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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcgcgtttcacagtctctctctcttctacgtacgctgagctgtgttggaatgtccgataaagctaatggaaaaagttttgaacgtgctcgatacgatagGCGGAGCGACTCTGGTATTCGACACGGAGCTTATCGCCGTCAACGGGAAGACATCTGGCGGTGCGAATCCAGAAACTGAAAGTGAGCTCTGATACGATGC

Basic information

species Zea mays
transcript GRMZM2G031204_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031204_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g68710.2 (Oryza sativa), 3'ss of exon 5
-------------------------------------------------------------------------------tgcgcgtttcacagtctctctctcttctacgt-acgctg------agctgtgttggaatgtccgataaagctaatggaaaaagttttgaacgtgctcg-atacgatagGCGGAGCGACTCTGGTATTCGACACGGAGCTTATCGCCGTCAACGGGAAGACATCTGGCGGTGCG---AATCCAGAAACTGAAAGTGAGCTCTGATACGATGC
                                                                               ||    ||| ||  | | || | | |  |  | ||  ||       |   |||   ||  |       |  ||     || | |     |||   ||| |  | ||||| ||||| || ||  | || ||||||||||||||||||||||| || |||||| | || |||||    |||   ||     || ||   || ||||       
gtatggtctgaatatttgtttgtttgcttgatggtttcttgtgaaagaattatccatgtgtagattctcaactttgacatggctattttaccatgtttcacacctacattttacattgccaacagggcatgtgataagttttttcccatttacctataatactgacatacggtttcgtaaccaatagGTGGAGCAACACTAATCTTTGACACGGAGCTTATCGCCGTCAATGGAAAGACAACCGGTGGTGCTAGCAATAGTGAGCTCTAAGGTCGTCTTTGATGTTC---
















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|211236506|gb|FL293611.1|FL293611
EST:     ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAG                         GCGGAGCGACTCTGGTCTTCGACACGGAGCTTATCGCCGTCAACGGGAAGA
genomic: ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAGgtatggctag ... gatacgatagGCGGAGCGACTCTGGTATTCGACACGGAGCTTATCGCCGTCAACGGGAAGA
EST: gi|211132103|gb|FL293587.1|FL293587
EST:     ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAG                         GCGGAGCGACTCTGGTCTTCGACAC
genomic: ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAGgtatggctag ... gatacgatagGCGGAGCGACTCTGGTATTCGACAC
EST: gi|211133032|gb|FL293601.1|FL293601
EST:     ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAG                         GCGGAGCGACTCTGGTCTTCGACACGGAGCTTATCG
genomic: ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAGgtatggctag ... gatacgatagGCGGAGCGACTCTGGTATTCGACACGGAGCTTATCG
EST: gi|166574032|gb|EG273567.1|EG273567
EST:     GCAAAGTATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAG                         GCGGAGCGACTCTGGTCTTCGACACGGAGCTTATCGCCGTCAACGGGAAGA
genomic: GCAAAG-ATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAGgtatggctag ... gatacgatagGCGGAGCGACTCTGGTATTCGACACGGAGCTTATCGCCGTCAACGGGAAGA
EST: gi|211133030|gb|FL293599.1|FL293599
EST:     ACCTGCAAAGATGGGCTATTGCGAGCGAGGCTCCCCACCGAAGATTCCAG                         GCGGAGCGACTCTGGTCTTCGACACGGAGCTTATCGCCGTCAACGGGAAGA
genomic: ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAGgtatggctag ... gatacgatagGCGGAGCGACTCTGGTATTCGACACGGAGCTTATCGCCGTCAACGGGAAGA
EST: gi|211133037|gb|FL293606.1|FL293606
EST:     ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAG                         GCGGAGCGACTCTGGTCTTCGACACGGAGCTTATCGCCGTCAACGGGAAGA
genomic: ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAGgtatggctag ... gatacgatagGCGGAGCGACTCTGGTATTCGACACGGAGCTTATCGCCGTCAACGGGAAGA
EST: gi|211240986|gb|FL293644.1|FL293644
EST:     ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAG                         GCGGAGCGACTCTGGTCTTCGACACGGAGCTTATCGCCGTCAACGGGAAGA
genomic: ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAGgtatggctag ... gatacgatagGCGGAGCGACTCTGGTATTCGACACGGAGCTTATCGCCGTCAACGGGAAGA
EST: gi|211133028|gb|FL293597.1|FL293597
EST:     ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAG                         GCGGAGCGACTCTGGTCTTCGACACGGAGCTTATCGCCGTCAACGGGAAGA
genomic: ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAGgtatggctag ... gatacgatagGCGGAGCGACTCTGGTATTCGACACGGAGCTTATCGCCGTCAACGGGAAGA
EST: gi|23357637|gb|BU645286.1|BU645286
EST:     ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAG                         GCGGAGCGACTCTGGTCTTCGACACGGAGCTTATCGCCGTCAACGGGAAGA
genomic: ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAGgtatggctag ... gatacgatagGCGGAGCGACTCTGGTATTCGACACGGAGCTTATCGCCGTCAACGGGAAGA
EST: gi|211238739|gb|FL293623.1|FL293623
EST:     ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAG                         GCGGAGCGACTCTGGTCTTCGACACGGA
genomic: ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAGgtatggctag ... gatacgatagGCGGAGCGACTCTGGTATTCGACACGGA
EST: gi|211238747|gb|FL293631.1|FL293631
EST:     ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAG                         GCGGAGCGACTCTGGGYCTTCGACACGGAGCTTATCGCCGTCAACGGG
genomic: ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAGgtatggctag ... gatacgatagGCGGAGCGACTCTGGTA-TTCGACACGGAGCTTATCGCCGTCAACGGG
EST: gi|211236504|gb|FL293609.1|FL293609
EST:     ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAG                         GCGGAGCGACTCTGGTCTTCGACACGGAGCTTATCGCCGTCCACGG
genomic: ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAGgtatggctag ... gatacgatagGCGGAGCGACTCTGGTATTCGACACGGAGCTTATCGCCGTCAACGG
EST: gi|211240992|gb|FL293650.1|FL293650
EST:     ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAG                         GCGGAGCGACTCTGGTCTTCGACACGGAGCTTATCGCCGTCAACGGG
genomic: ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAGgtatggctag ... gatacgatagGCGGAGCGACTCTGGTATTCGACACGGAGCTTATCGCCGTCAACGGG
EST: gi|108952959|gb|EC364521.1|EC364521
EST:     ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAG                         GCGGAGCGACTCTGGTCTTCGACACGGAGCTTATCGCCGTCAACGGGGAAG
genomic: ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAGgtatggctag ... gatacgatagGCGGAGCGACTCTGGTATTCGACACGGAGCTTATCGCCGTCAACGGG-AAG
EST: gi|211238746|gb|FL293630.1|FL293630
EST:     ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAG                         GCGGAGCGACTCTGGTCTTCGACACGGAGCTTATC
genomic: ACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAGgtatggctag ... gatacgatagGCGGAGCGACTCTGGTATTCGACACGGAGCTTATC

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: 49 (upstream exon), 49 (downstream exon)
Score: 76

GACCAAGGATTGCTAGGTATGTGCGTCGGTGAAAAGCGGAAGCTAAAGATACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAGgtatggctag ... gatacgatagGCGGAGCGACTCTGGTATTCGACACGGAGCTTATCGCCGTCAACGGGAAGACATCTGGCGGTGCGAATCCAGAAACTGAAAGTGAGCTCTGATACGATGC


Block sizes: 47 (upstream exon), 41 (downstream exon)
Score: 68

GACCAAGGATTGCTAGGTATGTGCGTCGGTGAAAAGCGGAAGCTAAAGATACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAGgtatggctag ... gatacgatagGCGGAGCGACTCTGGTATTCGACACGGAGCTTATCGCCGTCAACGGGAAGACATCTGGCGGTGCGAATCCAGAAACTGAAAGTGAGCTCTGATACGATGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

GACCAAGGATTGCTAGGTATGTGCGTCGGTGAAAAGCGGAAGCTAAAGATACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAGgtatggctag ... gatacgatagGCGGAGCGACTCTGGTATTCGACACGGAGCTTATCGCCGTCAACGGGAAGACATCTGGCGGTGCGAATCCAGAAACTGAAAGTGAGCTCTGATACGATGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 64

GACCAAGGATTGCTAGGTATGTGCGTCGGTGAAAAGCGGAAGCTAAAGATACCTGCAAAGATGGGCTATGGCGAGCGAGGCTCCCCACCGAAGATTCCAGgtatggctag ... gatacgatagGCGGAGCGACTCTGGTATTCGACACGGAGCTTATCGCCGTCAACGGGAAGACATCTGGCGGTGCGAATCCAGAAACTGAAAGTGAGCTCTGATACGATGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggaatgtccgataaagctaatggaaaaagttttgaacgtgctcgatacgatagGCGGAGCGACTCTGGTATTCGACACGGAGCTTATCGCCGTCAACGGGAAGACATCTGGCGGTGCGAATCCAGAAACTGAAAGTGAGCTCTGATACGATGC
                agctaat  putative branch site (score: 64)
                         aaaaagtttt  TA-rich tract