Sequence
atgc intronic sequence ATGC exonic sequencegtaatttgttccattccgattttgcatcagacatggttcgtttacctttgcttcattaactatctcaggccaatctgtgtgtcgtggatggaagtgaacgataatactgtcacactgttgatagtttgtcagttattttaagtaatgttctatttgtgcctttaaacttttgttgctttcatcttctacagATTATATTTCTGGAAACTATCTGTAACGATCCGAATATAATTGAAAGGAATGTACGTCTGAAGATACAGCAAAGTCCTGACTATGCTGACCA
Basic information
species | Oryza sativa |
transcript | LOC_Os05g07130.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g07130.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G021846_T01 (Zea mays), 3'ss of exon 11
gtaatttgttccattccgattttgcatcagacatggttcgtttacctttgcttcattaactatctcaggccaatctgtgtgtcgtggatggaagtgaacgataatactgtcacactgttgatagtttgtc---agttattttaagtaa-tgttct--atttgtgcctttaaacttttgttgctttcatcttctacagATTATATTTCTGGAAACTATCTGTAACGATCCGAATATAATTGAAAGGAATGTACGTCTGAAGATACAGCAAAGTCCTGACTATGCTGACCA
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-------------------------------------------------------------------------------------------------ccgtaaaatttctcaaaaaattgaccatttgtcttgatgcattttgtacatctgctcataattttgaccttctcgtaatgattgaagtcactttctgcagATTATATTTTTGGAGACAATATGTAATGATCCAAACATAATTGAAAGAAACATACGGCTGAAGATCCAACAAAGTCCAGACTATGCTGAACA
upper sequence: LOC_Os05g07130.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 17
gtaatttgttccattccgattttgcatcagacatggttcgtttacctttgcttcattaactatctcaggccaatctgtgtgtcgtggatggaagtgaacgataatactgtcacactgttgatagtttgtcagttattttaagtaatgttctatttgtgcctttaaacttttgttgctttcatcttctacagATTATATTTCTGGAAACTATCTGTAACGATCCGAATATAATTGAAAGGAATGTACGTCTGAAGATACAGCAAAGTCCTGACTATGCTGACCA
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------------------------------------------------------------------------------------------gtagtcaaagatggcactgaaataa-gtatatgatatgagaatgataa-atttagttttgaactcttctgatccatctttttgtgtttatgt----tgtagATAATCTTCCTGGAAACAATATGCAATGATAGAAATATAATTGAAAGGAATATTCGCCTTAAAATTCAGCAAAGTCCTGATTATGCAGAAGA
upper sequence: LOC_Os05g07130.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 12
gtaatttgttccattccgattttgcatcagacatggttcgtttacctttgcttcattaactatctcaggccaatctgtgtgtcgtggatggaagtgaacgataatactgtcacactgttgatagtttgtcagttattttaagtaatgttctatttgtgcctttaaacttttgttgctttcatcttctacagATTATATTTCTGGAAACTATCTGTAACGATCCGAATATAATTGAAAGGAATGTACGTCTGAAGATACAGCAAAGTCCTGACTATGCTGACCA
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------------------------------------------------------------------------------------------gtagtcaatgatggcactgaaataa-gtatatgatatgacaatgataa-atttagttttgaactcttctgatccatctttttgtgtttatgtttt----agATAATCTTCCTGGAAACAATATGCAATGATAGAAATATAATTGAAAGGAATATTCGCCTTAAAATTCAGCAAAGTCCTGATTATGCAGAAGA
upper sequence: LOC_Os05g07130.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 13
gtaatttgttccattccgattttgcatcagacatggttcgtttacctttgcttcattaactatctcaggccaatctgtgtgtcgtggatggaagtgaacgataatactgtcacactgttgatagtttgtcagttattttaagtaatgttctatttgtgcctttaaacttttgttgctttcatcttctacagATTATATTTCTGGAAACTATCTGTAACGATCCGAATATAATTGAAAGGAATGTACGTCTGAAGATACAGCAAAGTCCTGACTATGCTGACCA
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------------------------------------------------------------------------------------------gtagtcaaagatggcactgaaataa-gtataagatatgagaatgataa-atttaattttgaact----cttctgatccatctatttgttcttttgctgtagATAATCTTCCTGGAAACAATATGCAATGATAGAAATATAATTGAAAGGAATATTCGCCTTAAAATTCAGCAAAGTCCTGATTATGCAGAAGAMapped 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|58695801|gb|CK084488.1|CK084488EST: CAAGAAAACGAAGGTATATGCTAATGAAAATGGCTGAAGGGAACTGTAAG ATTATATTTCTGGAAACTATCTGTAACGATCCGAATATAATTGAAAGGACT
genomic: CAAGAAAACGAAGGTATATGCTAATGAAAATGGCTGAAGGGAACTGTAAGgtaatttgtt ... tcttctacagATTATATTTCTGGAAACTATCTGTAACGATCCGAATATAATTGAAAGGAAT
EST:
gi|84117327|gb|CD151094.1|CD151094EST: CAAGAAAACGAAGGTATATGCTAATGAAAATGGCTGAAGGGAACTGTAAG ATTATATTTCTGGAAACTATCTGTAACGATCCGAGTATAATTGAAAGGAAT
genomic: CAAGAAAACGAAGGTATATGCTAATGAAAATGGCTGAAGGGAACTGTAAGgtaatttgtt ... tcttctacagATTATATTTCTGGAAACTATCTGTAACGATCCGAATATAATTGAAAGGAAT
EST:
gi|29612781|gb|CB617794.1|CB617794EST: CAAGAAAACGAAGGTATATGCTAATGAAAATGGCTGAAGGGAACTGTAAG ATTATATTTCTGGAAACTATCTGTAACGAT
genomic: CAAGAAAACGAAGGTATATGCTAATGAAAATGGCTGAAGGGAACTGTAAGgtaatttgtt ... tcttctacagATTATATTTCTGGAAACTATCTGTAACGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaagtaatgttctatttgtgcctttaaacttttgttgctttcatcttctacagATTATATTTCTGGAAACTATCTGTAACGATCCGAATATAATTGAAAGGAATGTACGTCTGAAGATACAGCAAAGTCCTGACTATGCTGACCA
cttttgttgctttcat CT-rich tract
tttaaacttttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttgttccattccgattttgcatcagacatggttcgtttacctttgcttcattaactatctcaggccaatctgtgtgtcgtggatggaagtgaacgataatactgtcacactgttgatagtttgtcagttattttaagtaatgttctatttgtgcctttaaacttttgttgctttcatcttctacagATTATATTTCTGGAAACTATCTGTAACGATCCGAATATAATTGAAAGGAATGTACGTCTGAAGATACAGCAAAGTCCTGACTATGCTGACCA
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