Sequence
atgc intronic sequence ATGC exonic sequencegtgagttccttttctctttctgatgtcacaacaaatttcattctactagatttttgttcacccttttagtagtcaaactgatctggtctggttaaatgttctcaacactttcagCGGCTTGCAGTTGGCATCTTAATTTCCGGATTTGCTTTTGATGAGGATGACTTTTGTAGACCTTGGGAAGGATGGCAGGATAACCTAGAGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g02170.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g02170.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G092776_T05 (Zea mays), 3'ss of exon 7
-----gtgagttccttttctctttctgatgtcacaacaaatttcattctactagatttttgttcacccttttagtagtcaaactgatctggtctggttaaatgttctcaacactttcagCGGCTTGCAGTTGGCATCTTAATTTCCGGATTTGCTTTTGATGAGGATGACTTTTGTAGACCTTGGGAAGGATGGCAGGATAACCTAGAGAG
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agggtgtgagtcccttttttctctctc------------------tctgacaaaaatgctactcacccattttggaatgaaattgatctcgtctttgtaaatgttgctaattctt-cagCGCCTTGCTGTTGGCATCTTGGTTTCTGGATTTGCTTTTGATGAGGAGGATTTCTGGAAACCTTGGGAAGGATGGAAGGATAACCTAGAGAA
upper sequence: LOC_Os03g02170.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G092776_T01 (Zea mays), 3'ss of exon 8
--gtgagttccttttctctttctgatgtcacaacaaatttcattctactagatttttgttcacccttttagtagtcaaactgatctggtctggttaaatgttctcaacactttcagCGGCTTGCAGTTGGCATCTTAATTTCCGGATTTGCTTTTGATGAGGATGACTTTTGTAGACCTTGGGAAGGATGGCAGGATAACCTAGAGAG
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gtgtgagtcccttttttctctctc------------------tctgacaaaaatgctactcacccattttggaatgaaattgatctcgtctttgtaaatgttgctaattctt-cagCGCCTTGCTGTTGGCATCTTGGTTTCTGGATTTGCTTTTGATGAGGAGGATTTCTGGAAACCTTGGGAAGGATGGAAGGATAACCTAGAGAA
upper sequence: LOC_Os03g02170.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G092776_T04 (Zea mays), 3'ss of exon 8
gtgagttccttttctctttctgatgtcacaacaaatttcattctactagatttttgttcacccttttagtagtcaaactgatctggtctggttaaatgttctcaacactttcagCGGCTTGCAGTTGGCATCTTAATTTCCGGATTTGCTTTTGATGAGGATGACTTTTGTAGACCTTGGGAAGGATGGCAGGATAACCTAGAGAG
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gtgagtcccttttttctctctc------------------tctgacaaaaatgctactcacccattttggaatgaaattgatctcgtctttgtaaatgttgctaattctt-cagCGCCTTGCTGTTGGCATCTTGGTTTCTGGATTTGCTTTTGATGAGGAGGATTTCTGGAAACCTTGGGAAGGATGGAAGGATAACCTAGAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acccttttagtagtcaaactgatctggtctggttaaatgttctcaacactttcagCGGCTTGCAGTTGGCATCTTAATTTCCGGATTTGCTTTTGATGAGGATGACTTTTGTAGACCTTGGGAAGGATGGCAGGATAACCTAGAGAG
aactgat putative branch site (score: 3)
cactttc putative PPT
ttaaatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttccttttctctttctgatgtcacaacaaatttcattctactagatttttgttcacccttttagtagtcaaactgatctggtctggttaaatgttctcaacactttcagCGGCTTGCAGTTGGCATCTTAATTTCCGGATTTGCTTTTGATGAGGATGACTTTTGTAGACCTTGGGAAGGATGGCAGGATAACCTAGAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG