Sequence
atgc intronic sequence ATGC exonic sequence...aaattgagttgcaactaacgtcactcttgtgtctatgcttagctttttggttgcaagtaaagaaaagctgatttatgattatgttgtcctgcatctgcagCTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGAAGTTGCAGGATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G048277_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os09g24540.1 (Oryza sativa), 3'ss of exon 1
aaattgagttgcaactaacgtcactcttgtgtctatgcttagctttttggttgcaagtaaagaaaagctgatttatgattatgttgtc-ctgcatctgcagCTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGAAGTTGCAGGATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGA
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-tttaaagctcttttggttaggattattctgttcgtggtaaatttcatgttgtttttttttttttgggtacttgactgctgtgttgttactggtttttcagCTAGGCACGTACTGTGCGAGAAGCAAGGGAAGATCAATGAAGCTTACAAGAAGTTGCAGGATGGCTGGTTGGACAACGGGGACAAGGTCCCTCCTGCCGA
upper sequence: GRMZM2G048277_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G21080.1 (Glycine max), 3'ss of exon 2
--aaattgagttgc--aactaacgtcactcttgtgtctatgcttagcttttt----ggttgcaagtaaagaaaagctgatttatgattatgttgtcctgcatctg-cagCTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGAAGTTGCAGGATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGA
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gtaaaaaaatttccccatccacggataccattgtaaccatgattagttcttttcatagtttgtcttagaatgacattgacatctt-ttatggctttttattcctttcagCTAGGCATATCCTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGAAGCTGCAGGATGGTTGGCTTGGCAATGGAGACAAGGTCCCACCAGCTGA
upper sequence: GRMZM2G048277_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G33180.2 (Glycine max), 3'ss of exon 2
aaattgagttgcaactaacgtcactcttgtgtctatgcttagctttttggttgcaagtaaagaaaagctgatttatgattatgttgtcctgcatc-tgcagCTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGAAGTTGCAGGATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGA
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-------gtagaaaatttc-ccccatctgtaaccatgattaattcttt--tcatagtttgtcttagaatgacatatttttttggctttttattccgttcagCAAGGCATATCTTATGTGAGAAACAAGGTAAGATCAATGAAGCCTACAAGAAGCTGCAGGATGGTTGGCTTTGCAACGGAGATAAGGTCCCACCAGCTGA
upper sequence: GRMZM2G048277_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT1G26550.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------------------------------aaattgagttgcaa-ctaacgtcactcttgtgtctatgcttagctttttggttgcaagtaaagaaaagctgatttatgattatgttgtcctgcatctgcagCTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGAAGTTGCAGGATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGA
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gtgtgttttttggattcgtttctgtgcctgttacctttgttcatgagtaaaaaatactggtaaacaaatatggatccaaaagttctcttacaacttttg--tattagtacaatagcattaaagtcaaatctccaattgtttttgtttcagCAAGACATGTTTTGTGCGAGAAGCAAGGAAAGATCAACGAGGCCTACAAAAAGTTGCAGGATGGTTGGTTGAGCAACGGAGACAAGGTTCCTCCTGCTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttggttgcaagtaaagaaaagctgatttatgattatgttgtcctgcatctgcagCTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGAAGTTGCAGGATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGA
agctgat putative branch site (score: 4)
atttatgattatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaattgagttgcaactaacgtcactcttgtgtctatgcttagctttttggttgcaagtaaagaaaagctgatttatgattatgttgtcctgcatctgcagCTAGGCACGTATTGTGTGAGAAGCAGGGGAAGATCAATGAAGCTTATAAGAAGTTGCAGGATGGATGGCTGAATAATGGGGACAAAGTTCCTCCTGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA