Sequence
atgc intronic sequence ATGC exonic sequencegtgagtcttggttgtctggtattgtatcatattctgaagccacaatgaacttctgaggttaacttgttttcttactgcagTGTTGTGGGGTATACTTTACTCCTTACCATGATTGAGTATAAAACACTTGTAATGCGTGGAGACTTCGATCGTGCAAACGCTCTTTTACCATCTATACCA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g11840.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 16
----gtgagtcttggttgtctggtattgtatcatattctgaagccacaatgaacttctgaggttaacttgttttcttactgcagTGTTGTGGGGTATACTTTACTCCTTACCATGATTGAGTATAAAACACTTGTAATGCGTGGAGACTTCGATCGTGCAAACGCTCTTTTACCATCTATACCA
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gtgagttgatctttgtcacctaaatttcacttgtagtttttgtacacaag----ttctgtggctaatgtacttttttattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAGTATAAAACACTTGTAATGCGTGGGGATTTTGATCGTGCAAATGATGTTTTATCATCTATACCA
upper sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 16
gtgagtcttggttgtctggtattgtatcatattctgaagccacaatgaac---ttctgaggttaacttgttttcttactgcagTGTTGTGGGGTATACTTTACTCCTTACCATGATTGAGTATAAAACACTTGTAATGCGTGGAGACTTCGATCGTGCAAACGCTCTTTTACCATCTATACCA
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gtgagttc---atctttgttactaaattccact-tgtagtttttgtacacaagttctgtggctaatgtaccttattattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAATATAAAACACTTGTAATGCGTGGGGATTTCGATCGCGCGAATGATGTTTTATCATCTATACCA
upper sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 16
----------gtgagtcttggttgtctggtattgtatcatattctgaagccacaatgaacttctgaggttaact-tgttttcttactgcagTGTTGTGGGGTATACTTTACTCCTTACCATGATTGAGTATAAAACACTTGTAATGCGTGGAGACTTCGATCGTGCAAACGCTCTTTTACCATCTATACCA
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gtgagggagcttgggagctgcacttctgcaatctgactgc-ttttgttcttgtaattga--tctaaatttatttatgttatctta-tgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCTMapped 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|58600997|gb|CK011525.1|CK011525EST: GCTAACCAAAGCCGTGTCTAATCTTATTGACAAGCAATTTAA TGTTGTGGGGTATACTTTACTCCTTACCATGATTGAGTATAAAACACTTGT
genomic: GCTAACCAAAGCCGTGTCT-ATCTTATTGACAAGCAATTTAAgtgagtcttg ... cttactgcagTGTTGTGGGGTATACTTTACTCCTTACCATGATTGAGTATAAAACACTTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcatattctgaagccacaatgaacttctgaggttaacttgttttcttactgcagTGTTGTGGGGTATACTTTACTCCTTACCATGATTGAGTATAAAACACTTGTAATGCGTGGAGACTTCGATCGTGCAAACGCTCTTTTACCATCTATACCA
ttcttac putative branch site (score: 2)
cttgttttcttact CT-rich tract
ttttctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtcttggttgtctggtattgtatcatattctgaagccacaatgaacttctgaggttaacttgttttcttactgcagTGTTGTGGGGTATACTTTACTCCTTACCATGATTGAGTATAAAACACTTGTAATGCGTGGAGACTTCGATCGTGCAAACGCTCTTTTACCATCTATACCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA