Sequence
atgc intronic sequence ATGC exonic sequenceGTCAGACATGACTCTTGTGGAAGCTTTCAAAAGGATGCAGGTCATTGAAGATGAGGAAACAGAAGATGCACTAGATGAAAATGGAGAGCCCGATGAAGAGgtattgcgtgtggagtgtgcattttgctatccatgttcaacttattatgaaatttttcaactttcctttctagtgttgatgaccgtgtcactcaaccattgttccgtttatcctttctccttgattaaatgtctgtagtgctatattcatcatcatgttctgaaaataataacataggattcctcatag
Basic information
species | Oryza sativa |
transcript | LOC_Os06g05180.4 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 23
GTCAGACATGACTCTTGTGGAAGCTTTCAAAAGGATGCAGGTCATTGAAGATGAGGAAACAGAAGATGCACTAGATGAAAATGGAGAGCCCGATGAAGAGgtattgcgtgtggagtgtgcattttgctatccatgttcaacttattatgaaatttttcaactttcctttctagtgttgatgaccgtgtcactcaaccattgttccgtttatcctttctccttgattaaatgtctgtagtgctatattcatcatcatgttctgaaaataataacataggattcctcatag
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GTCAGACATGACTATTGTGGAAGCTTTCAAAAGGATGCAGGTTGTTCAGCATGAGGAACCTGAAGATGTGGCTGAGGAAAATGGAGAACTTGATCAACAGgtatctcatatgcattctgc-ttctattgcccatttcc----tagcatgcactatggaa---ttattttagaaacttgagatatgtactgatctattttcacatcggc---------------------------------------------------------------------------------
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 22
GTCAGACATGACTCTTGTGGAAGCTTTCAAAAGGATGCAGGTCATTGAAGATGAGGAAACAGAAGATGCACTAGATGAAAATGGAGAGCCCGATGAAGAGgtattgcgtgtggagtgtgcattttgctatccatgttcaacttattatgaaatttttcaactttcctttctagtgttgatgaccgtgtcactcaaccattgttccgtttatcctttctccttgattaaatgtctgtagtgctatattcatcatcatgttctgaaaataataacataggattcctcatag
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---------GATTCTTGTGGAAGCTTTCAAAAGGATGCAGGTCATTGAGCATGAGGAACCTGAAGATGCAGCTGAGGAAAATGGAGAACCTGATCAACAGGTATCTCATgtgcattctgcttcttactgtctattttgaact----atgca---ctatggtgctcttttggaaacctgatatat---ttacagatccattttcacatcggcccattcct----------------------------------------------------------------------
upper sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GRMZM2G095348_T01 (Zea mays), 5'ss of exon 23
GTCAGACATGACTCTTGTGGAAGCTTTCAAAAGGATGCAGGTCATTGAAGATGAGGAAACAGAAGATGCACTAGATGAAAATGGAGAGCCCGATGAAGAGgtattgcgtgtggagtgtgcattttgctatccatgttcaacttattatgaaatttttcaactttcctttctagtgttgatgaccgtgtcactcaaccattgttccgtttatcctttctccttgattaaatgtctgtagtgctatattcatcatcatgttctgaaaataataacataggattcctcatag
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GTCAGGCATGATTCTTGTGGAAGCTTTCAAAAGGATGCAGGTCATTGAGCATGAGGAACCTGAAGATGCAGCTGAGGAAAATGGAGAACCTGATCAACAGgtatctcatgtgcattctgcttcttactgtctattttgaact----atgca---ctatggtgctcttttggaaacctgatatat---ttacagatccattttcacatcgg-------------------------------------------------------------------------------Mapped 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|11370679|gb|AU164984.1|AU164984EST: ATGAGGAAACAGAAGATGCACTAGATGAAAATGGAGAGCCCGATGAAGAG GTTTTGGAAGAGANCAAAGTGGAGGAGAGCACAGATGAAGCTGTCGAAGTT
genomic: ATGAGGAAACAGAAGATGCACTAGATGAAAATGGAGAGCCCGATGAAGAGgtattgcgtg ... ttcctcatagGTTTTGGAAGAGAACAAAGTGGAGGAGAGCACAGATGAAGCTGTCGAAGTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTCAGACATGACTCTTGTGGAAGCTTTCAAAAGGATGCAGGTCATTGAAGATGAGGAAACAGAAGATGCACTAGATGAAAATGGAGAGCCCGATGAAGAGgtattgcgtgtggagtgtgcattttgctatccatgttcaacttattatgaaatttttcaactttcctttctagtgttgatgaccgtgtcactcaaccattgttccgtttatcctttctccttgattaaatgtctgtagtgctatattcatcatcatgttctgaaaataataacataggattcctcatag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA