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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGGACAAGCTCCTGCAAGGCAAGCCGCTCTGGGTGCAGGGATACCAAACACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagctaattcatctatccatgtttgtataattgatctgcttgctgttcattgttttttacacatgtgaagtgttcaggtgtgtgtgtatcatctgaccaattactctctgcacactctgcag

Basic information

species Zea mays
transcript GRMZM2G085474_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085474_T04 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os09g07830.1 (Oryza sativa), 5'ss of exon 4
TTGGGACAAGCTCCTGCAAGGCAAGCCGCTCTGGGTGCAGGGATACCAAACACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagctaattcatctatccatgtttgtataattgatctgcttgctgttcattgttttttacacatgtgaagtgttcaggtgtgtgtgtatcatctgaccaattactctctgcacactctgcag
||||| |||||||||||||| ||||| ||| | |||||||||||||||||||| |||||||||| | | ||||||||||| |||||||||||||||||||||        | |||||    |    ||| ||||| |          |||||||     || ||   |  |||    |     ||| | | | || | |   ||                       
TTGGGGCAAGCTCCTGCAAGACAAGCTGCTTTAGGTGCAGGGATACCAAACACAGTTGTTTGCAGCGCAGTTAACAAAGTTTGCGCATCTGGCATGAAAGgtta-----cagttcatgaggcagcctttctataaatt---------ctgttcaagaaattatatttacctgat-catgggcttgtttttatttcctttctgcag----------------------

upper sequence: GRMZM2G085474_T04 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA14G00760.1 (Glycine max), 5'ss of exon 4
TTGGGACAAGCTCCTGCAAGGCAAGCCGCTCTGGGTGCAGGGATACCAAACACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagctaattcatctatccatgtttgtataattgatctgcttgctgttcattgttttttacacatgtgaag--tgttcaggtgtgtgtgtatcatctgaccaattactctctgcacactctgcag
||||| |||||||||||||| ||||| ||||| || ||||| ||| | ||  | ||| | ||||| || ||||||||||| || ||||| || ||||||||| ||    ||||  |   |    | ||||| |  ||| | |  ||  |    | | |     |   || | ||   ||||| |||   ||                                      
TTGGGGCAAGCTCCTGCAAGACAAGCTGCTCTTGGAGCAGGAATATCCAATTCAGTTATCTGCACTACCGTTAACAAAGTTTGTGCATCAGGAATGAAAGgtgtgtttataataaaaacaattctatttgtttctttg-tatttttatttaaaaatatagaaaaaggatattaaccttgttctggttattgcag-----------------------------------
















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|211388472|gb|FL095521.1|FL095521
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGNTG
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
EST: gi|78114650|gb|DV533038.1|DV533038
EST:     ACTGTTGTTTGCACCACCTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
genomic: ACTGTTGTTTGCACCAC-TGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
EST: gi|211388476|gb|FL095525.1|FL095525
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
EST: gi|211388474|gb|FL095523.1|FL095523
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
EST: gi|149045418|gb|EE047840.2|EE047840
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
EST: gi|148965113|gb|EE015927.2|EE015927
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
EST: gi|31358163|gb|CD442520.1|CD442520
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
EST: gi|211391121|gb|FL095544.1|FL095544
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
EST: gi|211388481|gb|FL095530.1|FL095530
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
EST: gi|211383214|gb|FL095504.1|FL095504
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
EST: gi|211385842|gb|FL095512.1|FL095512
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTC
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTC
EST: gi|211385836|gb|FL095506.1|FL095506
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
EST: gi|211391119|gb|FL095542.1|FL095542
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
EST: gi|211385845|gb|FL095515.1|FL095515
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCA
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCA
EST: gi|211391123|gb|FL095546.1|FL095546
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGGATATTG
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATG-ATATTG
EST: gi|149008746|gb|EE040943.2|EE040943
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
EST: gi|211388484|gb|FL095533.1|FL095533
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGA
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGA
EST: gi|211391115|gb|FL095538.1|FL095538
EST:     ACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTT
genomic: ACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAA-Ggtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTT
EST: gi|37421375|gb|CF648386.1|CF648386
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
EST: gi|211388483|gb|FL095532.1|FL095532
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
EST: gi|211388477|gb|FL095526.1|FL095526
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
EST: gi|29130092|gb|CB380796.1|CB380796
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
EST: gi|211385847|gb|FL095517.1|FL095517
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
EST: gi|211391113|gb|FL095536.1|FL095536
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
EST: gi|211385843|gb|FL095513.1|FL095513
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
EST: gi|211388482|gb|FL095531.1|FL095531
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAA
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAA
EST: gi|211385838|gb|FL095508.1|FL095508
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
EST: gi|32863231|gb|CF002913.1|CF002913
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
EST: gi|149050402|gb|EE155650.2|EE155650
EST:     CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAG                         CTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG
genomic: CACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTG

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: 47 (upstream exon), 47 (downstream exon)
Score: 187

TTGGGACAAGCTCCTGCAAGGCAAGCCGCTCTGGGTGCAGGGATACCAAACACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTGTGGCAGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 157

TTGGGACAAGCTCCTGCAAGGCAAGCCGCTCTGGGTGCAGGGATACCAAACACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTGTGGCAGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 143

TTGGGACAAGCTCCTGCAAGGCAAGCCGCTCTGGGTGCAGGGATACCAAACACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTGTGGCAGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 340

TTGGGACAAGCTCCTGCAAGGCAAGCCGCTCTGGGTGCAGGGATACCAAACACTGTTGTTTGCACCACTGTTAACAAAGTCTGCGCATCTGGCATGAAAGgtctgaagct ... cactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTGTGGCAGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGA