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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAGgtattttatcatgtatttttttgggaatgtagaatctgatgactaatttttattaattatgttgaaattttggcaaaatttcacatgagaatgaatccag...

Basic information

species Zea mays
transcript GRMZM2G144618_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144618_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ11747 (Selaginella moellendorffii), 5'ss of exon 3
GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAGgta-------ttttatcatgtatttttttgggaatgtagaatctgatga-ctaatttttattaa--ttatgttgaaattttggcaaaatttcacatgagaatgaatccag
|      || || || |||||||||||||||||||| |||||||  |||||||       ||  | | |    | |||        ||||  || |  | ||  |  ||  |    || | ||||    ||||  |   | |   | ||           
GCGGATGCAGCCCAGGTTCCAGTTCATTGTCATGAATCGCAGGAGCACAGgtaagagtgattgcaactttctctctttgtttttcttagacgctaaaaaactcttccttgctggatttgttttgacgcgttggtgactgtgcctgtcag-----------
















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|211507640|gb|FL212617.1|FL212617
EST:     GAATGCTCAACCTAGATTCCAGTTCATNGTCATGAACCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
genomic: GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
EST: gi|71441642|gb|DR822692.1|DR822692
EST:     GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
genomic: GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
EST: gi|50322552|gb|CO517678.1|CO517678
EST:     GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
genomic: GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
EST: gi|211505290|gb|FL212613.1|FL212613
EST:     GAATGCTCAACCTAGATTCCAGTTCATNGTCATGAACCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
genomic: GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
EST: gi|50322824|gb|CO517950.1|CO517950
EST:     GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
genomic: GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
EST: gi|71448550|gb|DR829600.1|DR829600
EST:     GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
genomic: GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
EST: gi|89761719|gb|DY689622.1|DY689622
EST:     GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
genomic: GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
EST: gi|71443863|gb|DR824913.1|DR824913
EST:     GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
genomic: GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
EST: gi|211507637|gb|FL212614.1|FL212614
EST:     GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
genomic: GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
EST: gi|93012223|gb|EB637743.1|EB637743
EST:     GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
genomic: GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
EST: gi|211507639|gb|FL212616.1|FL212616
EST:     GAATGCTCAACCTAGATTCCAGTTCATGGTCATGAACCGCAGGAATACAG                         ATAATCTAGTTGA
genomic: GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGA
EST: gi|76286410|gb|DV025978.1|DV025978
EST:     GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
genomic: GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
EST: gi|149014053|gb|EE043578.2|EE043578
EST:     GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
genomic: GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
EST: gi|211507638|gb|FL212615.1|FL212615
EST:     GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTCTTTGGGAGATTTTGAATACCAACTCCAAGCT
genomic: GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTCTT-GGGAGATTTTGAATACCAACTCCAAGCT
EST: gi|76017159|gb|DT944329.1|DT944329
EST:     GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC
genomic: GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTC

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 3 RNA-Seq libraries.


Block sizes: 21 (upstream exon), 41 (downstream exon)
Score: 3

GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTCCTTATATTATGTACCGAAATGCTGCTCAAGAAGTTATAGGAATTTGGTT


Block sizes: 47 (upstream exon), 28 (downstream exon)
Score: 6

GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTCCTTATATTATGTACCGAAATGCTGCTCAAGAAGTTATAGGAATTTGGTT


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 9

GAATGCTCAACCTAGATTCCAGTTCATTGTCATGAACCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTCTTGGGAGATTTTGAATACCAACTCCAAGCTCCTTATATTATGTACCGAAATGCTGCTCAAGAAGTTATAGGAATTTGGTT