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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttcttttctgttcttttattgagtagcaaagattttcttggtaagagtaactggctgcttcatactccacctcaatattatgacacatgaatgtaacttaatagatcttctatattttttactctacctcaatattttcttgttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG

Basic information

species Oryza sativa
transcript LOC_Os06g37180.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G181151_T03 (Zea mays), 3'ss of exon 11
gtactttcttttctgttcttttattgagt-agcaaagattttcttggtaagagtaactggc------tgcttcatactccacctcaa-------tattatgacacatg-aatgtaacttaatagatcttc-tatattttttact---------------ctacctcaatattttcttgttac------tttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG----------------------------------------------------
|| ||||  ||| | || | || |||||| | | ||  || |      |   |   | ||       |  || |||    |  | |        |||| |  || ||   || ||   ||  |  | ||  | |||||||||||               ||   |  || |  ||   ||        |||||||| || ||||| ||||||||| |||||||||| |||||||||||||||                                                    
gtgcttttctttgtcttttattcttgagttatctaatgttataccttcacatgcggcaggtctggaattatttataactaaatttagcatttcttattttctcatatttgatatagaatatgaagtatttgtttattttttactaccttgatagcttatctgtgttgatgtgatcacattttattttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGGTAAGATAAGTTTTCTGTATGTTTTCAGCATTTATGTTGAAGGTTAGTTGTA

upper sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 10
gtactttcttttctgttcttttattgagt-agcaaagatt---ttcttggtaagagtaact---ggctgcttcatactccacctcaatattatga----------cacatgaatgtaacttaatagatcttctatattttttact---------------ctacctcaatattttcttgtta----ctttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
|| ||||  | | | |||| || |||||| | ||||  ||    | |      | | | ||   |  |  || |||    |  | |   || | |          || ||  || ||   |   |  ||||   |  ||||||||               ||   |  || |  |    |||    ||||||||| || ||||| || |||||| |||||||||| || ||||||||||||
gtgcttttctatgttttctattcttgagttatcaaatgttacactttcacatggggcagctctggaattatttataactaatttaacattttttattttttttctcatattgatatagaatgtgaagtctttgtttatttttactaccttgatagcttatctgtgttgatgtgatggcattatattctttcagATTTATCCACCTATTAATGTCCTGCCATCTCTTTCACGATTGATGAAG

upper sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 11
gtactttcttttctgttcttttattgagt-agcaaagattttcttggtaagagtaactggc------tgcttcatactccacctcaa-------tattatgacacatg-aatgtaacttaatagatcttc-tatattttttact---------------ctacctcaatattttcttgttac------tttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
|| ||||  ||| | || | || |||||| | | ||  || |      |   |   | ||       |  || |||    |  | |        |||| |  || ||   || ||   ||  |  | ||  | |||||||||||               ||   |  || |  ||   ||        |||||||| || ||||| ||||||||| |||||||||| |||||||||||||||
gtgcttttctttgtcttttattcttgagttatctaatgttataccttcacatgcggcaggtctggaattatttataactaaatttagcatttcttattttctcatatttgatatagaatatgaagtatttgtttattttttactaccttgatagcttatctgtgttgatgtgatcacattttattttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG

upper sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 12
gtactttcttttctgttcttttattgagtagcaaagattttcttggtaagagtaactggctgcttcatactccacctcaatattatgacacatgaatgtaacttaatagatct---tctatattttttactctacctcaatattttcttgttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
                                                     || |   ||     |  | ||| | | | || ||     | | |||||     | | |||   | ||| |  |      |    |||| |||  ||||   |  ||||| ||||| || |||||||||||||||||||| |||||  | ||||||
-----------------------------------------------------aatt--ttgaaagttgtttcactttagt-ttgtg---tgtaagtgtaaggcgttggttctagttttatgtaatagctggtgtaccaat-tttcgttgtgtttcacagATCTACCCTCCGATCAATGTCTTGCCATCTCTGTCTCGTCTCATGAAG

upper sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 11
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 10
gtactttcttttctgttcttttattgagtagcaaagattttcttggtaagagtaactggctgcttcatactccacctcaatattatgacacatgaatgtaacttaatagatcttctatattttttactctacctcaatattttcttgttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
    | |   ||||   |||  |   ||    ||  ||  || |  |    | | |  | | | |||||    |     |  |  |  ||  |||  || | | |    |  || || |   |||| |  | || ||| |  |  || |  |  ||||| |||||||| ||||||||  |||||||||| || ||||||||||||
---gtattggttctaa-cttcgagccaggcttaacaatactcatattctt-gcatccagtttcatcataggagat----acttcttcccatttgatcgttagtgatggaaggttgta-agcctttagttgatct-aatgtaatgatgatgatg-cagATCTACCCACCTATCAATGTGCTGCCATCTCTGTCGCGATTGATGAAG

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|33684047|gb|CF312286.1|CF312286
EST:     ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|24468720|gb|CA305669.1|CA305669
EST:     CATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: CATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|29665773|gb|CB662048.1|CB662048
EST:     ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|29681070|gb|CB677345.1|CB677345
EST:     CGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: CGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|86537237|gb|CI177443.1|CI177443
EST:     AGATATACAGTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCGTGCCATCTCTCTCTCGATTGATGAAG
genomic: AGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|29675288|gb|CB671563.1|CB671563
EST:     ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|58605789|gb|CK033822.1|CK033822
EST:     ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|29684019|gb|CB680294.1|CB680294
EST:     ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|58675652|gb|CK064339.1|CK064339
EST:     ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCG
genomic: ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCG
EST: gi|29630857|gb|CB635866.1|CB635866
EST:     ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|29630447|gb|CB635456.1|CB635456
EST:     CGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: CGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|218488216|gb|FG965996.1|FG965996
EST:     ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|58674437|gb|CK063123.1|CK063123
EST:     ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|58654849|gb|CK043529.1|CK043529
EST:     ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGA
genomic: ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGA
EST: gi|29678975|gb|CB675250.1|CB675250
EST:     ATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: ATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|700311|gb|D46602.1|D46602
EST:     CATTACCGAAGGNCAAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGGTTGATGAAG
genomic: CATTACCGAAGGACA-GATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|33675121|gb|CF303360.1|CF303360
EST:     ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTC
genomic: ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTC
EST: gi|300215980|gb|HO088606.1|HO088606
EST:     ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|58594202|gb|CF992510.1|CF992510
EST:     ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|86535166|gb|CI175372.1|CI175372
EST:     GACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: GACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|27554550|gb|CA998450.1|CA998450
EST:     ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|29678974|gb|CB675249.1|CB675249
EST:     ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|700095|gb|D46386.1|D46386
EST:     ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGA
genomic: ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCC-ATCAATGTCTTGCCATCTCTCTCTCGATTGATGA
EST: gi|29668005|gb|CB664280.1|CB664280
EST:     ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|58662859|gb|CK051545.1|CK051545
EST:     ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|29617704|gb|CB622716.1|CB622716
EST:     GCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: GCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|29684020|gb|CB680295.1|CB680295
EST:     ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|29669855|gb|CB666130.1|CB666130
EST:     ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|58688525|gb|CK077212.1|CK077212
EST:     ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|88902578|gb|CI088116.1|CI088116
EST:     ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|29665772|gb|CB662047.1|CB662047
EST:     ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
EST: gi|56157325|gb|D41816.2|D41816
EST:     ACATTACCGAA-GACAGATATACATTGACAGGCAGCTGCATAACAGACAG                         ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
genomic: ACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 60 (upstream exon), 72 (downstream exon)
Score: 87

ATATTACACATCCAACTCCTGATCTTACGGGGTACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttctt ... ttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatagatcttctatattttttactctacctcaatattttcttgttactttcagATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAG
                                     ttttcttgttactttc  CT-rich tract
       atcttctatatttttt  TA-rich tract