Sequence
atgc intronic sequence ATGC exonic sequence...caacacagcaggaaagagtcttgcctgcttgactagagaatgaaatggcacaatttggtacctaaaatggtcctgatttttaagataacattcctttcagGAGAGAGATAATATGCAGAAGACAGAGTTTTTGAAGGCATTATCAGATATGTGGAAGGATTTTGATTCCCGAGTTCTTCGATATAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G061681_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g42950.2 (Oryza sativa), 3'ss of exon 6
-----caacacagcaggaaagagtcttgcctgcttgactagagaatgaaatggcacaatttggtaccta-aaatggtcctgatttttaagataacattcctttcagGAGAGAGATAATATGCAGAAGACAGAGTTTTTGAAGGCATTATCAGATATGTGGAAGGATTTTGATTCCCGAGTTCTTCGATATAAA
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actaggagctttatctgcttgactgttgtttgtctaaacagacaacatact-----aatttgttacctagaaatggttataatctt-gatccaatatcgtcttcagGAGAGAGACAATATGCAGAAGACGGAGTTTCTGAAGGCATTATCGGATATGTGGAAGGACTTCGATTCCCGAGTTCTTCGGTATAAA
upper sequence: GRMZM2G061681_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G00470.1 (Glycine max), 3'ss of exon 6
-caacacagcaggaaagagtcttgcctgcttgactaga-gaatgaaatggcacaatttggtacctaaaatggtcctgatttttaagataacattcctttcagGAGAGAGATAATATGCAGAAGACAGAGTTTTTGAAGGCATTATCAGATATGTGGAAGGATTTTGATTCCCGAGTTCTTCGATATAAA
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gtaagatttttttagtttagccttttagcattacaaaatgtataacatg-ca-aattttagagttgaagt--tcttgatgat-gtgtcctcctttccttcagGAAAGAGATAACATGCAGAAGTCAGAGTTCTTAAAAGCATTGTCAGATATGTGGAAAGATTTTGATTCACGTGTATTGCGATACAAG
upper sequence: GRMZM2G061681_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA12G37070.1 (Glycine max), 3'ss of exon 6
-caacacagcaggaaagagtcttgcctgcttgactagagaatgaaatggcacaatttggtacctaaaatggtcctgatttttaagataacattcctttcagGAGAGAGATAATATGCAGAAGACAGAGTTTTTGAAGGCATTATCAGATATGTGGAAGGATTTTGATTCCCGAGTTCTTCGATATAAA
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gtaagatttttctagtttagccttttagcattacgaaatgttaacatg-ca-aattttagagttgaagt--tcttgatgat-gtgtcttcctttccttcagGAAAGAGATAACATGCAGAAGTCAGAGTTCTTAAAAGCATTGTCAGATATGTGGAAAGATTTTGATTCGCGCGTATTGCGATATAAG
upper sequence: GRMZM2G061681_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT1G71410.1 (Arabidopsis thaliana), 3'ss of exon 6
--------caacacagcaggaaagagtctt-gcctgcttgactagagaa---tgaaatggcacaatttg-gtacctaaaatggtcctgatttttaagataacattccttt----cagGAGAGAGATAATATGCAGAAGACAGAGTTTTTGAAGGCATTATCAGATATGTGGAAGGATTTTGATTCCCGAGTTCTTCGATATAAA
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gtacgtgtatatgcttccaataattgtttcagacagactgttcttagaagtcttagatgatggaaaatgtatctccacatttgataaccttttcggaacaattttctctttatccagGAAAGAGATAACATGCAAAAGTCCGAGTTCTTAAAAGCATTATCAGATATGTGGAAAGATTTTGATTCCCGTGTATTACGGTATAAG
upper sequence: GRMZM2G061681_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT1G22870.1 (Arabidopsis thaliana), 3'ss of exon 6
caacacagcaggaaagagtcttgcctgcttgactagagaatgaaatggc-acaatttggtacctaaaatggtcctgatttttaagataacattcctttcagGAGAGAGATAATATGCAGAAGACAGAGTTTTTGAAGGCATTATCAGATATGTGGAAGGATTTTGATTCCCGAGTTCTTCGATATAAA
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--gtat-gtatattaaattttaatcatcgtttcagacagacgtgattttgatagttggaaacatataaaacctttggggcatt--tttttatttattgcagGAGAGAGACAACATGCAGAAGTCTGAGTTCTTAAAAGCATTATCAGATATGTGGAAAGACTTTGATTCTCGTGTATTACGGTATAAG
upper sequence: GRMZM2G061681_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv18s0089g00030.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------caacacagcaggaaagagtcttgcc---tgcttgactagagaatgaaatggcacaatttggtacctaaaatggtcctgatttttaagataacattcctttcagGAGAGAGATAATATGCAGAAGACAGAGTTTTTGAAGGCATTATCAGATATGTGGAAGGATTTTGATTCCCGAGTTCTTCGATATAAA
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gtatgaagttatatttctttggatgtcacctgcttttgacataagattactaaaaaacattgtgcatgagaaggaaaaataagaagttggtggc--aatggaatctgagtaacaaattttatttttttgcagGAAAGGGATAACATGCAGAAGTCTGAGTTTCTAAAAGCATTATCGGATATGTGGAAAGATTTTGACTCTCGTGTTTTGCGTTATAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggcacaatttggtacctaaaatggtcctgatttttaagataacattcctttcagGAGAGAGATAATATGCAGAAGACAGAGTTTTTGAAGGCATTATCAGATATGTGGAAGGATTTTGATTCCCGAGTTCTTCGATATAAA
agataac putative branch site (score: 3)
cattcctttc CT-rich tract
atttttaagataacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caacacagcaggaaagagtcttgcctgcttgactagagaatgaaatggcacaatttggtacctaaaatggtcctgatttttaagataacattcctttcagGAGAGAGATAATATGCAGAAGACAGAGTTTTTGAAGGCATTATCAGATATGTGGAAGGATTTTGATTCCCGAGTTCTTCGATATAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG