Sequence
atgc intronic sequence ATGC exonic sequencegtaagacaataatagtttgtttgtttctttgtttgtttgttcgtgctataaatatttgcatggttgaaattgatagttaccctctctaccttctgtggctggctacgattgaaattaagttggaaatgtgctctgaaaaagatgtttgatttgtgttcctaaatattatgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g33240.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G064023_T04 (Zea mays), 3'ss of exon 3
gtaagacaataatagtttgtttgtttctttgtttgtttgttcgtgctataaatatttgcatggttgaaattgatagttaccctctctaccttctgtggctggctacgattgaaattaagttggaaatgtgctctgaaaaagatgtttgatttgtgttcctaaatattatgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
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-----------------------------------------------------------------------gtaagacagttcggcttcctgttgtacct---------tgtgttagagttg----tgtactctggatgggatgctgattgtgtttttgcaaatg---------cagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAGCAG
upper sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G063851_T02 (Zea mays), 3'ss of exon 3
gtaagacaataatagtttgtttgtttctttgtttgtttgttcgtgctataaatatttgcatggttgaaattgatagttaccctctctaccttctgtggctggctacgattgaaattaagttggaaatgtgctctgaaaaagatgtttgatttgtgttcctaaatattatgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
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-----------------------------------------------------------------------gtaagacagttcgtcttcctgttatgcct---tgtggtagagttttg--------tgtactctggatagcatgctga--ttgtgtttctgcaaatg-------cagGATCTTAAGTCCCAGTTGCAGGAATTGATTCCGGAACAACAG
upper sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G063909_T02 (Zea mays), 3'ss of exon 2
gtaagacaataatagtttgtttgtttctttgtttgtttgttcgtgctataaatatttgcatggttgaaattgatagttaccctctctaccttctgtggctggctacgattgaaattaagttggaaatgtgctctgaaaaagatgtt--tgatttgtgttcctaaatattatgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
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-------------------------------------------------------------------gtaggacagctcgtcttcctgc-tgctctacattgccgtaaac-acgtagagctgtgcatgtgctatggatgggatgctgatactgtgtgtttctgcaaattaaa--tgcagGATCTTAAGTCCCAGCTGCGGGAACTGATTCCGGAACAGCAGMapped 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|88695722|gb|CI737760.1|CI737760EST: CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTT GATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAGG
genomic: CCACGCTTGGTGGTGTGAGATGGCTGCAGATGCAGAGTCCATCTGATCTTgtaagacaat ... atgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaatgtgctctgaaaaagatgtttgatttgtgttcctaaatattatgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
tcctaaa putative branch site (score: 2)
tgctttc putative PPT
taaatattatgcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagacaataatagtttgtttgtttctttgtttgtttgttcgtgctataaatatttgcatggttgaaattgatagttaccctctctaccttctgtggctggctacgattgaaattaagttggaaatgtgctctgaaaaagatgtttgatttgtgttcctaaatattatgctttcagGATCTTAAGTCCCAGCTGCAGGAATTGATTCCCGAGCAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG