Sequence
atgc intronic sequence ATGC exonic sequence...ctctcaaccttctagtggctgtaagctatttacattgactgtataagttcgttttagtgagggtttagcaattagtgatcttttgaatatctgattccagGTTCTGAAAAAAGAGTTTCCAAGAGGAGCAGATATCATATATGAATCGGTTGGTGGGGAAATGTTTGACTTATGCTTGAATGCACTTGCAGTCCATGGAC
Basic information
species | Oryza sativa |
transcript | LOC_Os09g28570.2 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g28570.3 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G147191_T02 (Zea mays), 3'ss of exon 13
---------ctctcaaccttctagtggctgtaagctatttacattgactgtataagttcgttttagtgagggtttagcaattagtgatcttttgaatatctgattccagGTTCTGAAAAAAGAGTTTCCAAGAGGAGCAGATATCATATATGAATCGGTTGGTGGGGAAATGTTTGACTTATGCTTGAATGCACTTGCAGTCCATGGAC
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tgagttacattttgaaatctcaagtgtttgcaaaccacataaattgatgccttgtttgtttttttccatgtgtttattaatt---------taaaatgtttgaattcagGTTCTGAAGAAAGAGTTTCCAAGAGGTGTAGATATCATATATGAATCTGTAGGTGGGGAAATGTTTGACTTGTGCTTGAATGCACTTGCAGTCCATGGGC
upper sequence: LOC_Os09g28570.3 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G479068_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------------------------------------------------ctctcaaccttctagtggctgta--agctatttacattgactgtataagttcgtt--ttagtgagggtttagcaattagtgatctt-ttgaatatctgattccagGTTCTGAAAAAAGAGTTTCCAAGAGGAGCAGATATCATATATGAATCGGTTGGTGGGGAAATGTTTGACTTATGCTTGAATGCACTTGCAGTCCATGGAC
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gtaagttttggttcttgtctttcgtatttatctttcatactctagctgtttataatgcagagtttgttgtttatatttcaaatgtttaggctcgataacatttattttgattcctttctctgctgatatatgcgtgatatttattggtattctagtgtacatttatgttgtctaatgttcgattccagGTTCTGAAGAAAGAGTTTCCAAGAGGTGTAGATATCATATACGAATCAGTAGGAGGAGAAACGTTTGATGTGTGTCTGAATGCCCTAGCAGTCTATGGGC
upper sequence: LOC_Os09g28570.3 (Oryza sativa), 3'ss of exon 13
lower sequence: AT1G49670.1 (Arabidopsis thaliana), 3'ss of exon 13
ctctcaaccttctagtggctgtaagctatttacattgactgt-ataagttcgttttagtgagggtttagcaattagtgatcttttgaatatctgattccagGTTCTGAAAAAAGAGTTTCCAAGAGGAGCAGATATCATATATGAATCGGTTGGTGGGGAAATGTTTGACTTATGCTTGAATGCACTTGCAGTCCATGGAC
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--------------------gtaggtcttgtgtagaaacttttattagtatatgtggctaag----tgacaattattcatactggtctaatct--tcatagGTCTTGAAAAAGGAGTTTCCGAAGGGTGTAAATATCATCTATGAATCTGTAGGTGGTCAAATGTTTGACATGTGCTTGAATGCTCTTGCTGTTTACGGACMapped 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|58684560|gb|CK073247.1|CK073247EST: CCTTAGGAGTTGATAGAGTTATCAACTACCAAAATGAAAAGATCAAAGAT GTTCTGAAAAAAGAGTTTCCAAGAGGAGCAGATATCATATATGAATCGGTT
genomic: CCTTAGGAGTTGATAGAGTTATCAACTACCAAAATGAAAAGATCAAAGATgtaagcttgc ... ctgattccagGTTCTGAAAAAAGAGTTTCCAAGAGGAGCAGATATCATATATGAATCGGTT
EST:
gi|3766964|gb|AU031074.1|AU031074EST: CCTTAGGAGTTGATAGAGTTATCAACTACCAAAATGAAAAGATCAAAGAT GTTCTGAAAAAAGAGTTTCCAAGAGGAGCAGATATCATATATGAATCGGTT
genomic: CCTTAGGAGTTGATAGAGTTATCAACTACCAAAATGAAAAGATCAAAGATgtaagcttgc ... ctgattccagGTTCTGAAAAAAGAGTTTCCAAGAGGAGCAGATATCATATATGAATCGGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttcgttttagtgagggtttagcaattagtgatcttttgaatatctgattccagGTTCTGAAAAAAGAGTTTCCAAGAGGAGCAGATATCATATATGAATCGGTTGGTGGGGAAATGTTTGACTTATGCTTGAATGCACTTGCAGTCCATGGAC
atctgat putative branch site (score: 4)
ttttgaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctctcaaccttctagtggctgtaagctatttacattgactgtataagttcgttttagtgagggtttagcaattagtgatcttttgaatatctgattccagGTTCTGAAAAAAGAGTTTCCAAGAGGAGCAGATATCATATATGAATCGGTTGGTGGGGAAATGTTTGACTTATGCTTGAATGCACTTGCAGTCCATGGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA