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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtatccacattgcgtagtgtgtgccgcgtgaagggagaagaaaagaaaagaaaagaaaaacgctgcctggcatggcatgcatgcatgtgcgtgtgctcatctcatctcatctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATCAGATACCACTCGTTCTACC

Basic information

species Zea mays
transcript GRMZM2G126900_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126900_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g36560.1 (Oryza sativa), 3'ss of exon 7
gtcagtatccacattgcgtagtgt--gtgccgcgtgaagggagaagaaaagaaaagaaaag-----aaaaacgctgcctggcatggcatgcatgc----atgtgcgtgtgctcatctcatctcatctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATCAGATACCACTCGTTCTACC
   |  |  |||  | | | ||||   | |  |   ||  |   |  |  ||  ||| ||      |       | |   |  ||   |     |    ||||   |||| |  |      |  ||   |||||| |||||||||||||||  ||| |||||||| || ||  |||||||||||||||| || || |||||||
-gtaaaacacacggttcatcgtgtcgattcatcaccaattgcataccatggagcagagaaatcttcagttctagtactgaggttgtagttttctctgaaatgttgatgtgtttcttgttcttgttcatctcagGTTGCCAAGGAGAACAAGACCACTCTTCCTTCTGCAGGCTTGTTCATCATCAGATATCATTCATTCTACC
















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|31363556|gb|CD447913.1|CD447913
EST:     GCCTCGACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|88752150|gb|DY536291.1|DY536291
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGC
EST: gi|78076467|gb|DV504901.1|DV504901
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|76289997|gb|DV029565.1|DV029565
EST:     CCTNCA-CAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: CCT-CAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|148941675|gb|EC886622.2|EC886622
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|78119916|gb|DV538300.1|DV538300
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|148960892|gb|EE011574.2|EE011574
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCCTTCTTTCCGCGGGGCTGTTCATCAT
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCC-TTCCTTCCGCGGGGCTGTTCATCAT
EST: gi|45847402|gb|CN071345.1|CN071345
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|60339537|gb|DN206510.1|DN206510
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|76923451|gb|DV169494.1|DV169494
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|15554177|gb|BI644175.1|BI644175
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|93281927|gb|EB674191.1|EB674191
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|60397791|gb|DN230607.1|DN230607
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|78112469|gb|DV530863.1|DV530863
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACTTGTACCTG                         GGGGCCA-GGAGAACAA
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAA
EST: gi|15057218|gb|BI361190.1|BI361190
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|93016474|gb|EB641994.1|EB641994
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|78076468|gb|DV504902.1|DV504902
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|60359616|gb|DN226589.1|DN226589
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|78119915|gb|DV538299.1|DV538299
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|40303359|gb|CK347746.1|CK347746
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|14996904|gb|BI319057.1|BI319057
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|67041064|gb|CO467319.1|CO467319
EST:     GCCTCGACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGGCAAGGGAGA-CAAGTGCACCCTTCCTTCCGCGGGGCTGNTCATCAT
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGG-AGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCAT
EST: gi|149010866|gb|EE042255.2|EE042255
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|78088525|gb|DV516918.1|DV516918
EST:     CCCTCA-CAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: CC-TCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|76923453|gb|DV169495.1|DV169495
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|154130490|gb|EC872226.2|EC872226
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTG
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTG
EST: gi|149100878|gb|EE186973.2|EE186973
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCCTTC-GCGGGGCTGTTCATCAT
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCC-TTCCGCGGGGCTGTTCATCAT
EST: gi|50333620|gb|CO528746.1|CO528746
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|71325953|gb|DR799659.1|DR799659
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCA
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCA
EST: gi|60396286|gb|DN229155.1|DN229155
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|60347921|gb|DN214894.1|DN214894
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|14996932|gb|BI319072.1|BI319072
EST:     GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
EST: gi|211354362|gb|FL217076.1|FL217076
EST:     GCCTCGACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTG                         GTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC
genomic: GCCTCAACAAGGTGCTCATGTCATGGGGCCACGACGACTACATGTACCTGgtcagtatcc ... atctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcctggcatggcatgcatgcatgtgcgtgtgctcatctcatctcatctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATCAGATACCACTCGTTCTACC
                                    tctcatctcatctc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtatccacattgcgtagtgtgtgccgcgtgaagggagaagaaaagaaaagaaaagaaaaacgctgcctggcatggcatgcatgcatgtgcgtgtgctcatctcatctcatctcgtcagGTGGCCAAGGAGAACAAGTGCACCCTTCCTTCCGCGGGGCTGTTCATCATCAGATACCACTCGTTCTACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT