Sequence
atgc intronic sequence ATGC exonic sequencegtaaaccgtaagatacatatagtaattttgttttgcacaattgcattatatcactttgtcctttcctctggcactttgttagcatgtctagaataagtcaggtagactacatgtttcactatgtcctgatggcaatttcttggctaatattgtagGAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os12g03470.3 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G077299_T01 (Zea mays), 3'ss of exon 2
gtaaaccgtaagatacatatagtaattttgttttgcacaattgcattatatcactttgtcctttcctctggcactttgttagcatgtctagaataagtcaggtagactacatgtttcactatgtcctgatggcaatttcttggctaatattgtagGAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG
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------------gtg-agacagtgatttcttggtacacaccagccttat-------tgatcttac----aaggatttgtccatgtaagcggaatggtccaa-------acacacttggtcgtgttctca-gataaccaggttgctttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG
upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G006130_T06 (Zea mays), 3'ss of exon 2
gtaaaccgtaagatacatatagtaattttgttttgcacaattgcattatatcactttgtcctttcctctggcactttgttagcatgtctagaataagtcaggtagactacatgtttcactatgtcctgatggcaatttcttggctaatattgtagGAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG
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----------------------------------gtgaggcagtagtttatcggtagatgctagttccta----tgttttaccacatataa------tcagaaagaata-------------atccaaatat--actgcatggcc--tactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG
upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA19G30150.1 (Glycine max), 3'ss of exon 2
gtaaaccgtaagatacatatagtaattttgttttgcacaattgcattatatcactttgtcctttcctctggcactttgttagcatgtctagaataagtcaggtagactacatgtttcactatgtcctgatggcaat-----ttcttggctaatatt--gtagGAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG
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----------------------------------gtataatttaatta-attacttt------ttgtttggtatatttttaaga-gtccaggaagattt---tagagtgtg-attctaggatgttttgtttgcaataaagctaattgttggatctttggcagGAAATCAATCATGCAGGAGCTGGGGGATTGTGGGCTGAGCTTGTGAGGAATAGAG
upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G26120.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaaaccgtaagatacatatagtaattttgttttgcacaattgcattatatcactttgtcctttcctctggcactttgttagcatgtctagaataagtcaggtagactacatgtttcactatgtcctgatggcaatttcttggctaatattgtagGAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG
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------------------------------------ctaaatagaaactattttaatgtaactttactagtcatgatgtttaatgttttaatttagctctaataaaatttatga--------attctgatga-aatta----------attacagGAAATAAATCATGCTGGAGCAGGTGGACTATGGGCTGAACTTGTTAGCAATAGAG
upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaaaccgtaagatacatatagtaattttgttttgcacaattgcattatatcactttgtcctttcctctggcactttgttagcatgtctagaataagt-caggtagactacatgtttcactatgtcctgatggcaatttcttggctaatattgtagGAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG
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-----------------------------------------------gtttgttaatgttacggtctcaaatagatctttgcaatgtacgcaatgtgttcaaatcaatcataaacttta-tatgctct-atg-----ttc---------attatagGAGATCAACCATGCTGGTGCCGGTGGATTATGGGCCGAACTTGTTAGCAACAGAG
upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 3
gtaaaccgtaagatacatatagtaattttgttttgcacaattgcattatatcactttgtcctttcctctggcactttgttagcatgtctagaataagtcaggtagactacatgtttcactatgtcctgatggcaatttcttggctaatattgtagGAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG
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------------------------------------------gggttgtttcgaat--tctgagcaattagcaatttactgccactgtaattgtgtatatgttgattttgaagattga----gctttgtttgaaatgtctttg-------tgtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAACAGAGMapped 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|29627933|gb|CB632944.1|CB632944EST: GCTATTTGGAATATTTTTTGAG GAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: GCTATTTGGAATATTTTTTGAGgtaaaccgta ... aatattgtagGAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
EST:
gi|29667031|gb|CB663306.1|CB663306EST: TGCAACATGCTCGACAGATCCCCGACACGCTATTTGGAATATTTTTTGAG GAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
genomic: TGCAACATGCTCGACAGATCCCCGACACGCTATTTGGAATATTTTTTGAGgtaaaccgta ... aatattgtagGAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtagactacatgtttcactatgtcctgatggcaatttcttggctaatattgtagGAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG
ggctaat putative branch site (score: 3)
taatattgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaccgtaagatacatatagtaattttgttttgcacaattgcattatatcactttgtcctttcctctggcactttgttagcatgtctagaataagtcaggtagactacatgtttcactatgtcctgatggcaatttcttggctaatattgtagGAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA