Sequence
atgc intronic sequence ATGC exonic sequencegtaagtatattttattcttactgactccaggtgttttatctaaaataaggacaaaattagtatataatcatgttatgagataatttcagGTGTTCTCTGCTTTTGGTACTGTTCAAAAGATTGCAATGTTTGAGAAGAATGGTGGAATGCAGGCCTTAATTCAATATCCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os08g33830.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G178169_T01 (Zea mays), 3'ss of exon 7
gtaagtatatttta----ttcttactgactccaggtgttttatctaaaataaggacaaaattagtatataatcatgtta-tgagataatttcagGTGTTCTCTGCTTTTGGTACTGTTCAAAAGATTGCAATGTTTGAGAAGAATGGTGGAATGCAGGCCTTAATTCAATATCCAG
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gtaagaataacccagtaccttttgtttatttcaaataaag-agctgacatgaaagcaagct----gtatagttacattaatgtgataatttcagGTGTTTTCTGCTTTTGGTGCTGTTCAAAAAATTGCCATGTTTGAGAAGAATGGTGGAATGCAGGCTCTAATTCAATATCCAG
upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G082174_T05 (Zea mays), 3'ss of exon 5
gtaagtatatttta----ttcttactgactccaggtgttttatctaaaataaggacaaaattagtatataatcatgttatgagataatttcagGTGTTCTCTGCTTTTGGTACTGTTCAAAAGATTGCAATGTTTGAGAAGAATGGTGGAATGCAGGCCTTAATTCAATATCCAG
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gtaagaataacctagaaccttttgtttatttcaaacaaag-agctgactt--ggatgcaagctgtttagttacatga-atgcaataatttcagGTGTTTTCTGCTTTTGGAGCTGTTCAAAAAATTGCAATGTTTGAGAAGAATGGTGGAATGCAGGCTCTAATCCAATATCCAG
upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA18G49580.1 (Glycine max), 3'ss of exon 7
gtaagtatattttattcttactgactccaggtgttttatctaaaataaggacaaaattagtatataatcatgttatgagataatttcagGTGTTCTCTGCTTTTGGTACTGTTCAAAAGATTGCAATGTTTGAGAAGAATGGTGGAATGCAGGCCTTAATTCAATATCCAG-
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-tgagaat-ttgtattttt-ctg-cttaa-------tgtccaaacctgtaagtgatttataatctcacatcactggtctatctttacaggTGTTCTCTGCATTTGGTACTGTCCAGAAAATTGCTATATTTGAAAAGAACGGTCAAACTCAGGCACTGATTCAGTACCCTGG
upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA09G37080.1 (Glycine max), 3'ss of exon 8
gtaagtatattttattcttactgactccaggtgttttatctaaaataaggacaaaattagtatataatcatgttatgagataatttcagGTGTTCTCTGCTTTTGGTACTGTTCAAAAGATTGCAATGTTTGAGAAGAATGGTGGAATGCAGGCCTTAATTCAATATCCAG
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gtgagaat-ttgcattttt-ctg-cttaa-------tatccaaacctgtaagtgatttataatctcacatcaccggtctatctttacagGTGTTCTCTGCATTTGGTACTGTCCAGAAAATTGCTATATTTGAAAAGAATGGTCAAACTCAGGCACTAATTCAGTACCCTG
upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G01150.2 (Arabidopsis thaliana), 3'ss of exon 5
gtaagtatattttattcttactgactccaggtgttttatctaaaataaggacaaaattagtatataatcatgttatgagataatttcagGTGTTCTCTGCTTTTGGTACTGTTCAAAAGATTGCAATGTTTGAGAAGAATGGTGGAATGCAGGCCTTAATTCAATATCCAG
||||| | | | || | | | | | | | ||||| | | | | | ||| | | | | | | ||||||| ||||| | ||| ||||| || |||||||| || ||||||||||||||| || ||| || ||||||||||| | |
gtaagga-acaacagtcatgcacatttctgct------tctaag---cattcttagtctctcaaaaataacatcctttgcttctcatagGTGTTTTCTGCATATGGAACTGTCCAGAAGATTGCTATATTTGAGAAGAATGGTTCAACGCAAGCATTAATTCAATACTCTG
upper sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv14s0108g01030.t01 (Vitis vinifera), 3'ss of exon 7
gtaagtatattttattcttactgactccaggtgttttatctaaaataaggacaaaattagtatataatcatgttatgagata-atttcagGTGTTCTCTGCTTTTGGTACTGTTCAAAAGATTGCAATGTTTGAGAAGAATGGTGGAATGCAGGCCTTAATTCAATATCCAG
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gtgagtaattctatttatgatttcctccaatgatcttttttatcatgtgggatgtact--catactgtgatgtcggatcacctatttcagGTATTCTCTGCATTTGGTACTGTCCAGAAAATTGCCATATTTGAGAAGAATGGTGGGATGCAGGCTCTAATTCAATATCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatctaaaataaggacaaaattagtatataatcatgttatgagataatttcagGTGTTCTCTGCTTTTGGTACTGTTCAAAAGATTGCAATGTTTGAGAAGAATGGTGGAATGCAGGCCTTAATTCAATATCCAG
atctaaa putative branch site (score: 3)
aaaattagtatataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtatattttattcttactgactccaggtgttttatctaaaataaggacaaaattagtatataatcatgttatgagataatttcagGTGTTCTCTGCTTTTGGTACTGTTCAAAAGATTGCAATGTTTGAGAAGAATGGTGGAATGCAGGCCTTAATTCAATATCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA