Sequence
atgc intronic sequence ATGC exonic sequence...atgttctaggctatctgacatgcaatagaataaattccatggacttcatgatactagcaatttaatgattgcctctataatttttttgctccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTCACCTGCTTGATGCAGATTTCAACAAGAACAGAAGACTTTATTGTGGACACTCTTAAGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G039096_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g06190.1 (Oryza sativa), 3'ss of exon 2
-------atgttctaggctatctgacatgcaatagaataaattccatggacttcatgatactagcaatttaatgattgcctctataatttttttgctccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTCACCTGCTTGATGCAGATTTCAACAAGAACAGAAGACTTTATTGTGGACACTCTTAAGC
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ttcattcatgttatgggc-atctgttatggaataaaacaacttctgaggcctt-gcagtgttaggaacttaagctttatttc---ggttcgtctgtt--gttttcagGTTGACTTGGAGCACAATCAATATAGGTCATTTCAGGGTTTGACCTGCTTGATGCAGATTTCAACAAGAACAGAGGATTTTGTTGTAGACACCCTTAAAC
upper sequence: GRMZM2G039096_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G13920.1 (Glycine max), 3'ss of exon 2
---atgttctaggctatctgac-atgcaatagaataaattcca---tggacttcatgatactagcaatttaatgattgcctctataatttttttgctcc--attttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTCACCTGCTTGATGCAGATTTCAACAAGAACAGAAGACTTTATTGTGGACACTCTTAAGC
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gtaaaaacaaacatcacttcattgtgcattaagttttactttgaactttccttcttgac-ctattatgtgtgcaactatatataatgattcatgatttgtaatatttagGTTGATTTGGAGCATAATCAATATCGCACTTTCCAAGGCTTGACTTGCCTGATGCAAATCTCAACAAGGACTGAAGATTTTATTGTTGACACTTTGAAAC
upper sequence: GRMZM2G039096_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G24130.1 (Glycine max), 3'ss of exon 3
----atgttctaggctatctgacatgcaataga---ataaattccatggacttcatgatactagcaatttaatgattgcctctataatttttttgctccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTCACCTGCTTGATGCAGATTTCAACAAGAACAGAAGACTTTATTGTGGACACTCTTAAGC
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gctgatattcc--cctttcttgtagtcactccctccattacttccattcattgcattcttttgacttatttatgtata-----atgacttgaagttgaaatgtatagGTTGATTTGGAACATAATCAATATCGGTCTTTCCAAGGTTTGACTTGCCTGATGCAAATTTCAACAAGGACTGAAGATTTTATTGTTGACACATTGAAAC
upper sequence: GRMZM2G039096_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT5G35910.1 (Arabidopsis thaliana), 3'ss of exon 2
atgttctaggctatctgacatgc-aatagaataaattcca--tggacttcatgatactagcaatttaatgattgcctctataatttttttgctccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTCACCTGCTTGATGCAGATTTCAACAAGAACAGAAGACTTTATTGTGGACACTCTTAAGC
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---ctctccttgattagataagccaaaaaaatatattcaagtttgagttgccaatgcttatttctcccctttctcttaagttttttgtttttgctctttttagGTTGATCTGGAGCATAATCAGTATAGATCTTTTCAAGGATTGACATGCTTGATGCAAATTTCCACCAGAACAGAGGATTATATAGTTGATACATTTAAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatgatactagcaatttaatgattgcctctataatttttttgctccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTCACCTGCTTGATGCAGATTTCAACAAGAACAGAAGACTTTATTGTGGACACTCTTAAGC
atttaat putative branch site (score: 4)
tttttttgctccattt putative PPT
tctataattttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgttctaggctatctgacatgcaatagaataaattccatggacttcatgatactagcaatttaatgattgcctctataatttttttgctccattttcagGTAGATCTGGAGCATAATCAATATAGGTCATTTCAGGGCTTCACCTGCTTGATGCAGATTTCAACAAGAACAGAAGACTTTATTGTGGACACTCTTAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC