Sequence
atgc intronic sequence ATGC exonic sequence...tatctttcaaagcaagagtcacactttttaatgctctatgtttctgctcaaatcactgaaaattgtcaagtactaaattcgttgatttgtgttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g40830.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G094614_T02 (Zea mays), 3'ss of exon 4
----tatctttcaaagcaagagtcacac-tttttaatgctctatgtttctgctcaaatcactgaaaattgtcaagtactaaattcgttgatttgtgttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG----------------------
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ctatgctgtatgaaagtcattacctcatgcttttagtttgcaatatttccttgcatatc---gaagatttctagagattgatactgt--atgttctcttcggtagGTCTACTTGTGTGAGAAACTATCTCTTACAAATGAGATGTACTTTGCCATCACCCTTGATAGGAAAACTGCTGGTCCGGTATGCCATTTATCTCAAATAT
upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G094614_T01 (Zea mays), 3'ss of exon 4
----tatctttcaaagcaagagtcacac-tttttaatgctctatgtttctgctcaaatcactgaaaattgtcaagtactaaattcgttgatttgtgttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG
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ctatgctgtatgaaagtcattacctcatgcttttagtttgcaatatttccttgcatatc---gaagatttctagagattgatactgt--atgttctcttcggtagGTCTACTTGTGTGAGAAACTATCTCTTACAAATGAGATGTACTTTGCCATCACCCTTGATAGGAAAACTGCTGGTCCG
upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G064695_T03 (Zea mays), 3'ss of exon 4
----tatctttcaaagcaagagtcacac-tttttaatgctctatgtttctgctcaaatcactgaaaattgtcaagtactaaattcgttgatttgtgttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG
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ctatgctgtatgaaagtcattacctcatgcttttagtttgcaatatttccttgca---tattgaagatttctagagattga--tactctatgttctcttcggcagGTCTACTTGTGTGAGAAACTATCTCTTACTAATGAGATGTACTTCGCCATCACCCTTGATAGGAAAACTGCTGGTCCG
upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 4
tatctttcaaagcaagagtcacactttttaatgctctatgtttctgctcaaatcactgaaaattgtcaagtactaaattcgttgatttgtg---ttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG
| | | | || ||| | | | | | | | | ||| ||| || | | || ||||| || | |||| |||||| ||||| ||||| || ||||||||||| |||||||||||||| || || || || || | | | |||||||||
tgctactttattttgtttttggtctctttcaatccttttatatagagatata-cacaaaaaggggttggttgtttgat--gttgaattttccattttttacagGTTTACTTGTGTGAAAAGCTGTCACTTGTAAATGAGATGTACTTTGCTATAACACTGGATCGTACGAGTGCTGGTCCA
upper sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G20420.1 (Arabidopsis thaliana), 3'ss of exon 4
tatctttcaaagcaagagtcacacttt-ttaatgctctatgtttctgctcaaatcactgaaaattgtcaagtac-----taaattcgttg-atttgtgttttga-cagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG
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-------------gtttgttatctgttattcatgattggtgttttttcttctattattgtcactgctcttgcacctttgtttattcattgtgtcttcattttgagcagGTTTACTTGTGTGAGAAATTGTCACTCGTCAATGAGATGTACTTTTCCATTATTCTGGACCGTAAATCTGCTGGACCGMapped 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|88730444|gb|CI754057.1|CI754057EST: AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAG GTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
genomic: AGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAGgttagttttt ... gttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctcaaatcactgaaaattgtcaagtactaaattcgttgatttgtgttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG
tactaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatctttcaaagcaagagtcacactttttaatgctctatgtttctgctcaaatcactgaaaattgtcaagtactaaattcgttgatttgtgttttgacagGTCTACTTATGTGAGAAACTGTCACTTGTTAATGAGATGTACTTCGCCATCACCCTTGACAGGAATACTGCTGGTCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG