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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatcatgtattttttggtactgtttaatctgcaatacaggtattttatcatgtattttttggtattgtataataaggaattacaggtattgtat...

Basic information

species Zea mays
transcript GRMZM2G101596_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101596_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g14580.1 (Oryza sativa), 5'ss of exon 3
GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtat--tttatcatgtattttttggtactgtttaatctgcaatacaggtattttatcatgtattttttggtattgtataataaggaattacaggtattgtat-
|||||| || ||||||||||||||  |||||||||||||  | ||||||||||   |  || |    ||| |||||  | ||  |  || | |     || ||    ||||   |       ||||| ||   |    |  |  | |      
GAATGCGCAGCCCAGATTCCAGTTTGTTGTCATGAATCGTCGTAATACAGgtacgctgcatgaaaattttcttggttttcttagagttgaagtttctataattggctatgt---tacaacctttgtaaaacctgtgcgtgaaattgtcaatct

upper sequence: GRMZM2G101596_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ11747 (Selaginella moellendorffii), 5'ss of exon 3
GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtatt--ttatcatgtattttttggtactgtttaatctgcaatacaggtattttatcatgtattttttggtattgtataataaggaattacaggtattgtat
|      || ||||| ||||||||||||||||||||||||||||  |||||||    | ||     | ||| |     |||||    |  |    |   |  |  || |   |   || || |||     |  |  | |     | |     
GCGGATGCAGCCCAGGTTCCAGTTCATTGTCATGAATCGCAGGAGCACAGgtaagagtgattgca-actttctctctttgtttttcttagacgctaaaaaactcttccttgctggatttgttttgacgcgttggtgactgtgcctgtcag--

upper sequence: GRMZM2G101596_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ22541 (Selaginella moellendorffii), 5'ss of exon 3
GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatcatgtattttttggtactgtttaatctgcaatacaggtattttatcatgtattttttggtattgtataataaggaattacaggtattgtat-----
|      || ||||| |||||||||||||||||||||||||| |  |||||||        || |  | |   |     ||  | |    || | |      | |  ||  ||  |||  |||| |  | | |  ||   | |  ||  |     
GCGGATGCAGCCCAGGTTCCAGTTCATTGTCATGAATCGCAGAAGCACAGgtaagagtgattgcaactctctctctctctttgtttttcttagacgctaaaaaactcgtccttgctggatttgttt--tgacgcgttggtgattgtgcctgtcag

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|211391322|gb|FK987371.1|FK987371
EST:     GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
EST: gi|93282402|gb|EB674666.1|EB674666
EST:     GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
EST: gi|211393952|gb|FK987388.1|FK987388
EST:     GAATGCTCAACCCAGATTCCAGTTCAT-GTCATGAATCGCAGGAATACAG                         ATNATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
EST: gi|37419345|gb|CF647353.1|CF647353
EST:     GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
EST: gi|13125936|gb|BG316611.1|BG316611
EST:     GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
EST: gi|91056521|gb|EB166939.1|EB166939
EST:     GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
EST: gi|211391326|gb|FK987375.1|FK987375
EST:     GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
EST: gi|211393953|gb|FK987389.1|FK987389
EST:     GAATGCTCAACCCAGATTCCAGTTCAT-GTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGA
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGA
EST: gi|76928738|gb|DV171746.1|DV171746
EST:     GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
EST: gi|93281394|gb|EB673658.1|EB673658
EST:     GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
EST: gi|211393955|gb|FK987391.1|FK987391
EST:     GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTTTTTGGGAGATTTTGAATACCAACTACAAGCT
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTT-GGGAGATTTTGAATACCAACTACAAGCT
EST: gi|76010496|gb|DT937666.1|DT937666
EST:     GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
EST: gi|7304674|gb|AW600613.1|AW600613
EST:     GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
EST: gi|211393947|gb|FK987383.1|FK987383
EST:     GAATGCTCAACCCAGATTCCAGTTCATCGTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTTTTGGGAGATTT-GAATACCAACTACAAGCTC
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
EST: gi|211391329|gb|FK987378.1|FK987378
EST:     GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTTTTGGG
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGG
EST: gi|76909432|gb|DV163378.1|DV163378
EST:     GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
EST: gi|91048464|gb|EB158882.1|EB158882
EST:     GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
EST: gi|76011730|gb|DT938900.1|DT938900
EST:     GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
EST: gi|89758076|gb|DY687416.1|DY687416
EST:     GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
EST: gi|211393949|gb|FK987385.1|FK987385
EST:     AATGCTCAACCCAGGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
genomic: AATGCTCAACCCAG-ATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
EST: gi|211393951|gb|FK987387.1|FK987387
EST:     GAATGCTCAACCCAGATTCCAGTTCATGGTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
EST: gi|149112671|gb|EE191401.2|EE191401
EST:     GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
EST: gi|148999366|gb|EE036307.2|EE036307
EST:     GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
EST: gi|211393954|gb|FK987390.1|FK987390
EST:     GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAAC
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAAC
EST: gi|211393950|gb|FK987386.1|FK987386
EST:     GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
EST: gi|78114665|gb|DV533053.1|DV533053
EST:     GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAG                         ATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC
genomic: GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTC

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), 46 (downstream exon)
Score: 44

GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTCCTTATATAATGTACCGCAATGCTGCTCAAGAAGTTATAGGAATCTGGTT


Block sizes: 41 (upstream exon), 47 (downstream exon)
Score: 51

GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTCCTTATATAATGTACCGCAATGCTGCTCAAGAAGTTATAGGAATCTGGTT


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

GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTCCTTATATAATGTACCGCAATGCTGCTCAAGAAGTTATAGGAATCTGGTT


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 49

GAATGCTCAACCCAGATTCCAGTTCATTGTCATGAATCGCAGGAATACAGgtattttatc ... ttgttaacagATAATCTAGTTGAAGATCTTTTGGGAGATTTTGAATACCAACTACAAGCTCCTTATATAATGTACCGCAATGCTGCTCAAGAAGTTATAGGAATCTGGTT