Sequence
atgc intronic sequence ATGC exonic sequencegtaaggcttcattttaaggtctcataattattctttttacaatatgtcgctgttatttttatactgttctattgtaaaaaatatacttctttagGCTGGACAACCAGAGCTGATTTCTCTTGAGAAGTCACTTAAGGAGGCAATGGTTCCTGCAGGAACTGCAAGAGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g19690.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g19690.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G135968_T01 (Zea mays), 3'ss of exon 2
gtaaggcttcattttaaggtctcataattattctttttacaatatgtcgctgttatttttatactgttctattgtaaaaaatatacttctttagGCTGGACAACCAGAGCTGATTTCTCTTGAGAAGTCACTTAAGGAGGCAATGGTTCCTGCAGGAACTGCAAGAGAG
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gtaatgcctcatttagataa-taatgaat-ttcttttcacaa-atgt----gttatcct-atcgtcacccattgcaa---------ttttctagGCTGGACAACCGGAGCTGATATCTCTCGAGAAGTCACTGAAGGAGGCCATGCAACCTGCAGGAATTGCAAGAGAT
upper sequence: LOC_Os03g19690.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA07G36730.1 (Glycine max), 3'ss of exon 2
----gtaaggcttcattttaaggtctcataattat-tctttttacaatatgtcgctgttatttttatactgttctattgtaaaaaatatactt-ctttagGCTGGACAACCAGAGCTGATTTCTCTTGAGAAGTCACTTAAGGAGGCAATGGTTCCTGCAGGAACTGCAAGAGAG
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cctagtcaaaaattgtcacctggctatgcatcgaaatcaaattttactttagaaatattatggattaaccaagacaatttaaaattaattgtcgctgtagGCTGGACAGCCTGAACTGATAGCACTTGAGAAAGAACTGAAAGAGGCAATGGTTCCTGCAGGAAAAGCAAGAGAG
upper sequence: LOC_Os03g19690.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv05s0077g00820.t01 (Vitis vinifera), 3'ss of exon 2
------gtaaggcttcattttaaggtctcataattattctttttacaatatgtcgctgttatttttat--actgttctattgtaaaaaatatacttctttagGCTGGACAACCAGAGCTGATTTCTCTTGAGAAGTCACTTAAGGAGGCAATGGTTCCTGCAGGAACTGCAAGAGAG
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atggcaatgaagccaaagaatggaatgcaac--tttatcttttgagtcggtgcaagtgctactccttttaaccattacattatgtatttgtcctcactacagGCTGGGCAACCAGAGCTGATAGCACTGGAGAAGGCACTGAAAGAGGCCATGGTTCCTGCTGGAACTGCTAGAGAG
upper sequence: LOC_Os03g19690.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv05s0077g00250.t01 (Vitis vinifera), 3'ss of exon 2
------gtaaggcttcattttaaggtctcataattattctttttacaatatgtcgctgttatttttat--actgttctattgtaaaaaatatacttctttagGCTGGACAACCAGAGCTGATTTCTCTTGAGAAGTCACTTAAGGAGGCAATGGTTCCTGCAGGAACTGCAAGAGAG
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atggcaatgaagccaaagaatggagtgcaac--tttatcttttgagtcggtgcaagtgctactccttttaaccattacataatgtatttgtctacactacagGCTGGGCAACCAGAGCTGATAGCACTGGAGAAGGCACTGAAAGAGGCCATGGTTCCTGCTGGAACTGCTAGAGAG
upper sequence: LOC_Os03g19690.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv05s0077g00200.t01 (Vitis vinifera), 3'ss of exon 1
---gtaaggcttcattttaaggtctcataattat-tctttttacaatatgtcgctgttatttttat--actgttctattgtaaaaaatatacttctttagGCTGGACAACCAGAGCTGATTTCTCTTGAGAAGTCACTTAAGGAGGCAATGGTTCCTGCAGGAACTGCAAGAGAG
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atggcaatgatgccaaagaatggagtgcaactttatcttttgagtcggtgcaagtgctactccttttaaccattacattatgtatttgtctacactacagGCTGGGCAACCAGAGCTGATAGCACTGGAGAAGGCACTGAAAGAGGCCATGGTTCCTGCTGGAACTGCTAGAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatatgtcgctgttatttttatactgttctattgtaaaaaatatacttctttagGCTGGACAACCAGAGCTGATTTCTCTTGAGAAGTCACTTAAGGAGGCAATGGTTCCTGCAGGAACTGCAAGAGAG
tacttcttt CT-rich tract
ttatttttatactgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggcttcattttaaggtctcataattattctttttacaatatgtcgctgttatttttatactgttctattgtaaaaaatatacttctttagGCTGGACAACCAGAGCTGATTTCTCTTGAGAAGTCACTTAAGGAGGCAATGGTTCCTGCAGGAACTGCAAGAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA