Sequence
atgc intronic sequence ATGC exonic sequencegtgagtcaaatattatctattgatatttatagattgatacttttaacgaatttcatactgaaataactagttttgtcactgtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
Basic information
species | Oryza sativa |
transcript | LOC_Os06g05180.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 12
gtgagtcaaatattatctattgatatttatagattg-atacttttaacgaattt-catactgaaataactagttttgtcactgtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
|||| |||| |||||| | || | | | ||| || | || | || |||| | | ||| ||| || |||| |||||| |||| ||||||||||| ||||||||||||||||||||||||||||||||||||||||| || ||||||||
gtgaatcaagtattattttttcttgggtggaaattttgtatgtaaaatgtatgagtttactattaaccttttctttatca-tgcatttatagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 13
gtgagtcaaa--tattatctattgatatttatagattgatacttttaacgaatttcatactgaaataactagttttgtcactgtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
|||||||||| |||||| | | | | | ||| | | | | || ||| ||| | | | | ||| ||| ||| ||| ||||| |||| ||||||||||| ||||||||||||||||||||||||||||||||||||||||| || ||||||||
gtgagtcaaaagtattatttttccttgggtggaaatt--ttgtatgtatgagtttaatattaacct---tttgtttatca-tgtgtttatagAATGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
gtgagtcaaatattatctattgatatttatagattgatacttttaacgaat-ttcatactgaaataactagttttgtcactgtattt---ttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
|| ||| | | | || ||| ||||| || ||||| | ||||| | |||| || |||||| | | || | ||||||| || |||||||| || ||||| ||||| |||| || || ||||||||||||||||| |||||||||||
gtaagt--actttgattaggtgacatttagttatctgctcttttccttcttattcattgtttaata--taattttgttattaatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 2
gtgagtcaaatattatctattgatatttatagattgatacttttaacgaatttcatactgaaa-taactagttttgtcactgtattttt-----agAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
|| ||| | || ||| || || || | |||||| ||| ||||| | || |||||| | | || || ||||||| || ||||||||||| ||||| ||||| | || || ||||||||||||||||| || |||||||||||
gtaagt--gcttgcatgaggtgacatc---agctttctgcttttattt--cttcttactgtttcttgttaattttgttaaaattttcttgtgtcagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 13
gtgagtcaaatattatctattgatatttatagattgatacttttaacgaatttcatactgaaataactagttttgtcactgtattttt-----agAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
|| | | | | | || || | |||||| ||| ||||| | || |||||| | | || || ||||||| || ||||||||||||||||| |||| | || || ||||||||||||||||| || || ||||||||
-----gtaagtgcttgcatgaggtggcatcagctttctgcttttattt--cttcttactgt--ttcttatttttgttaaatttttcttgtgtcagAACCTGTACTGGGCTGATAGCGGTGATTTAGTGACGATTGCTAGTGATACATCATTCTATATCCTTAAGTACAAT
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 13
gtgagtcaaatattatctattgatatttatagattgatacttttaa--cgaatttcatactgaaataactagttttgtcactgtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
|| ||| | | | || ||| || || || ||||| | ||| | | || | | | | || | | | | | ||||||| || |||||||| || ||||| ||||| |||| || |||||||||||||||||||| |||||||||||
gtaagt--actttgattaggtgacatctagttatctgctcttttccttcttattcgttgtttaatttaattttgttatttatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGTGATACATCATTCTACATTCTGAAGTACAAT
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 17
----------------------------------------------------------------------------------------------------gtgagtcaaatattatctattgatatttatagattgatacttttaacgaatttcatactgaaataactagttttgtcactgtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
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gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaagagttccttatctgaaatttaaacgcaaaagcagattggtactgctcgcttatt-cacttttaacgtttttgtttattcaatgt---ttcagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
----------------------------------------------------gtgagtcaaatattatctattgatatttatagattgatacttttaacgaatttcatactgaaataactagttttgtcactgtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
| || ||| | || | | | || | | | || | | || | || | || | | | |||| |||| |||||||||||||| || ||||| |||| || || || |||||||| ||||||||||| ||||||||||
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttg-tcccaattagtgtctttactaactctttactcccatgaa-aaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 13
gtgagt-caaatattat---ctattgatatttatagattgatacttttaacgaatttca-----tactgaaataactagttttgtcactgtattttt-----------agAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
|| || | || || || || ||| | | | | | | | | | || | | |||| |||| | | ||||| ||||||| |||||||||||||| || || | || || || || |||||||||||||| ||||| |||||||||||
gtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT
upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 13
--gtgagtcaaatattatctattgatatttatagattgatacttttaacgaatttcatactgaaataactagttttgtcactgtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
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gcatgttctcaaaaagcttacttcacaattaccaggttttggccacagagaaactaatagttcatttctttgggtggtttcaatatttc-agAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAATMapped 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|58660118|gb|CK048798.1|CK048798EST: ATGACTGGGCTGACTGTAGACTAATACGCCGCATTGATGTGAATGTCAAA AACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACA
genomic: ATGACTGGGCTGACTGTAGACTAATACGCCGCATTGATGTGAATGTCAAAgtgagtcaaa ... gtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACA
EST:
gi|29630380|gb|CB635389.1|CB635389EST: ATGACTGGGCTGACTGTAGACTAATACGCCGCATTGATGTGAATGTCAAA AACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACA
genomic: ATGACTGGGCTGACTGTAGACTAATACGCCGCATTGATGTGAATGTCAAAgtgagtcaaa ... gtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatacttttaacgaatttcatactgaaataactagttttgtcactgtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
aaataac putative branch site (score: 2)
tattttt putative PPT
aaataactagtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtcaaatattatctattgatatttatagattgatacttttaacgaatttcatactgaaataactagttttgtcactgtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG