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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACGAGATGTGCAAGAACGTCAGGTACGCTAACGTCTATGACCCCGACGACGACTGGCCGGAGCCCGCCGAATACACGCACATGCTCGGCGTCCTAAAGgtacgtacgtacttgtgctgctattccatatggaacatttcctctgttttatgagctaaatctcgtcatgcatgttattgcaaccgacag

Basic information

species Zea mays
transcript GRMZM2G328908_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G328908_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os08g17390.1 (Oryza sativa), 5'ss of exon 1
GTACGAGATGTGCAAGAACGTCAGGTACGCTAACGTCTATGACCCCGACGACGACTGGCCGGAGCCCGCCGAATACACGCACATGCTCGGCGTCCTAAAGgtacgtacgtacttgtgctgctattccatatggaa-catttcctct-------gttttatgagcta-aatctcgtcatgcatgttattgcaaccgacag-
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GTACGAGATGTGCAAGAACGTCAGGTACGCCGACGTCTACGACCCCGACGACGACTGGCCCGAGCCCGCCGAGTACACCCACCAGCTCGGCGTGCTCAAGgtaaaccaaaaattatgtcactgctacgtacagaaatagtcactcaaagtggggatgtatatgttttaaactcgatcgagaagggattatgtccactcgt
















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|211358043|gb|FL050070.1|FL050070
EST:     ACGACTGGCCGGAGCCCGCCGAATA-ACGCACATGCTCGGCGTCCTAAAG                         AATAGGTACTATGATCTGATCATCCTC-ACGAGGCTGGCGGGGATCGG-CA
genomic: ACGACTGGCCGGAGCCCGCCGAATACACGCACATGCTCGGCGTCCTAAAGgtacgtacgt ... caaccgacagAATAGGTACTATGATCTGATCATC-TCCACGAGGCTGGCGGGGATCGGGCA
EST: gi|148956817|gb|EC902716.2|EC902716
EST:     ACGACTGGCCGGAGCCCGCCGAATACACGCACATGCTCGGCGTCCTAAAG                         AATAGGTACTATGATCTGATCATCTCCACGAGGCTGGCGGGGATCGGGCAC
genomic: ACGACTGGCCGGAGCCCGCCGAATACACGCACATGCTCGGCGTCCTAAAGgtacgtacgt ... caaccgacagAATAGGTACTATGATCTGATCATCTCCACGAGGCTGGCGGGGATCGGGCAC
EST: gi|211358048|gb|FL050075.1|FL050075
EST:     ACGACTGGCCGGAGCCCGCCGAATACACGCACATGCTCGGCGTCCTAAAG                         AATAGGTACTATGATCTGATCATCTCCACGAGGCTGGCGGGGATCGGGCAC
genomic: ACGACTGGCCGGAGCCCGCCGAATACACGCACATGCTCGGCGTCCTAAAGgtacgtacgt ... caaccgacagAATAGGTACTATGATCTGATCATCTCCACGAGGCTGGCGGGGATCGGGCAC
EST: gi|148994671|gb|EE034192.2|EE034192
EST:     ACGACTGGCCGGAGCCCGCCGAATACACGCACATGCTCGGCGTCCTAAAG                         AATAGGTACTATGATCTGATCATCTCCACGAGGCTGGCGGGGATCGGGCAC
genomic: ACGACTGGCCGGAGCCCGCCGAATACACGCACATGCTCGGCGTCCTAAAGgtacgtacgt ... caaccgacagAATAGGTACTATGATCTGATCATCTCCACGAGGCTGGCGGGGATCGGGCAC
EST: gi|148941964|gb|EC886951.2|EC886951
EST:     ACGACTGGCCGGAGCCCGCCGAATACACGCACATGCTCGGCGTCCTAAAG                         AATAGGTACTATGATCTGATCATCTCCACGAGGCTGGCGGGGATCGGGCAC
genomic: ACGACTGGCCGGAGCCCGCCGAATACACGCACATGCTCGGCGTCCTAAAGgtacgtacgt ... caaccgacagAATAGGTACTATGATCTGATCATCTCCACGAGGCTGGCGGGGATCGGGCAC
EST: gi|148956152|gb|EC901927.2|EC901927
EST:     ACGACTGGCCGGAGCCCGCCGAATACACGCACATGCTCGGCGTCCTAAAG                         AATAGGTACTATGATCTGATCATCTCCCCGAGGCTGGCGGGGATCGGGCAC
genomic: ACGACTGGCCGGAGCCCGCCGAATACACGCACATGCTCGGCGTCCTAAAGgtacgtacgt ... caaccgacagAATAGGTACTATGATCTGATCATCTCCACGAGGCTGGCGGGGATCGGGCAC
EST: gi|148957850|gb|EC904001.2|EC904001
EST:     ACGACTGGCCGGAGCCCGCCGAATACACGCACATGCTCGGCGTCCTAAAG                         AATAGGTACTATGATCTGATCATCTCCACGAGGCTGGCGGGGATCGGGCAC
genomic: ACGACTGGCCGGAGCCCGCCGAATACACGCACATGCTCGGCGTCCTAAAGgtacgtacgt ... caaccgacagAATAGGTACTATGATCTGATCATCTCCACGAGGCTGGCGGGGATCGGGCAC
EST: gi|149012944|gb|EE042734.2|EE042734
EST:     ACGACTGGCCGGAGCCCGCCGAATACACGCACATGCTCGGCGTCCTAAAG                         AATAGGTACTATGATCTGATCATCTCCACGAGGCTGGCGGGGATCGGGCAC
genomic: ACGACTGGCCGGAGCCCGCCGAATACACGCACATGCTCGGCGTCCTAAAGgtacgtacgt ... caaccgacagAATAGGTACTATGATCTGATCATCTCCACGAGGCTGGCGGGGATCGGGCAC
EST: gi|148955410|gb|EC900982.2|EC900982
EST:     ACGACTGGCCGGAGCCCGCCGAATACACGCACATGCTCGGCGTCCTAAAG                         AATAGGTACTATGATCTGATCATCTCCACGAGGCTGGCGGGGATCGGGCAC
genomic: ACGACTGGCCGGAGCCCGCCGAATACACGCACATGCTCGGCGTCCTAAAGgtacgtacgt ... caaccgacagAATAGGTACTATGATCTGATCATCTCCACGAGGCTGGCGGGGATCGGGCAC

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: 288

GTACGAGATGTGCAAGAACGTCAGGTACGCTAACGTCTATGACCCCGACGACGACTGGCCGGAGCCCGCCGAATACACGCACATGCTCGGCGTCCTAAAGgtacgtacgt ... caaccgacagAATAGGTACTATGATCTGATCATCTCCACGAGGCTGGCGGGGATCGGGCACGCGCTCTTCCTTTTCATGTCGTCGGCGCGCGACAAGGTCGGCTACGTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 55

GTACGAGATGTGCAAGAACGTCAGGTACGCTAACGTCTATGACCCCGACGACGACTGGCCGGAGCCCGCCGAATACACGCACATGCTCGGCGTCCTAAAGgtacgtacgt ... caaccgacagAATAGGTACTATGATCTGATCATCTCCACGAGGCTGGCGGGGATCGGGCACGCGCTCTTCCTTTTCATGTCGTCGGCGCGCGACAAGGTCGGCTACGTTT




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