Sequence
atgc intronic sequence ATGC exonic sequencegttggtcaaaattttattattattcttttcttttctagagtacttgcttctggtcaaaatgttttgacctttatatctgtacctcagTATGCTTTGCATCATGGTGAGAGCGGAGAACCTGATGAATGGAGAATGTACAAGAAGTAAGCTTTGGCTTGTAGATTTGGCTGGAAGTGAACGATTAGCT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g02290.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g02290.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G092232_T01 (Zea mays), 3'ss of exon 9
gttggtcaaaattttattat--tattcttttcttttc-tagagtacttgcttctggtcaaaatg-------ttttgacctttat---atctgtacctcagTATGCTTTGCATCATGGTGAGAGCGGAGAACCTGATGAATGGAGAATGTACAAGAAGTAAGCTTTGGCTTGTAGATTTGGCTGGAAGTGAACGATTAGCT
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gttggacactgttttcatataatatccttttttattcgttggctgattgcttgatgtccaaatggttcttcttttaatctttattataacttttcttcagCATGCTATGCATCACGGTGAGGGCTAAGAACCAGCTTAATGGAGAGTGTACAAGTAGTAAGCTTTGGCTTGTAGATTTGGCTGGAAGTGAGCGTTTAGCC
upper sequence: LOC_Os03g02290.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT2G22610.2 (Arabidopsis thaliana), 3'ss of exon 11
gttggtcaaaattttattattattcttttcttttctagagtacttgcttctggtcaaaatgttttgacctt-tatatctgtacctcagTATGCTTTGCATCATGGTGAGAGCGGAGAACCTGATGAATGGAGAATGTACAAGAAGTAAGCTTTGGCTTGTAGATTTGGCTGGAAGTGAACGATTAGCT
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-gtatcatatatgcctcttttgctgtcttgtttgaatgtttgccatcacattatgagggttgtttaatattgtaaaccctta---cagCATGCTCTCTATAATGGTGAAAGCAAAGAACCTGATGAATGGTGATTGCACAAAAAGCAAGCTTTGGCTTGTAGATTTAGCTGGAAGTGAGAGATTGGCA
upper sequence: LOC_Os03g02290.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv00s0218g00050.t01 (Vitis vinifera), 3'ss of exon 11
gttggtcaaaattttatta--ttattcttttct-tttctagagtacttgcttctggtcaaaatgtt--ttgacctttatatctgtacctcagTATGCTTTGCATCATGGTGAGAGCGGAGAACCTGATGAATGGAGAATGTACAAGAAGTAAGCTTTGGCTTGTAGATTTGGCTGGAAGTGAACGATTAGCT
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-gtattcaacttcccaaaagctttctcttttctgtttccttattcatcatattttgataagttgtgaataaaatttcaccaattttgttcagCATGCTTTGTATAATGGTAAAAGCAAAAAACTTAATGAATGGCGACTGTACAAAGAGCAAGCTTTGGCTTGTGGATTTGGCTGGCAGTGAAAGGCTTGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctagagtacttgcttctggtcaaaatgttttgacctttatatctgtacctcagTATGCTTTGCATCATGGTGAGAGCGGAGAACCTGATGAATGGAGAATGTACAAGAAGTAAGCTTTGGCTTGTAGATTTGGCTGGAAGTGAACGATTAGCT
ttttgac putative branch site (score: 3)
aaaatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggtcaaaattttattattattcttttcttttctagagtacttgcttctggtcaaaatgttttgacctttatatctgtacctcagTATGCTTTGCATCATGGTGAGAGCGGAGAACCTGATGAATGGAGAATGTACAAGAAGTAAGCTTTGGCTTGTAGATTTGGCTGGAAGTGAACGATTAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG