Sequence
atgc intronic sequence ATGC exonic sequencegtaaagcatgtgtaacatgaaaatgcccagtgcattggtgcctctataataatatgacagattaacatttcctttctatgcagTATTTGATGCCCTTTGTGGAAAAAGAGAAATATGAACTCCCAAGCAAATGTAGACTTCATCCTGGTAATGACATGTTTCGGGAACAGGAGCAGCATAAGA
Basic information
species | Oryza sativa |
transcript | LOC_Os12g13130.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g13130.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G095323_T03 (Zea mays), 3'ss of exon 3
gtaaagcatgtgtaacatgaaaatgcccag--------tgcattggtgcctctataataatatgacagattaacatttcctttctatgcagTATTTGATGCCCTTTGTGGAAAAAGAGAAATATGAACTCCCAAGCAAATGTAGACTTCATCCTGGTAATGACATGTTTCGGGAACAGGAGCAGCATAAGA
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--gtagcagatgcaacctaacagttctgtgattttatatgcattgctgcatccataacattgttacatgtcaactcccatttcttatgcagTATTTGATGCCCTTCGTGGAAAAAGAAAAATATGAACTCCCAAGCAAATGTAGACTTCGTCCTGATAATGACATGTTTCGGGAGCAAGAGCAACATAAGA
upper sequence: LOC_Os12g13130.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G10750.1 (Glycine max), 3'ss of exon 3
gtaaagcatgtgtaacatgaaaatgcccagtgcattggtgcctctataataatatgacagatt-----aacatttcctttcta-tgcagTATTTGATGCCCTTTGTGGAAAAAGAGAAATATGAACTCCCAAGCAAATGTAGACTTCATCCTGGTAATGACATGTTTCGGGAACAGGAGCAGCATAAGA
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----------ggtattagaatatatccaaacaaataactctctcaatgatattagtgtgcattctcttgatatatgatttttcctgcaGTATTTGATGCCCTTTGTGGAGAAAGAAAAATACCACATCTCAAAAAGGTGTAGGCTTCACCCTGACAATGACATATACAGAGATCAGGAGCAACATAAG-
upper sequence: LOC_Os12g13130.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G43130.1 (Glycine max), 3'ss of exon 3
gtaaagcatgtgtaacatgaaaatgcccagtgcattggtgcctctataataatatgacagatt-----aacatttcctttcta-tgcagTATTTGATGCCCTTTGTGGAAAAAGAGAAATATGAACTCCCAAGCAAATGTAGACTTCATCCTGGTAATGACATGTTTCGGGAACAGGAGCAGCATAAGA
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-----------gtattagaatatatccaagcaaataactctctcaatgatattagtgtgcattctcttgatatataatttttgctgcagTATTTGATGCCATTTGTGGAGAAAGAAAAATACCACATCTCAAAAAGGTGTATGCTTCACCCTGACAATGACATATACAGAGATCAGGAGCAACATAAGT
upper sequence: LOC_Os12g13130.4 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv14s0219g00070.t01 (Vitis vinifera), 3'ss of exon 3
------------gtaa--agcatgtgtaacatgaaaatgcccagtgcattggt--gcctctataataatatgacagattaacatttcct-ttctatgcagTATTTGATGCCCTTTGTGGAAAAAGAGAAATATGAACTCCCAAGCAAATGTAGACTTCATCCTGGTAATGACATGTTTCGGGAACAGGAGCAGCATAAGA
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gtattggtggatgaaactatcatctgtttttggtcactgccccctgaaatatttggtgtgcctcactgcttggtacataatctggtgatattttgcgcagTATTTGATGCCCTTTGTGGAGAAAGAGGGCTATCAGATCTCAAGTAGCTGTAGGCTTCATCATGAAAATGACCTGTACAGGGATCAGGAGCAGCATAAAAMapped 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|218496856|gb|FG966014.1|FG966014EST: TGCATTGCTCAAGGGAAAGAAGCCGTGCAGCTTGGAAAGCTATTGATGAG TATTTGATGCCCTTTGTGGAAAAAGAGAAATATGAACTCCCAAGCAAATGT
genomic: TGCATTGCTCAAGGGAAAGAAGCCGTGCAGCTTGGAAAGCTATTGATGAGgtaaagcatg ... ttctatgcagTATTTGATGCCCTTTGTGGAAAAAGAGAAATATGAACTCCCAAGCAAATGT
EST:
gi|58674107|gb|CK062793.1|CK062793EST: TGCATTGCTCAAGGGAAAGAAGCCGTGCAGCTTGGAAAGCTATTGATGAG TATTTGATGCCCTTTGTGGAAAAAGAGAAATATGAACTCCCAAGCAAATGT
genomic: TGCATTGCTCAAGGGAAAGAAGCCGTGCAGCTTGGAAAGCTATTGATGAGgtaaagcatg ... ttctatgcagTATTTGATGCCCTTTGTGGAAAAAGAGAAATATGAACTCCCAAGCAAATGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtgcattggtgcctctataataatatgacagattaacatttcctttctatgcagTATTTGATGCCCTTTGTGGAAAAAGAGAAATATGAACTCCCAAGCAAATGTAGACTTCATCCTGGTAATGACATGTTTCGGGAACAGGAGCAGCATAAGA
gattaac putative branch site (score: 2)
catttcctttctat CT-rich tract
tataataatatgacag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagcatgtgtaacatgaaaatgcccagtgcattggtgcctctataataatatgacagattaacatttcctttctatgcagTATTTGATGCCCTTTGTGGAAAAAGAGAAATATGAACTCCCAAGCAAATGTAGACTTCATCCTGGTAATGACATGTTTCGGGAACAGGAGCAGCATAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG