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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagccttgtaactgtcatatgtattctgttttctcgtgcttcatgttgcaataattttattagcagccatagcactaacaataaagagtctgcttgtaatgcagGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG

Basic information

species Zea mays
transcript GRMZM2G381051_T03
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G381051_T03 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os05g03480.4 (Oryza sativa), 3'ss of exon 10
gtaaagccttgtaactgtcatatgtattctgttttctcgtgcttcatgttgcaataattttattagcagccat--agcactaacaataaagagtctgcttgtaatgcagGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
||| | ||  | |||| | | || | | ||||||| || || |||  | ||||| | |||| ||| ||| | |   | || ||| ||||  |||   ||| |||||||||||||| |||| ||||||||||| || |||||||| |||||
gtatatccaggaaactcttacatatgtcctgttttatcctgtttctaggtgcaaca-ttttgttaacagacgtctggtaccaaccataacaagttatcttttaatgcagGGGAAATTGGCAGATATGTACACCTCCTTGCAGTCATCAAG
















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|148952108|gb|EC897900.2|EC897900
EST:     GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
genomic: GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaagcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
EST: gi|24763821|gb|CA398992.1|CA398992
EST:     GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCCGATATGTACACCTCGTTGCAGTCGTCAAG
genomic: GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaagcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
EST: gi|40333869|gb|CK367939.1|CK367939
EST:     GGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
genomic: GGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaagcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
EST: gi|148928298|gb|EE284912.2|EE284912
EST:     GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
genomic: GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaagcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
EST: gi|149073601|gb|EE161904.2|EE161904
EST:     GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
genomic: GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaagcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
EST: gi|37375704|gb|CF624307.1|CF624307
EST:     GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
genomic: GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaagcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
EST: gi|148949902|gb|EC895400.2|EC895400
EST:     GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
genomic: GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaagcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
EST: gi|31352282|gb|CD436639.1|CD436639
EST:     GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCCGATATGTACACCTCGTTGCAGTCGTCAAG
genomic: GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaagcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
EST: gi|60356707|gb|DN223680.1|DN223680
EST:     GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
genomic: GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaagcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
EST: gi|5871129|gb|AW017570.1|AW017570
EST:     GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
genomic: GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaagcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
EST: gi|15214937|gb|BI431104.1|BI431104
EST:     GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
genomic: GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaagcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
EST: gi|8576983|gb|BE129620.1|BE129620
EST:     GCCAGAGGGAGCAATTCGGCCGTCCAATTGGGGAATTTCAGTTCATACAG                         GGGCAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
genomic: GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaagcctt ... tgtaatgcagGGG-AAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
EST: gi|40333885|gb|CK367955.1|CK367955
EST:     GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
genomic: GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaagcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
EST: gi|78086928|gb|DV515321.1|DV515321
EST:     GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
genomic: GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaagcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
EST: gi|16925518|gb|BM078586.1|BM078586
EST:     GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
genomic: GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaagcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
EST: gi|86474638|gb|DY241008.1|DY241008
EST:     GCCAGAGGGAGCAATTCGGCCGTCCAATTGGGGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
genomic: GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaagcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
EST: gi|6095776|gb|AW120443.1|AW120443
EST:     GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
genomic: GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaagcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
EST: gi|37394249|gb|CF634396.1|CF634396
EST:     GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
genomic: GCCAGAGGGAGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaagcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
EST: gi|6020797|gb|AW065725.1|AW065725
EST:     ATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
genomic: ATTTCAGTTCATACAGgtaaagcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
EST: gi|37375650|gb|CF624276.1|CF624276
EST:     AGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
genomic: AGCAATTCGGCCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaagcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataattttattagcagccatagcactaacaataaagagtctgcttgtaatgcagGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG
                       cactaac  putative branch site (score: 1)
                                       tctgctt  putative PPT
                          taacaataaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagccttgtaactgtcatatgtattctgttttctcgtgcttcatgttgcaataattttattagcagccatagcactaacaataaagagtctgcttgtaatgcagGGGAAAATGGCTGATATGTACACTTCGTTGCAGTCGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT