Sequence
atgc intronic sequence ATGC exonic sequencegtccgtacagcgccctgcattctacttaatcacaatctcctgacacattgaaaaatgttctaatttgttggtatctgaaattctgaatctgaattctgcttcattttttagGTGAGGACGATCGATGAGATGCGGGAGAGGGTGAGGATGCGTGGCCTCCGATGCCATCTCATGTACTGCAGGAATGCAACAAGGCTTCAAGTTGTTCCTC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g69030.3 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g69030.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM5G875238_T01 (Zea mays), 3'ss of exon 10
gtccgtacagcgccctgcattctacttaatcacaatctcctgacacattgaaaaatgttctaatttg--ttggtatctgaaattctgaatctgaattctgcttcatttttta-gGTGAGGACGATCGATGAGATGCGGGAGAGGGTGAGGATGCGTGGCCTCCGATGCCATCTCATGTACTGCAGGAATGCAACAAGGCTTCAAGTTGTTCCTC
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-----------gttagggaat-tctttaataaca-----cgtgtgcatccttaattcctccagttaaaaccagttgctgta----tgaatctgaattatgttttcctgcttaagGTGAAAACGGTCGATGAGATGAGGGAGCGGCTGAGGATGCGTGGTCTCCGCTGCCACATCATGTACTGCAGGAACTCGACAAGGCTTCAGGTTGTCCCTC
upper sequence: LOC_Os01g69030.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G140107_T01 (Zea mays), 3'ss of exon 11
gtccgtacagcgccctgcattctacttaatcacaatctcctgacacattgaaaaatgttct-aatttgttggtatctgaaatt-ctgaatctgaattctgcttcattttttagGTGAGGACGATCGATGAGATGCGGGAGAGGGTGAGGATGCGTGGCCTCCGATGCCATCTCATGTACTGCAGGAATGCAACAAGGCTTCAAGTTGTTCCTC
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------------------------gttag--ggagttctttattttgtgcatacgtatccttaatgcctacttatgaccgattgctgagtctgaattctatctgtgtggttagGTGAAAACGGTCGATGAGATGAGGGAGAGGCTGAGGATGCGTGGTCTCCGGTGCCACATCATGTACTGCAGGAACTCGACAAGGCTTCAGGTTGTCCCTCMapped 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|58609199|gb|CK037232.1|CK037232EST: AGTCCTGCAACCCCCACTGTGTCTCCTTCTTCATCAAAGACCCCAATAAG GTGAGGACGATCGATGAGATGCGGGGGAGGATGAGGATGCGTGGCCTCCGA
genomic: AGTCCTGCAACCCCCACTGTGTCTCCTTCTTCATCAAAGACCCCAATAAGgtccgtacag ... cattttttagGTGAGGACGATCGATGAGATGCGGGAGAGGGTGAGGATGCGTGGCCTCCGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttctaatttgttggtatctgaaattctgaatctgaattctgcttcattttttagGTGAGGACGATCGATGAGATGCGGGAGAGGGTGAGGATGCGTGGCCTCCGATGCCATCTCATGTACTGCAGGAATGCAACAAGGCTTCAAGTTGTTCCTC
ttctaat putative branch site (score: 2)
ttctgcttcatttttt putative PPT
ttcatttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtccgtacagcgccctgcattctacttaatcacaatctcctgacacattgaaaaatgttctaatttgttggtatctgaaattctgaatctgaattctgcttcattttttagGTGAGGACGATCGATGAGATGCGGGAGAGGGTGAGGATGCGTGGCCTCCGATGCCATCTCATGTACTGCAGGAATGCAACAAGGCTTCAAGTTGTTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG