Sequence
atgc intronic sequence ATGC exonic sequence...tcgtttcaccctgcaaaggtgtcttgcctttgttgtttttggttctgaaatacttgaggtgaattgtcatactaattgtacaggtttggctgttttgtagGCTGCCTTATGCTCTATAAGGATCGTACGGAAGGTTCCAGATTTGGCAGAGAACTTCATGGGCTCTGCTGTTTCACTACTGAAGGAAAAACATCACGGGG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g07090.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g07090.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G017421_T02 (Zea mays), 3'ss of exon 3
---tcgtt-tcaccctgcaaaggtgtcttgcctttgttgtttttggttctgaaatacttgaggtgaattg-tcatactaattgtacaggtttggctgttttgtagGCTGCCTTATGCTCTATAAGGATCGTACGGAAGGTTCCAGATTTGGCAGAGAACTTCATGGGCTCTGCTGTTTCACTACTGAAGGAAAAACATCACGGGG
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ctttcgttcttgtccaatcaccagtgcttatccttcttggtt--agtttgttaatgtgtgctgtggagaggtctcgttgattgtctagcttt---tgttttttagGCTGCTTTATGCTCTATAAGGATTGTGCGAAAAGTTCCAGACTTGGCGGAAAATTTCATGAGTGCTGCTGCATCATTACTGAAGGAAAAACATCATGGTG
upper sequence: LOC_Os06g07090.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 2
tcgtttcaccctgcaaaggtgtcttgcctttgttgtttt--tggttctgaaatacttgaggtgaattgtcatactaattgtacaggtttggctgttttgtagGCTGCCTTATGCTCTATAAGGATCGTACGGAAGGTTCCAGATTTGGCAGAGAACTTCATGGGCTCTGCTGTTTCACTACTGAAGGAAAAACATCACGGGG
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-tgagttatta-ataaaactgttcccatttaactgcatgaatgatgagtgatgactaatcattatttattctcataaattaactgtgctcactgctatatagGCAGCATTATGCTCTATAAGGATCATAAAGAAAGTTCCAGACTTGGCAGAAAATTTTATCAATCCTGCTACTTCCTTACTCAGAGAGAAGCATCATGGGG
upper sequence: LOC_Os06g07090.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 3
-tcgtttcaccctgcaaaggtgtcttgcctttgttgtttt-tggttctgaaatacttgaggtgaattgtcatactaattgtacaggtttggctgttttgtagGCTGCCTTATGCTCTATAAGGATCGTACGGAAGGTTCCAGATTTGGCAGAGAACTTCATGGGCTCTGCTGTTTCACTACTGAAGGAAAAACATCACGGGG
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agggtttaatacttaatgtttctctttatttatttggtctattgtatgtctttattctttcttgact-ttgaattgattac-ctactttgtgtaaaaaatagGCAGCATTATGCTCTATAAGGATTATAAGGAAAGTTCCAGATCTGGCAGAAAATTTTATGCATCCTGCTACCAACTTACTTAAAGAAAAGCACCATGGAGMapped 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|87015454|gb|CI303060.1|CI303060EST: CTGAGGTGGAGAGGCTATTGCAAAGTAGGGAACCAAATACCAAGAAGAAG GCTGCCTTATGCTCTATAAGGATCGTACGGAAGGTTCCAGATTTGGCAGAG
genomic: CTGAGGTGGAGAGGCTATTGCAAAGTAGGGAACCAAATACCAAGAAGAAGgtatatgttt ... tgttttgtagGCTGCCTTATGCTCTATAAGGATCGTACGGAAGGTTCCAGATTTGGCAGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaatacttgaggtgaattgtcatactaattgtacaggtttggctgttttgtagGCTGCCTTATGCTCTATAAGGATCGTACGGAAGGTTCCAGATTTGGCAGAGAACTTCATGGGCTCTGCTGTTTCACTACTGAAGGAAAAACATCACGGGG
tactaat putative branch site (score: 1)
ctgtttt putative PPT
atactaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcgtttcaccctgcaaaggtgtcttgcctttgttgtttttggttctgaaatacttgaggtgaattgtcatactaattgtacaggtttggctgttttgtagGCTGCCTTATGCTCTATAAGGATCGTACGGAAGGTTCCAGATTTGGCAGAGAACTTCATGGGCTCTGCTGTTTCACTACTGAAGGAAAAACATCACGGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA