Sequence
atgc intronic sequence ATGC exonic sequence...tggcactatctaaagaattgtctataaactaggaacaataagatcgcatcgtactattcttcacattaaaacatttcttacccccaaaattgatgtgcagGGTGTGGATCCCACTATTCGAGCTGAAGTTTGGGAATTTCTTCTTGGCTGCTATGCCTTGAGTAGTACCTCAGAGTATAGGAGGAAACTAAGAGCTGTTA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g01010.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g01010.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G031043_T01 (Zea mays), 3'ss of exon 4
tggcactatctaaagaattgtctataaactaggaacaataagatcgcatcgtactattcttcacattaaaacatttcttacccccaaaattgatgtgcagGGTGTGGATCCCACTATTCGAGCTGAAGTTTGGGAATTTCTTCTTGGCTGCTATGCCTTGAGTAGTACCTCAGAGTATAGGAGGAAACTAAGAGCTGTTA
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ttgcatcagtgtttttttttgttatcaacagaatgctgaattatgaaaaatgcatgaaaatggccatgtaataagttctatctctattgatgatgtgcagGGTGTGGATCCTTCTATTCGAGCGGAAGTTTGGGAATTTCTTATTGGCTGCTACACCTTAAGTACTACAGCGGAATATAGGGGAAAACTAAGAGCTGCTC
upper sequence: LOC_Os01g01010.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G59570.1 (Arabidopsis thaliana), 3'ss of exon 3
tggcac-tatctaaagaattgtctataaactaggaacaataagatcgcatcgtactattcttcacattaaaacatttcttacccccaaaattgatgtgcagGGTGTGGATCCCACTATTCGAGCTGAAGTTTGGGAATTTCTTCTTGGCTGCTATGCCTTGAGTAGTACCTCAGAGTATAGGAGGAAACTAAGAGCTGTTA
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--gtatgtttgcagatgattttttagctgctcagg-ctatcccattgttgtttgttctttaacatggtattctaatgcatttcctttgtgctttttttaagGGAATCGATCCATCCATAAGAGCTGAAGTTTGGGAATTTCTCCTTGGCTGTTATGCATTAAGCAGCACCTCTGAGTATCGTACGCAACTCAGGGTAGCTC
upper sequence: LOC_Os01g01010.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT2G43490.2 (Arabidopsis thaliana), 3'ss of exon 3
tggcactatctaaagaattgtctataaactaggaacaataagatcgcatcgtactattcttcacattaaaacatttcttacccccaaaattgatgtgcagGGTGTGGATCCCACTATTCGAGCTGAAGTTTGGGAATTTCTTCTTGGCTGCTATGCCTTGAGTAGTACCTCAGAGTATAGGAGGAAACTAAGAGCTGTTA
|| || | ||| | | | | ||| | | ||||||| || || | | | | | || | |||| | || || ||||| |||||||||||||||||||||| ||||| || ||||| ||||| || ||||| ||||| | | |||| || | | |
------------gtatgttttcactttggtagaagaacttgtaacgcttttgattattcttt-cagtacagtggta-taatgtatgatgtttttcattagGGAATCGACCCATCTATTAGAGCTGAAGTTTGGGAATTTCTCCTTGGTTGTTATGCGTTGAGCAGCACCTCTGAGTACCGTAATCAACTCAGGGTAGCTC
upper sequence: LOC_Os01g01010.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv00s0914g00010.t01 (Vitis vinifera), 3'ss of exon 3
-tggcactatctaaagaattgtctataaactaggaacaataagatcgcatcg--tactattcttcacattaaaacatttcttacccccaaaattgatgtgcagGGTGTGGATCCCACTATTCGAGCTGAAGTTTGGGAATTTCTTCTTGGCTGCTATGCCTTGAGTAGTACCTCAGAGTATAGGAGGAAACTAAGAGCTGTTA
| || | | | ||||| | | |||| | | || || | | || || ||| ||| || | ||||||||||||| |||| | || ||||||||||||||||||||||| || ||||| | | || ||| ||||||| | ||| |||| || | | |
attttttcat-tgcaatttcttctatgagttttctttcataaagatttaagaactcctgttttccttatccttgcaattc--accttttgtgctgcatggtagGGTGTGGATCCATCTATAAGGGCAGAAGTTTGGGAATTTCTTCTTGGTTGTTATGCACTTGGAAGCACCACAGAGTACCGTAGGCAACTGAGGACGGCCA
upper sequence: LOC_Os01g01010.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv00s0226g00160.t01 (Vitis vinifera), 3'ss of exon 3
--tggcactatctaaagaattgtctataaactaggaacaataagatcgcatcgtactattcttcacattaaaacatttcttacccccaaaattgatgtgcagGGTGTGGATCCCACTATTCGAGCTGAAGTTTGGGAATTTCTTCTTGGCTGCTATGCCTTGAGTAGTACCTCAGAGTATAGGAGGAAACTAAGAGCTGTTA
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gttgctgcttcttcaatttgtcttcttttgttaaggagattccagcaagaac-tcctgttttcctactgatcagaattcacatttttttgctgcatg-gtagGGTGTGGATCCATCTATAAGGGCTGAAGTTTGGGAATTTCTTCTTGGTTGTTATGCAGTTGACAGCACCGCAGAGCATCGGAGGCAACTAAGGACAGCCAMapped 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|29675456|gb|CB671731.1|CB671731EST: ATGGAAAGGTCATAGGTTTCCGTAAAGCCCTAAAATTCATTGTCTTAGGG GGTGTGGATCCCACTATTCGAGCTGAAGTTTGGGAATTTCTTCTTGGCTGC
genomic: ATGGAAAGGTCATAGGTTTCCGTAAAGCCCTAAAATTCATTGTCTTAGGGgtgagttaat ... tgatgtgcagGGTGTGGATCCCACTATTCGAGCTGAAGTTTGGGAATTTCTTCTTGGCTGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatcgtactattcttcacattaaaacatttcttacccccaaaattgatgtgcagGGTGTGGATCCCACTATTCGAGCTGAAGTTTGGGAATTTCTTCTTGGCTGCTATGCCTTGAGTAGTACCTCAGAGTATAGGAGGAAACTAAGAGCTGTTA
attaaaacatttctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggcactatctaaagaattgtctataaactaggaacaataagatcgcatcgtactattcttcacattaaaacatttcttacccccaaaattgatgtgcagGGTGTGGATCCCACTATTCGAGCTGAAGTTTGGGAATTTCTTCTTGGCTGCTATGCCTTGAGTAGTACCTCAGAGTATAGGAGGAAACTAAGAGCTGTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT