Sequence
atgc intronic sequence ATGC exonic sequence...aatttcagtgtggtctttgttaaaaccttgaattcagtggtcagattttggcttaaaataaagaagatcattcaagaatgttgattttgttcctctgtagGTACGCAAATTCAGCAAACATTGCAGAAGTTGTGACAAATGTGTCGATGGGTTTGATCATCATTGTCGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0122g00920.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g49560.1 (Oryza sativa), 3'ss of exon 4
aatttcagtgtggtctttgttaaaaccttgaattcagtg-gtcagattttggcttaaaataaagaagatcattcaagaatgttgattt-tgttcctctgtagGTACGCAAATTCAGCAAACATTGCAGAAGTTGTGACAAATGTGTCGATGGGTTTGATCATCATTGTCGT
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--atttaacatatttgtttacagcagtttttattcactgtatatgctaataatccaaagttttggttcatactcagtaccctttccttgtacattgatatagGTGCGGAAAAATAGTAAACATTGTCGGAGTTGTGACAAATGTGTTGATGGTTTTGATCATCATTGCCGG
upper sequence: Vv18s0122g00920.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G010011_T02 (Zea mays), 3'ss of exon 5
aatttcagtgtggtctttgttaaaaccttgaattcagtggtcagattttggcttaaaataaagaagatcattcaagaatgttgattttg--ttcctctgtagGTACGCAAATTCAGCAAACATTGCAGAAGTTGTGACAAATGTGTCGATGGGTTTGATCATCATTGTCGT
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--tctttgtattaattttcagtgcactttatgtttggacacatggtatcaacacaaagttttaatcgatactaagtgcagttccctttgtattgtgatacagGTGCGCAAACATAGCAAGCACTGTCGAAGTTGCGACAAGTGTGTTGATGGGTTTGATCATCACTGCCGG
upper sequence: Vv18s0122g00920.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G01720.1 (Glycine max), 3'ss of exon 4
aatttcagtgtggtctttgttaaaaccttgaattcagtggtcagattttggcttaaaataaagaag-atcattcaagaatgttgattttgttcc--tctgtagGTACGCAAATTCAGCAAACATTGCAGAAGTTGTGACAAATGTGTCGATGGGTTTGATCATCATTGTCGT
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-attttaaaata--tctagttgaagagttttctttcctttccttacctcaccagagtattgaaaaccatgatgtatttacatctttttaattatattttgcagGTGCAGAAGTTTAGTAAGCATTGTCGAAGTTGTGACAAATGTGTTGATGGATTTGATCACCATTGTCGG
upper sequence: Vv18s0122g00920.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G01810.1 (Glycine max), 3'ss of exon 6
---aatttcagtgtggtctttgttaaaaccttgaattcagtggtcagattttggcttaaaataaagaagatcattcaagaatgttgattttgttcctctgtagGTACGCAAATTCAGCAAACATTGCAGAAGTTGTGACAAATGTGTCGATGGGTTTGATCATCATTGTCGT
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taaaatatctagttgaagagttttctttcctttccttgcctcaccagaatatggaaaaaaaaccatgatgtatttacatctttttagttatattt---tgcagGTTCGGAAGTTCAGTAAGCATTGTCGAAGTTGTGACAAATGTGTTGATGGATTTGATCACCATTGTCGG
upper sequence: Vv18s0122g00920.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S96_102V6.1 (Physcomitrella patens), 3'ss of exon 3
aatttcagtg--tggtctttgttaaaaccttgaattcagtggtcagattttggcttaaaataaagaagatcattcaagaatgttgattttgttcctctgtagGTACGCAAATTCAGCAAACATTGCAGAAGTTGTGACAAATGTGTCGATGGGTTTGATCATCATTGTCGT
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-gttgtattggtcaatgcttgtgaggggatctc-tctagcagcaaaatttcttttgtactaaaattgtgatagtaaaaactgtgtttgttctcgatttgtagGTTCGGAAGTACAGTAAACATTGCAGAAGCTGCGACAAATGTGTTGATGGCTTTGACCACCATTGTCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttggcttaaaataaagaagatcattcaagaatgttgattttgttcctctgtagGTACGCAAATTCAGCAAACATTGCAGAAGTTGTGACAAATGTGTCGATGGGTTTGATCATCATTGTCGT
tgttgat putative branch site (score: 4)
ttttgttcctctgt CT-rich tract
ttaaaataaagaagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatttcagtgtggtctttgttaaaaccttgaattcagtggtcagattttggcttaaaataaagaagatcattcaagaatgttgattttgttcctctgtagGTACGCAAATTCAGCAAACATTGCAGAAGTTGTGACAAATGTGTCGATGGGTTTGATCATCATTGTCGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - taaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cattcaa