Sequence
atgc intronic sequence ATGC exonic sequenceATTGCAGATGGTGAGCGCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAAgtaagttcatatttgctatttaaacgaatgcatcattcgcatattgatgttttccaatagaaccaacttgatgcttgcaaatgagtcccaagtttctttt...
Basic information
species | Oryza sativa |
transcript | LOC_Os02g11830.2 |
intron # | 11 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G124886_T01 (Zea mays), 5'ss of exon 11
ATTGCAGATGGTGAGCGCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAAgtaagttcatatttgctatttaaacgaatgcatcattcgcatattgatgttttccaatagaaccaacttgatgcttgcaaatgagtcccaagtttctttt----------
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ATCGCAGATGGTGATCGGTTACCATTGGCCGTGAAGGAGTTGGGAAGCTGTGATCTTTATCCACAAgtaagtttacctatgata---gaatggatgcttcaattg-----tgatcttcatca--tgactcaactaaatgcttgaaacttagttctattttctttttaatgtccaaa
upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G141587_T02 (Zea mays), 5'ss of exon 11
ATTGCAGATGGTGAGCGCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAAgtaagttcatatttgctatttaaacgaatgcatcattcgc-atattgatgttt--tccaatagaaccaacttgatgcttgcaaatgagtcccaagtttctttt---
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ATCGCAGATGGTGATCGGTTACCGTTGGCCGTGAAGGAGTTGGGAAGCTGTGACCTTTATCCACAAgtaagtttacctgtgata---aaatggatgcttcaattgtgatcttcatcatgagtcaactaaatgttgtgtgagattttcat-tga--cttaattctatttgagt
upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 11
ATTGCAGATGGTGAGCGCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAAgtaagttcatatttgctat--ttaaacgaatgcatcattcgcatattgatgttttccaatagaaccaac-ttgatgcttgcaa-atgagtcccaagtttctttt
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ATTGCTGATGGAGAAAGGCTACCATTGGCTGTTAAGGAGTTGGGCACCTGTGATCTCTATCCACAAgtgagtgaacatcccttttccttgatgttaagtcacattcttttgcattacttctctattttttttatcatttatgctcacatcatgtgatagggacttg----
upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 11
ATTGCAGATGGTGAGCGCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAAgtaagttcatatttgctatttaaacgaatgcatcattcgcatattgat-gttttccaatagaaccaacttgatgcttgcaaatgagtcccaagtttctttt
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ATTGCTGATGGAGAAAGGTTACCATTGGCTGTTAAGGAGTTGGGCACCTGTGATCTCTATCCTCAAgtgagtgaacatcctttttccgtaatattaagtcacattcttttgcattacttctctatattttatcatttatgctcatat-tatgtgatagggacttagg
upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 11
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 11
ATTGCAGATGGTGAGCGCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAAgtaagttcatatttgctatttaa-acgaatgcatcattcgcatattgatgttttccaatagaaccaacttgatgcttgcaaatgagtcccaagtttctttt-----
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GCTACTGATGGAGAAAGACTTCCCTTGTCTGTTAAAGAGTTGGGGACCTGTGATCTTTATCCACAAgtgagc-----gttactatccagcacctttgaaactttcctgttgtgttgaattatcattggatct-tttggggtaaacactttcggtgcatgtcccacttaaatg
upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 11
lower sequence: AT3G15980.5 (Arabidopsis thaliana), 5'ss of exon 11
--------------------ATTGCAGATGGTGAGCGCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAAgtaagttcatatttgctatttaa-acgaatgcatcattcgcatattgatgttttccaatagaaccaacttgatgcttgcaaatgagtcccaagtttctttt-----
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CTTTCATCTCTCTACCTTAGGCTACTGATGGAGAAAGACTTCCCTTGTCTGTTAAAGAGTTGGGGACCTGTGATCTTTATCCACAAgtgagc-----gttactatccagcacctttgaaactttcctgttgtgttgaattatcattggatct-tttggggtaaacactttcggtgcatgtcccacttaaatg
upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 11
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 11
ATTGCAGATGGTGAGCGCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAAgtaagttcatatttgctatttaaacgaatgcatcattcgcatattgatgttttccaatagaaccaacttgatgcttgcaaatgagtcccaagtttctttt-------
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GTTACTGATGGAGAAAGGTTGCCCTTGAGTGTTAAAGAGTTGGGGACCTGTGATCTTTATCCACAAgtgagtgttactacagcactcggtccaatg-attttatg-atgttg-tggcttattatatagttcattt----cggaaaaacattttctgcgttgctggtatgattg
upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 11
ATTGCAGATGGTGAGCGCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAAgtaagttcatatttgctatttaaacgaatgcatcattcgcatattgatgttttccaatagaaccaacttgatgcttgcaaatgagtcccaagtttctttt-----
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GTTACAGATGGAGAAAGATTGCCTTTGGCTGTGAAAGAGTTGGGAACCTGTGACCTTTATCCTCAAgtaagtt---ggttcttttctagccacatgc--tatccaagtgatgatttcatgtgccatttttgttgaagtgtgaattcatttacctgatgtgacctttccaaa
upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 11
ATTGCAGATGGTGAGCGCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAAgtaagttcatatttgctatttaaacgaatgcatcattcgcatattgatgttttccaatagaaccaacttgatgcttgcaaatgagtcccaagtttctttt-------
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GTTACTGATGGAGAAAGATTGCCTTTGGCTGTTAAGGAGTTAGGAACCTGTGATCTTTACCCACAAgtgagttga--ctgtcttctggcattatttaattttttctatggtgctttatttcattat--tttgctt--tgctttggtgtg-gtttcatgtcctttgctcccaccMapped 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|300215876|gb|HO088502.1|HO088502EST: GCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAA AGTTTAAGGCACAATCCAAATGGAAGATTTGTTGTTGTATGTGGAGATGGA
genomic: GCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAAgtaagttcat ... ttcatttcagAGTTTAAGGCACAATCCAAATGGAAGATTTGTTGTTGTATGTGGAGATGGA
EST:
gi|29680637|gb|CB676912.1|CB676912EST: GCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAA AGTTTAAGGCACAATCCAAATGGAAGATTTGTTGTTGTATGTGGAGATGGA
genomic: GCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAAgtaagttcat ... ttcatttcagAGTTTAAGGCACAATCCAAATGGAAGATTTGTTGTTGTATGTGGAGATGGA
EST:
gi|29671007|gb|CB667282.1|CB667282EST: GCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAA AGTTTAAGGCACAATCCAAATGGAAGATTTGTTGTTGTATGTGGAGATGGA
genomic: GCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAAgtaagttcat ... ttcatttcagAGTTTAAGGCACAATCCAAATGGAAGATTTGTTGTTGTATGTGGAGATGGA
EST:
gi|29613910|gb|CB618923.1|CB618923EST: GCTTACCCTTGGCTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAA AGTTTAAGGCACAATCCAAATGGAAGATTTGTTGTTGTATGTGGAGATGGA
genomic: GCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAAgtaagttcat ... ttcatttcagAGTTTAAGGCACAATCCAAATGGAAGATTTGTTGTTGTATGTGGAGATGGA
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
70 (upstream exon),
60 (downstream exon)
Score:
36ATTGCAGATGGTGAGCGCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAAgtaagttcat ... ttcatttcagAGTTTAAGGCACAATCCAAATGGAAGATTTGTTGTTGTATGTGGAGATGGAGAATACATAATCTACACCGCATTGGCATGGAGAAATAGATCATTCGGGT
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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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATTGCAGATGGTGAGCGCTTACCCTTGGTTGTGAAGGAGTTGGGAACCTGTGATCTTTATCCACAAgtaagttcatatttgctatttaaacgaatgcatcattcgcatattgatgttttccaatagaaccaacttgatgcttgcaaatgagtcccaagtttctttt
- - - - - - - - - - - - - - - - AAGGAG