Sequence
atgc intronic sequence ATGC exonic sequencegtatgctcgacaaccaaatctcaattcatgtaactttctggcacaaatctacacattttcatacaaaatttttgtgatagATGATGGAAAATTGCAAGCAGAATCAGATTCTGGTGAATTCTGGGTTCTTTTTGGAGGTTTTGCACCAATAGGGAAGAAAGCTATATGTGACGATGATGT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g24220.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G081322_T01 (Zea mays), 3'ss of exon 6
---gtatgctcgacaaccaaatctca-attcatgtaacttt------ctggcacaaatctacacattttcatacaaaatttttgtgatagATGATGGAAAATTGCAAGCAGAATCAGATTCTGGTGAATTCTGGGTTCTTTTTGGAGGTTTTGCACCAATAGGGAAGAAAGCTATATGTGACGATGATGT
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gtgagatgagaatgagacgaatctcatacatgtgaaacgtcagcaagttcacacacacttatacatttttttgtt--gccttgataatagATGATGGGAAACTGCAAGCAGAATCAGATTCAGGAGAATTCTGGGTCCTTTTTGGAGGTTTTGCGCCAATAGGGAAAAAAGCAATAAGTGATGATGATGT
upper sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G323479_T01 (Zea mays), 3'ss of exon 11
---gtatgctcgacaaccaaatctcaattcat----gtaactttctggca--caaatctacacattttcatacaaaatttttgtgatagATGATGGAAAATTGCAAGCAGAATCAGATTCTGGTGAATTCTGGGTTCTTTTTGGAGGTTTTGCACCAATAGGGAAGAAAGCTATATGTGACGATGATGT
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gtgagatgacaatgatacaattttcatttcatacatgtaaaatgtcagcaagtaaacacacacttatacctttcttgccttaataatagACGACGGGAAATTGCAAGCAGAATCAGATTCAGGAGAATTCTGGGTCGTTTTTGGAGGCTTTGCGCCAATAGGGAAGAAAGCAGTAAGTGATGATGATGT
upper sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 7
-----------------------------------------------------gtatgctcga-caaccaaatctcaattc-atgt---aactttctggcacaa-atctacacattttcatacaaaatttttg--tgatagATGATGGAAAATTGCAAGCAGAATCAGATTCTGGTGAATTCTGGGTTCTTTTTGGAGGTTTTGCACCAATAGGGAAGAAAGCTATATGTGACGATGATGT
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gtaagttgtattagacgcattacaactaatatttgaatatcttctttttcacgttttgatcagtcaatcaagcagcagttggatgctcaatcaatttattgcggtactcatgcatgtata-ataatttccttgcataacagATGATGGAAAATTAGATACAGAATCAGATTCTGGCGAGTTCTGGGTCCTCTTTGGGGGGTTTGCTCCAATAGCAAGGAAAGTTGCGAGTGAGGATGAAAT
upper sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G41740.1 (Arabidopsis thaliana), 3'ss of exon 6
---------------------------------------gtatgctcgacaaccaaat-ctcaattcatgtaactttctggcacaaatctacacattttcatacaaaatttttgtgatagATGATGGAAAATTGCAAGCAGAATCAGATTCTGGTGAATTCTGGGTTCTTTTTGGAGGTTTTGCACCAATAGGGAAGAAAGCTATATGTGACGATGATGT
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gtaagccaattgcaccttcttcctcagtttcctttaagtcaatgaacagtgttttaatacttaaagaataggttttgtgtgtggaaacttatctatattcatactttcctgctataacagATGACGGAAAATTAGATACAGAATCAGATTCTGGTGCATTTTGGGTCCTCTTTGGTGGTTTTGCTCCAATCGGAAGGAAAGTTGCCAATGATGATGACATMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|29674447|gb|CB670722.1|CB670722EST: ACATTTAAAGGAGACATACCACAATGGAGTGTGTGATGTTGCGATTGTTG ATGATGGAAAATTGCAAGCAGAATCAGATTCTGGTGAATTCTGGGTTCTTT
genomic: ACATTTAAAGGAGACATACCACAATGGAGTGTGTGATGTTGCGATTGTTGgtatgctcga ... tttgtgatagATGATGGAAAATTGCAAGCAGAATCAGATTCTGGTGAATTCTGGGTTCTTT
EST:
gi|11442605|gb|BF430508.1|BF430508EST: ACATTTAAAGGAGACATACCACAATGGAGTGTGTGATGTTGCGATTGTTG ATGATGGAAAATTGCAAGCAGAATCAGATTCTGGTGAATTCTGGGTTCTTT
genomic: ACATTTAAAGGAGACATACCACAATGGAGTGTGTGATGTTGCGATTGTTGgtatgctcga ... tttgtgatagATGATGGAAAATTGCAAGCAGAATCAGATTCTGGTGAATTCTGGGTTCTTT
EST:
gi|58670145|gb|CK058831.1|CK058831EST: GTTGCGATTGTTG ATGATGGAAAATTGCAAGCAGAATCAGATTCTGGTGAATTCTGGGTTCTTT
genomic: GTTGCGATTGTTGgtatgctcga ... tttgtgatagATGATGGAAAATTGCAAGCAGAATCAGATTCTGGTGAATTCTGGGTTCTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatgtaactttctggcacaaatctacacattttcatacaaaatttttgtgatagATGATGGAAAATTGCAAGCAGAATCAGATTCTGGTGAATTCTGGGTTCTTTTTGGAGGTTTTGCACCAATAGGGAAGAAAGCTATATGTGACGATGATGT
atgtaac putative branch site (score: 3)
tttttgt putative PPT
acattttcatacaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctcgacaaccaaatctcaattcatgtaactttctggcacaaatctacacattttcatacaaaatttttgtgatagATGATGGAAAATTGCAAGCAGAATCAGATTCTGGTGAATTCTGGGTTCTTTTTGGAGGTTTTGCACCAATAGGGAAGAAAGCTATATGTGACGATGATGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA