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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGCCTCTGTTCGTGATCCCTCATGAGAAGCACAGAGATGAAATCGAGGAGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAGgtaggtggcgctactagtacatatacatgataatctccagtccagaatgaaatggaaccttaatttgaatatgaaacatcacttaattacctgaccgacttccaattaag

Basic information

species Zea mays
transcript GRMZM2G328908_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G328908_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g17390.1 (Oryza sativa), 5'ss of exon 4
CAAGCCTCTGTTCGTGATCCCTCATGAGAAGCACAGAGATGAAATCGAGGAGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAGgtaggtggcgctactagtacatatacatgat-aatctccagtccagaatgaaatggaaccttaatttgaatatgaaacatcacttaattac--ctgaccgacttccaattaag------------
 ||||||||||| |||||||||||| |||||||||| || ||  | ||||||   |||||| | ||||| |  ||||||||||||||||| || ||||| ||||||  |  |  |  | | |    |  || | | | || ||   ||  |  |   | | |  ||   |  | | |   || ||  |||   ||||  |  |||   ||  |            
GAAGCCTCTGTTTGTGATCCCTCATCAGAAGCACAGGGAAGAGGTTGAGGAGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAAgtaggtt-ctttgatgcttcttcattacaatcactttgcaatctgaaaacaccttagatcatctttcacaggtaacattacaattctttattactgagtgttttctttttgtgatccatgataag
















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|13558898|gb|BG550253.1|BG550253
EST:     CCCCAGGCCAG                         CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
genomic: CCCCAGGCCAGgtaggtggcg ... tccaattaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
EST: gi|7135782|gb|AW498263.1|AW498263
EST:     AGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAG                         CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
genomic: AGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAGgtaggtggcg ... tccaattaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
EST: gi|18650231|gb|BM499050.1|BM499050
EST:     AGAAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAG                         CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
genomic: AGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAGgtaggtggcg ... tccaattaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
EST: gi|4647713|gb|AI622788.1|AI622788
EST:     AGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAG                         CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
genomic: AGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAGgtaggtggcg ... tccaattaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
EST: gi|149040130|gb|EE046781.2|EE046781
EST:     AGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAG                         CTCACCTGCTTCATCAACGATTCTGCGGGGGTGGTCGCGACCAATACCGCT
genomic: AGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAGgtaggtggcg ... tccaattaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
EST: gi|16919363|gb|BM074154.1|BM074154
EST:     AGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAG                         CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
genomic: AGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAGgtaggtggcg ... tccaattaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
EST: gi|110219083|gb|EC900981.1|EC900981
EST:     AGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAG                         CTCACCTGCCTCATCAACGATTCTGCCGGGGTGGTCGCGACCAATACCGCT
genomic: AGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAGgtaggtggcg ... tccaattaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
EST: gi|71772626|gb|DR970554.1|DR970554
EST:     GACACAAGCATCCTGTTCATCACCACCCCAGGCCAG                         CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
genomic: GACACAAGCATCCTGTTCATCACCACCCCAGGCCAGgtaggtggcg ... tccaattaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
EST: gi|32849587|gb|CD989268.1|CD989268
EST:     AGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAG                         CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
genomic: AGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAGgtaggtggcg ... tccaattaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
EST: gi|116820958|gb|EC864226.1|EC864226
EST:     AGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAG                         CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
genomic: AGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAGgtaggtggcg ... tccaattaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
EST: gi|148934032|gb|EC878040.2|EC878040
EST:     AGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAG                         CTCACCTGCTTCATCAACGATTCTGCCGGCGTCGTCGCGACCAATACCGCT
genomic: AGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAGgtaggtggcg ... tccaattaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
EST: gi|13126121|gb|BG316691.1|BG316691
EST:     AGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAG                         CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
genomic: AGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAGgtaggtggcg ... tccaattaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
EST: gi|148996082|gb|EE035341.2|EE035341
EST:     AGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAG                         CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
genomic: AGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAGgtaggtggcg ... tccaattaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
EST: gi|13490410|gb|BG517174.1|BG517174
EST:     AGAAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAG                         CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
genomic: AGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAGgtaggtggcg ... tccaattaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
EST: gi|13126546|gb|BG317116.1|BG317116
EST:     AGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAG                         CTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT
genomic: AGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAGgtaggtggcg ... tccaattaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCT

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 2 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 385

CAAGCCTCTGTTCGTGATCCCTCATGAGAAGCACAGAGATGAAATCGAGGAGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAGgtaggtggcg ... tccaattaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 62

CAAGCCTCTGTTCGTGATCCCTCATGAGAAGCACAGAGATGAAATCGAGGAGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAGgtaggtggcg ... tccaattaagCTCACCTGCCTCATCAACGACTCTGCCGGCGTCGTCGCGACCAATACCGCTGCCGTGCAGCTCGCCAACGCCCGCGACAAGCCATG




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