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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatgaagttgccaatgtgatttttcacctgttataattgattatcttagctgcctaaagaatacctcacctgttgtaatcaatttctattccctatcagGAAGGTGATCCCCGCTTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGATGGGAAAAGTTATAGCACTAACCTGGCTTACACTCCACCAGAGTTTCTAC

Basic information

species Zea mays
transcript GRMZM2G054634_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G054634_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g42110.1 (Oryza sativa), 3'ss of exon 4
----------------------------------------------------------------------------------------atatgaag--ttgccaat-gtgatttttcacctgttataatt-----gattatcttagctgcctaaagaatacctcacctgttgtaatcaatttctattccctatcagGAAGGTGATCCCCGCTTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGATGGGAAAAGTTATAGCACTAACCTGGCTTACACTCCACCAGAGTTTCTAC
                                                                                        |   | |   || |  ||    ||||   || |  |  |  |     |||     || || || | ||||| |      ||   | ||  |||        |||||||||||||||||| ||  |||||||||||||| |||||||||||||||| ||||||||||||||||||||||| ||||||||||| || || ||||||||||
gtatgtttgttgctgctagtacattccactcaaaacaccttttgtttctgctgattttgcattgcttttcacttccttcctcctgtgaactcggatgctttctgatcaaaatttactactttctgaagctttgctgatgtctgtaactaccgagagaattctaactttggcatgatttatt--------ctatcagGAAGGTGATCCTCGGCTGTCAAGTTTTGGACTAATGAAGAACAGCCGCGATGGGAAAAGTTATAGCACTAATCTGGCTTACACCCCGCCTGAGTTTCTAC

upper sequence: GRMZM2G054634_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G16420.1 (Glycine max), 3'ss of exon 4
atatgaagttgccaatgtgatttttcacctgt-tataattgattatct--tagctgcctaaagaatacctcacctgttgtaatcaatttctat-tccctatcagGAAGGTGATCCCCGCTTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGATGGGAAAAGTTATAGCACTAACCTGGCTTACACTCCACCAGAGTTTCTAC
     | |     ||||| ||   |  | ||   || |||| ||   |  ||  || |||||  ||   |      |||| |  ||||| |   |  || |||||| |||||||||||||| || ||||||||  | ||||| || || || ||||||||||| || || |||||  | ||||| |||||||| || ||| | |
----tacgcgaggaatgtcataaatgccatgaacatcattggttcattagtacatgtctaaattatggattgaaatttgttactaatttattcatttctgtcagGATGGTGATCCCCGCTTATCTAGTTTTGGGCTTATGAAAAATAGTCGAGATGGGAAAAGCTACAGTACTAATTTAGCTTATACTCCACCTGAATTTTTGC

upper sequence: GRMZM2G054634_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S156_133V6.1 (Physcomitrella patens), 3'ss of exon 4
atatgaagttgccaatgtgatttttcacctgttataattgattatcttagct---gcctaaagaatacctcacctgttgtaatcaatttctattccctatcagGAAGGTGATCCCCGCTTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGATGGGAAAAGTTATAGCACTAACCTGGCTTACACTCCACCAGAGTTTCTAC
 | ||  |||     | |||  |  |  ||| |     ||   || ||| ||   | ||| | ||    |    | ||   ||   | |||      |||||||| || || || ||  | ||  |||||||  | |||||||||||| | ||||||||||| || ||||| || |||||||||||||| || ||||   || 
ttttgtggtttttcctttgaactagc-tctgcttggtatgtggatgttaactaaagtctagaaaacggttagtttattt--atggttatctgcaatttatcagGATGGAGACCCACGTCTCTCCTGTTTTGGGCTCATGAAGAACAGCAGAGATGGGAAAAGCTACAGCACCAATCTGGCTTACACTCCTCCTGAGTACTTAA

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|89248037|gb|DY619823.1|DY619823
EST:     ACAGGAAAATCTATCATGATTTGAATGCTTATAGGGTACTTTTTGATGAG                         GAAGGTGATCCCCGCTTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGAT
genomic: ACAGGAAAATCTATCATGATTTGAATGCTTATAGGGTACTTTTTGATGAGgtacacaaca ... tccctatcagGAAGGTGATCCCCGCTTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGAT
EST: gi|211485328|gb|FL295172.1|FL295172
EST:     ACAGGAAAATCTATCATGATTTGAATGCTTATAGGGTACTTTTTGATGAG                         GAAGGTGATCCCCGCTTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGAT
genomic: ACAGGAAAATCTATCATGATTTGAATGCTTATAGGGTACTTTTTGATGAGgtacacaaca ... tccctatcagGAAGGTGATCCCCGCTTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGAT
EST: gi|71760095|gb|DR958032.1|DR958032
EST:     ACAGGAAAATCTATCATGATTTGAATGCTTATAGGGTACTTTTTGATGAG                         GAAGGTGATCCCCGCTTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGAT
genomic: ACAGGAAAATCTATCATGATTTGAATGCTTATAGGGTACTTTTTGATGAGgtacacaaca ... tccctatcagGAAGGTGATCCCCGCTTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGAT
EST: gi|211485330|gb|FL295174.1|FL295174
EST:     ACAGGAAAATCTATCATGATTTGAATGCTTATAGGGTACTTTTTGATGAG                         GAAGGTGATCCCCGCTTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGAT
genomic: ACAGGAAAATCTATCATGATTTGAATGCTTATAGGGTACTTTTTGATGAGgtacacaaca ... tccctatcagGAAGGTGATCCCCGCTTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGAT
EST: gi|211485329|gb|FL295173.1|FL295173
EST:     ACAGGAAAATCTATCATGATTTGAATGCTTATAGGGTACTTTTTGATGAG                         GAAGGTGATCCCCGCTTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGAT
genomic: ACAGGAAAATCTATCATGATTTGAATGCTTATAGGGTACTTTTTGATGAGgtacacaaca ... tccctatcagGAAGGTGATCCCCGCTTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGAT
EST: gi|78122641|gb|DV541025.1|DV541025
EST:     ACAGGAAAATCTATCATGATTTGAATGCTTATAGGGTACTTTTTGATGAG                         GAAGGTGATCCCCGCTTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGAT
genomic: ACAGGAAAATCTATCATGATTTGAATGCTTATAGGGTACTTTTTGATGAGgtacacaaca ... tccctatcagGAAGGTGATCCCCGCTTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGAT
EST: gi|32930139|gb|CF034951.1|CF034951
EST:     ACTTTTTGATGAG                         GAAGGTGATCCCCGCTTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGAT
genomic: ACTTTTTGATGAGgtacacaaca ... tccctatcagGAAGGTGATCCCCGCTTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttagctgcctaaagaatacctcacctgttgtaatcaatttctattccctatcagGAAGGTGATCCCCGCTTGTCAAGTTTTGGATTAATGAAGAACAGCCGTGATGGGAAAAGTTATAGCACTAACCTGGCTTACACTCCACCAGAGTTTCTAC
                  acctcac  putative branch site (score: 3)
                                      tttctattccctatc  putative PPT
                               taatcaatttctatt  TA-rich tract