttctgctactgtaactctctttcttcaagtggtttttatttgctaagaagcagtgctcctgt---------------ttcta-cagATATGTGCATGGCGATGTAAAACCAGAGAATTTTCTGCTTGGGCCTCCTGGAACTCCTGAAGAGAAAAAACTTTTCCTTGTAGACCTCGGCTTAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaaaaaaaaaaaagatatagtgctgttataatgactcctgcaacttctggcagGTATGTGCATGGGGATGTAAAGCCTGAGAACTTTTTGCTTGGTCCTCCAGGAACTAATGAGGAGAAAAAACTGTTTCTTGTTGACCTTGGATTAG
cttct CT-rich tract
aaaaaaaaaagatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaaaaaaaaaaaaaaaaaaagatatagtgctgttataatgactcctgcaacttctggcagGTATGTGCATGGGGATGTAAAGCCTGAGAACTTTTTGCTTGGTCCTCCAGGAACTAATGAGGAGAAAAAACTGTTTCTTGTTGACCTTGGATTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgtt