Sequence
atgc intronic sequence ATGC exonic sequence...tgcagagcatcattttaattgtttcttcaatcaagttttacgcttactgactggtatttggtattttgtatctaattgtccacccttctttctattgcagCAAGCAGCTCTAGTACTCAATGCATCCAGGCGCTTTAGATACACATTGGACTTGAAAAGGGAGGAACAAAGGGAGGAAGTTATAAGCAAAATTCGTGCAC
Basic information
species | Oryza sativa |
transcript | LOC_Os04g51610.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G140328_T04 (Zea mays), 3'ss of exon 1
---tgcagagcatcattttaa--ttgtttcttcaatcaagttttacgcttactgactggtatttggtattttgtatctaattgtccacccttctttctattgcagCAAGCAGCTCTAGTACTCAATGCATCCAGGCGCTTTAGATACACATTGGACTTGAAAAGGGAGGAACAAAGGGAGGAAGTTATAAGCAAAATTCGTGCAC
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gctcgcttctccctctctaaacatttttcctttgctaaattgatttgcttgatatcattcttttgata-----tgtttggtttttaataccttatattattgcagCAAGCAGCCCTTGTGCTGAATGCATCAAGGCGCTTTAGGTACACACTCGATTTGAAAAAGGAGGAACAAAATGAGGAAATCAGGAGAAAAATTCGTGCAA
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G391042_T02 (Zea mays), 3'ss of exon 1
tgcagagcatcattttaattgtttcttca-atcaagttttacgcttactgact-ggtatttggtattt--tgtatctaattgtccacccttctttctattgcagCAAGCAGCTCTAGTACTCAATGCATCCAGGCGCTTTAGATACACATTGGACTTGAAAAGGGAGGAACAAAGGGAGGAAGTTATAAGCAAAATTCGTGCAC
|| || | | ||| | || | || | | | | | ||| | ||| | | | || | | | || |||||||||||||||| || || || |||||||| ||||||||||| ||||| | || ||||||| ||||||||||| |||||| | | || ||||| |||||||
----agttttctttcctaaaatatctaaatatttcctgctagagtgattagtttgatatctttcttttgacatgtttggtttctaatacattttgttattgcagCAAGCAGCACTTGTGCTGAATGCATCAAGGCGCTTTAGGTACACTCTTGATTTGAAAAAGGAGGAACAAAAGGAGGAGATCAGGAGAAAAATCCGTGCAC
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA07G00630.1 (Glycine max), 3'ss of exon 3
tgcagagcatcattttaattgtttcttcaatcaagttttacgcttactgactggtat-ttggtattttgtatctaat-tgtccacccttctttctat-tgcagCAAGCAGCTCTAGTACTCAATGCATCCAGGCGCTTTAGATACACATTGGACTTGAAAAGGGAGGAACAAAGGGAGGAAGTTATAAGCAAAATTCGTGCAC
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---ggattgtgactttagccagtgtaattttgacgaggtgcattagtgtagcggtatgtctgctttttgcaaggcatctaactgaagtttcacccatgtacagCAAGCAGCACTCGTGCTCAATGCGTCCAGGCGTTTTAGATATACTTTGGACTTGAGAAAGGAAGAAGAGAAAGAGCAAAAGAAACACTTGATTAGAGCCC
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA15G00340.1 (Glycine max), 3'ss of exon 1
tgcagagcatcattttaattgtttcttcaatcaagttttacgcttactgactggtatttggtattttgtatctaattgtccacccttctttctattgcagCAAGCAGCTCTAGTACTCAATGCATCCAGGCGCTTTAGATACACATTGGACTTGAAAAGGGAGGAACAAAGGGAGGAAGTTATAAGCAAAATTCGTGCAC
| | | | | | | | | | || || ||| || | |||| |||||| | | | | | ||||||||||||||| | || |||||||| |||||||| ||||| ||||| | |||||||||| ||| || | | ||| || | ||||| ||| | | |
-----------------gtaataacgttactataatctctctctctctctctg---catgattttttctatctatcttattaactgtaatgaatttgcagCAAGCAGCTTTCGTGCTCAATGCGTCCAGGCGTTTTAGGTACACTCTTGACTTGAAAAAGGAAGAGGAGAAAGAGCAAAAGAAAAGCATGATTAGATCCC
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 3
tgcagagcatcattttaattgtttc--ttcaatcaagttttacgcttactgactggtatttggtattttgtatctaattgtccacccttctttctat-tgcagCAAGCAGCTCTAGTACTCAATGCATCCAGGCGCTTTAGATACACATTGGACTTGAAAAGGGAGGAACAAAGGGAGGAAGTTATAAGCAAAATTCGTGCAC
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---tgattgtggtttaattcagtgtaattttggcgaggtgcatttgtgtagaagtatgtctgctttttggaaggcatctaactgaagtttcacccatgtacagCAAGCAGCACTCGTGCTCAATGCGTCCAGGCGTTTTAGATATACTTTGGACTTGAGAAAGGAAGAAGAGAAAGAGCAAAAGAAACACTTGATTAGAGCCC
upper sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 1
tgcagagcatcattttaattgtttcttcaatcaagttttacgcttactgactggtatttggtattttgtatctaattgtccacccttctttctattgcagCAAGCAGCTCTAGTACTCAATGCATCCAGGCGCTTTAGATACACATTGGACTTGAAAAGGGAGGAACAAAGGGAGGAAGTTATAAGCAAAATTCGTGCAC
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-gta-ataataatacttaatctctctgcattcagttaattaattaattaattt---ttctatctatcttatcttattaactgaaatgcatt----tgcagCAAGCAGCTTTCGTCCTCAATGCGTCCAGGCGTTTTAGATACACTCTTGACTTGAAAAAGGAAGAGGAGAAAGAGCAAAAGAAAAGCATGATTAGATCCCMapped 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|58600052|gb|CK010580.1|CK010580EST: AGGGTGCTCCCGTCGAGAGTCTCAAAAAATGGCGG CAAGCAGCTCTAGTACTCAATGCATCCAGGCGCTTTAGATACACATTGGAC
genomic: AGGGTGCTCCCGTCGAGAGTCTCAAAAAATGGCGGgtaagccgca ... tctattgcagCAAGCAGCTCTAGTACTCAATGCATCCAGGCGCTTTAGATACACATTGGAC
EST:
gi|88401968|gb|CI593680.1|CI593680EST: CGACATCCCGGCTAATGGTGCTCCCGTCGAGAGTCTCAAAAAATTGGCGG CAAGCAGCTCTAGTACTCAATGCATCCAGGCGCTTTAGATACACATTGGA
genomic: CGACATCCCGGCTAAGGGTGCTCCCGTCGAGAGTCTCAAAAAAT-GGCGGgtaagccgca ... tctattgcagCAAGCAGCTCTAGTACTCAATGCATCCAGGCGCTTTAGATACACATTGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actgactggtatttggtattttgtatctaattgtccacccttctttctattgcagCAAGCAGCTCTAGTACTCAATGCATCCAGGCGCTTTAGATACACATTGGACTTGAAAAGGGAGGAACAAAGGGAGGAAGTTATAAGCAAAATTCGTGCAC
ttgtccacccttcttt CT-rich tract
tattttgtatctaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgcagagcatcattttaattgtttcttcaatcaagttttacgcttactgactggtatttggtattttgtatctaattgtccacccttctttctattgcagCAAGCAGCTCTAGTACTCAATGCATCCAGGCGCTTTAGATACACATTGGACTTGAAAAGGGAGGAACAAAGGGAGGAAGTTATAAGCAAAATTCGTGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA