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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataagttttctgtatgttttcagcatttatgttgaaggttagttgtaagaaccacttaacaactcctgcag

Basic information

species Zea mays
transcript GRMZM2G181151_T04
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G181151_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 12
ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataagttttctgtatgttttcagcat---------ttat----gttgaaggtta-----------------gttgtaagaaccacttaacaactcctgcag
|| || ||||| ||||||||| |||||||||| ||||||||||||||||| |||| | |  ||  |||   ||   |||         | ||    |||  | | ||                 ||| |||||||    ||| || || |||||
ATATACCCACCCATCAATGTCTTGCCATCTCTCTCTCGATTGATGAAGgtgagattactcatcaatataaatttcacataaactggtttcataacagttacatgctacaataatttccatttgcgttctaagaactgtctaataattcttgcag

upper sequence: GRMZM2G181151_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA10G42940.2 (Glycine max), 5'ss of exon 12
ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataagttt--tctgtatgttttcagcatttatgttgaaggttagttgtaagaaccacttaacaactcctgcag------------------------------------------
|| || ||||| ||||||||||| || || |||||||| |||||||||||||| | | | |  | ||| || | |||   |     || || || |    ||    |   ||   || |   |||                                           
ATATACCCACCAATCAATGTCCTCCCGTCACTATCTCGGTTGATGAAGgtaaggttaatctcgtttgtttgatatcaaggtgc---tttaaagtgataaatattttctgtttcttaattaaagcaagtggttcacacactaaaggtgcatcattggtcacttttgcag

upper sequence: GRMZM2G181151_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA20G24070.1 (Glycine max), 5'ss of exon 13
ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataagttttctgtatgttttcagcatttatg-ttgaaggttagttgtaagaaccacttaacaactcctgcag-------------------------------------------
|| || ||||| ||||| ||||| ||||| |||||||| ||||||||||||||   | | ||  |  |||||      |   || || || || |    ||    |   ||   || |  ||||                                            
ATATACCCACCAATCAACGTCCTCCCATCACTATCTCGGTTGATGAAGgtaaggataatctt--gcttgtttgatatctaggtgctttaaagtgataaatattttctgattcttaattaatgcaaagtggttcacgctctaatggtgcatcattggtcacttctgcag

upper sequence: GRMZM2G181151_T02 (Zea mays), 5'ss of exon 12
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 5'ss of exon 11
ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataagttttctgtatgtttt-cagcatttatgttgaaggttagttgtaagaac-cacttaacaac-tcctgcag---------------------
|| || || ||||| ||||| ||||||||||| |||||| ||||||||||  |||      ||||  |    |  |   || | || | ||  | | | |   | |   ||  || |  |  ||                        
ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAGgtgcgatcctacatctgcgtacaatatattcttcaagtggtagaatggatattgtatcatgctagacgatattttgtgtgtatttactctacttggatgc

upper sequence: GRMZM2G181151_T02 (Zea mays), 5'ss of exon 12
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 5'ss of exon 11
ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataagttttctgtatgttttcagcatttatgttgaaggttagttgtaagaaccacttaacaactcctgcag-------------------------
|| || |||||||||||||| ||||||||||| || ||||||||||||||  |     | |  | |||  || |     |||||   |  |||   | ||    |    ||   | || |||                           
ATCTACCCACCTATCAATGTGCTGCCATCTCTGTCGCGATTGATGAAGgtgcggcct-tatattatatccttgcgtttgttatgaccagcgttttctttatcttcagtatacttattcgtgcccactacatttttcaagtcacagagtg

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|60355003|gb|DN221976.1|DN221976
EST:     ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
genomic: ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
EST: gi|16925493|gb|BM078561.1|BM078561
EST:     ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
genomic: ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
EST: gi|4646659|gb|AI491497.2|AI491497
EST:     CTATCAATGTCCTGCCATCTCTATTTCGATTGATGAAG                         AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
genomic: CTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
EST: gi|32945219|gb|CF050038.1|CF050038
EST:     ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
genomic: ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
EST: gi|211017023|gb|FL053488.1|FL053488
EST:     CGATTGATGAAG                         AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
genomic: CGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
EST: gi|60343435|gb|DN210408.1|DN210408
EST:     ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
genomic: ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
EST: gi|211222466|gb|FL437622.1|FL437622
EST:     AGATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
genomic: AGATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
EST: gi|60352479|gb|DN219452.1|DN219452
EST:     ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
genomic: ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
EST: gi|211122809|gb|FL454319.1|FL454319
EST:     TCGATTGATGAAG                         AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
genomic: TCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
EST: gi|67019767|gb|CO448516.1|CO448516
EST:     ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
genomic: ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
EST: gi|37401251|gb|CF637988.1|CF637988
EST:     ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
genomic: ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
EST: gi|211222467|gb|FL437623.1|FL437623
EST:     ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
genomic: ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
EST: gi|194716931|gb|FK934090.1|FK934090
EST:     ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
genomic: ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
EST: gi|30307203|gb|CD001876.1|CD001876
EST:     AGATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
genomic: AGATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
EST: gi|213188201|gb|FM181912.1|FM181912
EST:     ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
genomic: ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
EST: gi|60395817|gb|DN228687.1|DN228687
EST:     ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
genomic: ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
EST: gi|24767815|gb|CA402951.1|CA402951
EST:     ATTTATCCACCTATCAATGTCCTGCCGTCTCTCTCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCAGATGTGTCTAAT
genomic: ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
EST: gi|6563648|gb|AW231375.1|AW231375
EST:     CTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
genomic: CTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
EST: gi|4646712|gb|AI491575.2|AI491575
EST:     CTATCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGCATGGCACGTAGAGACCATTCGGATGTGTCTAAT
genomic: CTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
EST: gi|60396754|gb|DN229618.1|DN229618
EST:     ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
genomic: ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
EST: gi|211019798|gb|FL053491.1|FL053491
EST:     CTATCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
genomic: CTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
EST: gi|32933748|gb|CF038560.1|CF038560
EST:     ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
genomic: ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
EST: gi|32942169|gb|CF046988.1|CF046988
EST:     ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
genomic: ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
EST: gi|211222468|gb|FL437624.1|FL437624
EST:     ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG                         AGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT
genomic: ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAAT

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 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 435

ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 605

ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 507

ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 482

ATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGgtaagataag ... actcctgcagAGTGCTATTGGTGAGGGCATGACACGTAGAGACCATTCGGATGTGTCTAATCAG