Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgttcaataataagcgtaatagtactgtatcatatctgacaaatttccacagatcttgtgtttgacttgaaacttgtggtaatcaattttgttttgtatgtgtgatttatgtttttggtaattattatgcacactcctccacagGTAATTCCTCCTGGGATGGATTTCAGCAGTGTTGTGGTTCCTGAAGATACCAGCGATGGAGATGATGGCAAAGACTTTGAGATTGCCTCGCCGAGGTCAC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g69030.4 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g69030.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G875238_T01 (Zea mays), 3'ss of exon 4
gtaagtgttcaataataagcgtaatagtactgtatcatatctgacaaatttccacagatcttgtgtttgacttgaaacttgtggtaatcaattttgttttgtatgtgtgatttatgtttttggtaattattatgcacactcctccacagGTAATTCCTCCTGGGATGGATTTCAGCAGTGTTGTGGTTCCTGAAGATACCAGCGATGGAGATGATGGCAAAGACTTTGAGATTGCCTCGCCGAGGTCAC
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--------------gtaagtataaaaat-ctctgttatccatgccaagta---gtaagtgctg--ttcaacataaa--taattaaaatccatt---------------aatccatatat---gtattgattagagaactttgttggcagGTGATTCCTCCGGGAATGGATTTCAGCAATGTTGTAGTTCATGAAGACATTGATGGGGATGGTGACGTCAAAGATGATATCGTTGGTTTGGAGGGTGCCT
upper sequence: LOC_Os01g69030.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G140107_T01 (Zea mays), 3'ss of exon 5
gtaagtgttcaataataagcgtaatagtactgtatcatatctgacaaatttccacagatcttgtgtttgacttgaaacttgtggtaatcaattttgttttgtatgtgtgatttatgtttttggtaattattatgcacactcctccacagGTAATTCCTCCTGGGATGGATTTCAGCAGTGTTGTGGTTCCTGAAGATACCAGCGATGGAGATGATGGCAAAGACTTTGAGATTGCCTCGCCGAGGTCAC
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----------------------------------------------------------------gtaagtatttaaacctctcttg-tccataccaagtagtaaatgctgt-----tttactgtgttgattagagaactttgttgacagGTGATTCCTCCAGGAATGGATTTCAGCAATGTTGTGGTTCATGAAGACATTGATGGGGATGGTGACAGCAAAGATGATATCGTTGGTTTGGAGGGTGCTT
upper sequence: LOC_Os01g69030.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv05s0029g01140.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------------gtaagtgttcaataataa--gcgtaatagtactgtatcatatctgacaaatttccacagatcttgtgtttgacttgaaacttgtggtaatcaattttgttttgtatgtgtgatttatgttt-------ttggtaattattatgcacactcctccacagGTAATTCCTCCTGGGATGGATTTCAGCAGTGTTGTGGTTCCTGAAGATACCAGCGATGGAGATGATGGCAAAGACTTTGAGATTGCCTCGCCGAGGTCAC----
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gtacgaagactatcttttacattttatctatccatgcattatgaggatttgagattgaatgcatgttaatgtc-tacttgacctgagaacgcatttccattctaccgtcttcactaaccttaaagaagaatcacttactaaaggtcacaagaattttgtttaattgaatcaaaaattaccattaaaaatattttgcagGTTATTCCTCCTGGGATGGACTTTAGCAGTGTTGAGGTTCAGGAGGATGCCCCTGAAGTGGATGG----AGAACTCACGGCACTTGCTAGCTCTGATGGTTCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttttgtatgtgtgatttatgtttttggtaattattatgcacactcctccacagGTAATTCCTCCTGGGATGGATTTCAGCAGTGTTGTGGTTCCTGAAGATACCAGCGATGGAGATGATGGCAAAGACTTTGAGATTGCCTCGCCGAGGTCAC
cactcctcc CT-rich tract
atttatgtttttggta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgttcaataataagcgtaatagtactgtatcatatctgacaaatttccacagatcttgtgtttgacttgaaacttgtggtaatcaattttgttttgtatgtgtgatttatgtttttggtaattattatgcacactcctccacagGTAATTCCTCCTGGGATGGATTTCAGCAGTGTTGTGGTTCCTGAAGATACCAGCGATGGAGATGATGGCAAAGACTTTGAGATTGCCTCGCCGAGGTCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG