Sequence
atgc intronic sequence ATGC exonic sequence...tcagctgtttagcttttatttagaaactgggaaagattgttattttgtatcctttaattgaaagatgtggtgccagagtttcaatttttattttacacagGCAAAGTGATGAATCTTGGAAGATGGGTGATATTGTGCACACACTGACTAACAGAAGGTGGTCAGAGAAGTGTGTTACTTATGCTGAAAGTCATGATCAA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g32660.2 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G032628_T01 (Zea mays), 3'ss of exon 15
-tca-gctgtttagcttttatttagaaactgggaaagattgt-tattttgtatcctttaattgaaagatgtggtgccagagtttcaatttttattttac---acagGCAAAGTGATGAATCTTGGAAGATGGGTGATATTGTGCACACACTGACTAACAGAAGGTGGTCAGAGAAGTGTGTTACTTATGCTGAAAGTCATGATCAA
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ataatgatacacaaactctcctgtgcgttcgagagaaaaaatgccttctgcattcact--ttgagatatgtggt----gagtttcaatttctatttaaccgcacagGCAAAGTGATGAAACTTGGAAGATGGGTGATATTGTGCACACACTGACAAATAGGAGGTGGTTAGAGAAGTGTGTAACTTATGCTGAAAGTCATGATCAA
upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA03G35020.1 (Glycine max), 3'ss of exon 15
tcagctgtttagcttttatttagaaactgggaaagattgttattttgtatcctttaattgaaagatgtggtgccag-agtttcaat--ttttattttacacagGCAAAGTGATGAATCTTGGAAGATGGGTGATATTGTGCACACACTGACTAACAGAAGGTGGTCAGAGAAGTGTGTTACTTATGCTGAAAGTCATGATCAA
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-catcatttcatctccaat--gaccactgtcattcgttcttactgtttgtaagtagtgtgaaaagaaaatcatgtgtaatttcagcggtgtccttttgtgtagGAAGAATGATGAAGACTGGAAAATGGGTGATATTGTCCACACATTAACAAACAGAAGGTGGCTGGAAAAATGTGTAGCTTATGCTGAAAGTCATGACCAG
upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 15
lower sequence: AT5G03650.1 (Arabidopsis thaliana), 3'ss of exon 15
tcagctgtttagcttttatttagaaactgggaaagattgttattttgtatcctttaattgaaagatgtggtgccagagtttcaatttttattttacacagGCAAAGTGATGAATCTTGGAAGATGGGTGATATTGTGCACACACTGACTAACAGAAGGTGGTCAGAGAAGTGTGTTACTTATGCTGAAAGTCATGATCAA
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-------gtgagtgttttctgcattttcttttaagttccatctgctttaatatttggt-gaaataagtg-tcttactctcctccatgttatgctgtgaagGAAGAGAGATGAAGACTGGCAAATGGGCGACATCATTTACACACTTACCAACAGAAGGTGGTCAGAGAAGTGTATCTCTTATGCTGAAAGTCACGATCAA
upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 15
lower sequence: Vv08s0007g03750.t01 (Vitis vinifera), 3'ss of exon 15
tcagctgtttagcttttatttagaaac----tgggaaagattgttattttgtatcctttaattgaaagatgtggtgccagagtttcaatttttattttacacagGCAAAGTGATGAATCTTGGAAGATGGGTGATATTGTGCACACACTGACTAACAGAAGGTGGTCAGAGAAGTGTGTTACTTATGCTGAAAGTCATGATCAA
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tttggtataccaggtcaagaaagagttgttttaccatagtttattaattttttccttcatgttattataattcatttcaca--tgcaaatgctat--gatgcagGAAACCTGATGAATATTGGAAAATGGGTGACATTATTCACACGCTCACCAATAGAAGGTGGTTGGAAAAATGTGTTGCTTATGCTGAAAGTCATGACCAAMapped 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|66912774|gb|CX099622.1|CX099622EST: ATGGCTGTTCCTGACAAATGGATTGAACTCCTCAA GCAAAGTGATGAATCTTGGAAGATGGGTGATATTGTGCACACACTGACTAA
genomic: ATGGCTGTTCCTGACAAATGGATTGAACTCCTCAAgtaagtgttt ... ttttacacagGCAAAGTGATGAATCTTGGAAGATGGGTGATATTGTGCACACACTGACTAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtatcctttaattgaaagatgtggtgccagagtttcaatttttattttacacagGCAAAGTGATGAATCTTGGAAGATGGGTGATATTGTGCACACACTGACTAACAGAAGGTGGTCAGAGAAGTGTGTTACTTATGCTGAAAGTCATGATCAA
ctttaat putative branch site (score: 4)
tttttatttt putative PPT
agagtttcaattttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcagctgtttagcttttatttagaaactgggaaagattgttattttgtatcctttaattgaaagatgtggtgccagagtttcaatttttattttacacagGCAAAGTGATGAATCTTGGAAGATGGGTGATATTGTGCACACACTGACTAACAGAAGGTGGTCAGAGAAGTGTGTTACTTATGCTGAAAGTCATGATCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG