Sequence
atgc intronic sequence ATGC exonic sequencegtaatgtagttgcttgacattactaatgttctttcttccaatactttttcatgacccgtgacctcattttaaacaaaatatacttcttttgcagTATCTGATGGAGTTCAACAGCACACCAGGGGATCTTATGGAACTTTCTCCTTTATTTTCTGATGACAGTCGTGTTGCTGAGGCAGCTTCAATTGCACAGA
Basic information
species | Oryza sativa |
transcript | LOC_Os12g13590.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA16G01660.1 (Glycine max), 3'ss of exon 5
gtaatgtagttgcttgacattactaatgttctttcttccaatactttttcatgacccgtgacctcattttaaacaaaatatactt--cttttgcagTATCTGATGGAGTTCAACAGCACACCAGGGGATCTTATGGAACTTTCTCCTTTATTTTCTGATGACAGTCGTGTTGCTGAGGCAGCTTCAATTGCACAGA
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--------gtaataccagtttgttcat-tttttttttttaat--tttaccatcatttgtgttaggaaatttacctatggttaattaatttctgcagTACTTAATGGAATTCAATAGCAGCCCAGGCGACCTGATGGAGCTTTCACCTCTTTTTTCTGATGATAGCCGTGTTGCTGATGCTGCTTCGATTGCCCAGA
upper sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G05160.1 (Glycine max), 3'ss of exon 5
gtaatgtagttgcttgacattactaatgttctttcttccaatactttttcatgacccgtgacctcattttaaacaaaatatacttcttttgcagTATCTGATGGAGTTCAACAGCACACCAGGGGATCTTATGGAACTTTCTCCTTTATTTTCTGATGACAGTCGTGTTGCTGAGGCAGCTTCAATTGCACAGA
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-----gtaataccagttcgttcatttggtttttaattttacca-tcatttgtgttaggaaatttacctatggttgattaata-----tctgcagTACTTAATGGAATTCAATAGCAGTCCAGGCGACCTGATGGAGCTTTCACCTCTTTTTTCTGATGATAGCCGTGTTGCTGAGGCTGCTTCGATTGCCCAGA
upper sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G12370.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaatgtagttgcttgacattactaatgttctttcttccaatactttttcatgacccgtgacctcattttaaacaaaatatacttcttttgcagTATCTGATGGAGTTCAACAGCACACCAGGGGATCTTATGGAACTTTCTCCTTTATTTTCTGATGACAGTCGTGTTGCTGAGGCAGCTTCAATTGCACAGA
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-----gtaagtgtgcatctatgttgcaagg--ttggtcacatatttagtta-gatgaatg--cttaaagtaatcct--tgttcaacaaatgcagTACCTAATGGAGTTCAACGGCAGCCCAGGGGATCTTATGGAGCTTTCCGCTTTGTTTTCTGATGATAGCCGCGTAGCTGAGGCTGCTTCTATCGCTCAGA
upper sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv15s0046g02200.t01 (Vitis vinifera), 3'ss of exon 5
gtaatgtagttgcttgacattactaatgttctttcttccaatactttttcatgacccgtgacctcattttaaacaaaatatacttcttttgcagTATCTGATGGAGTTCAACAGCACACCAGGGGATCTTATGGAACTTTCTCCTTTATTTTCTGATGACAGTCGTGTTGCTGAGGCAGCTTCAATTGCACAGA
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-----gta-ttatctatcaagacacataaaattgattaccat----ttgcataga--atgagttaatatcactttgttgatttcatctctgcagTACTTGATGGAGTTCAATAGCAGCCCAGGCGACCTGATGGAACTTTCACCTCTATTTTCTGATGATAGTCGTGTTGCTGAGGCTGCTTCAATCGCACAGAMapped 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|58677372|gb|CK066059.1|CK066059EST: GTGCAGAATCCCAGAGGGAAACTGCTAGTCAGACAATAGATCTCATCAAG TATCTGATGGAGTTCAACAGCACACCAGGGGGATCTTATGGAACTTTCTCC
genomic: GTGCAGAATCCCAGAGGGAAACTGCTAGTCAGACAATAGATCTCATCAAGgtaatgtagt ... tcttttgcagTATCTGATGGAGTTCAACAGCACACCA-GGGGATCTTATGGAACTTTCTCC
EST:
gi|29669744|gb|CB666019.1|CB666019EST: GAATCCCAGAGGGAAACTGCTAGTCAGACAATAGATCTCATCAAG TATCTGATGGAGTTCAACAGCACACCAGGGGATCTTATGGAACTTTCTCCT
genomic: GAATCCCAGAGGGAAACTGCTAGTCAGACAATAGATCTCATCAAGgtaatgtagt ... tcttttgcagTATCTGATGGAGTTCAACAGCACACCAGGGGATCTTATGGAACTTTCTCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatactttttcatgacccgtgacctcattttaaacaaaatatacttcttttgcagTATCTGATGGAGTTCAACAGCACACCAGGGGATCTTATGGAACTTTCTCCTTTATTTTCTGATGACAGTCGTGTTGCTGAGGCAGCTTCAATTGCACAGA
tacttctttt CT-rich tract
tcattttaaacaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgtagttgcttgacattactaatgttctttcttccaatactttttcatgacccgtgacctcattttaaacaaaatatacttcttttgcagTATCTGATGGAGTTCAACAGCACACCAGGGGATCTTATGGAACTTTCTCCTTTATTTTCTGATGACAGTCGTGTTGCTGAGGCAGCTTCAATTGCACAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT