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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggttcgtgtgtttcatactggaattttttgctctctgtgcagcttcgtgtttgatttgttcctcagctgtgcccagcacttcatatttcatatttgttcttctttacggtagctatttcgactgactgtatttattccaagcacatttttttaatgattgcgttcaaaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGCACGTGAAGATCAACCTTGATGGCACTGGTGTCGCCGAGTGTAGCACAGG

Basic information

species Zea mays
transcript GRMZM2G094255_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094255_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g52710.1 (Oryza sativa), 3'ss of exon 1
gtggttcgtgtgtttcatactggaatttt------ttgctctctgtgcagctt----------cgtgtttgatttgttcctcagctgtgcccag---cacttcatatttca----tatttgttcttctttacggtagctatttcgactgactgtatttattccaagcacatttttttaatgattgcgttcaaaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGCACGTGAAGATCAACCTTGATGGCACTGGTGTCGCCGAGTGTAGCACAGG
|||| |  || ||     | | |  ||||      |||| ||   ||    ||            || ||||  | | |   ||| ||   |||   || |   |||| ||    |  ||  |||  |||  |  ||||| | | | | | | |  || ||  ||         | |  |  ||| ||||  |||  ||||  |  || ||||| ||||| || |||||||||||||| ||||| |||||||| |||||||||||||| |||||||||||||| ||||| || ||||||||
gtggattctgcgtcgtcgattaggcttttgttctgttgcgcttcatgtgatttgctaccatgctatgcttgacatctccactagcagtaggcagtagcagtagctattccaagagttcttactctcttttgtgaaagctaatcctatttaatttgattttttaaa--------ctctggt--ttgtgttcggaattctcagCGTTGTCCAGGATAGGAGAAGTCAAGAGGGTGACCAAGGAGACGAATGTGCATGTGAAGATCAACCTGGATGGCACTGGTGTTGCCGATTGCAGCACAGG
















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|76281018|gb|DV020586.1|DV020586
EST:     GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAG                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGgtggttcgtg ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|94478729|gb|EB707687.1|EB707687
EST:     GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAG                         GTGGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATG
genomic: GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGgtggttcgtg ... aaatcttcagG---ATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATG
EST: gi|211006666|gb|FL081503.1|FL081503
EST:     GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAG                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGgtggttcgtg ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|211006657|gb|FL081494.1|FL081494
EST:     GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAG                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGgtggttcgtg ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|211003886|gb|FL081493.1|FL081493
EST:     GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAG                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGgtggttcgtg ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|149110134|gb|EE293952.2|EE293952
EST:     GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAG                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGgtggttcgtg ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|88757021|gb|DY541162.1|DY541162
EST:     GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAG                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGgtggttcgtg ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|211006669|gb|FL081506.1|FL081506
EST:     GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAG                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGgtggttcgtg ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|211006664|gb|FL081501.1|FL081501
EST:     GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAG                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGgtggttcgtg ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|91056439|gb|EB166857.1|EB166857
EST:     GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAG                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGgtggttcgtg ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|31611949|gb|CD568571.1|CD568571
EST:     GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAG                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGgtggttcgtg ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|211006668|gb|FL081505.1|FL081505
EST:     GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAG                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGgtggttcgtg ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|211006671|gb|FL081508.1|FL081508
EST:     GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAG                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGgtggttcgtg ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|211006662|gb|FL081499.1|FL081499
EST:     GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAG                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGgtggttcgtg ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|101397352|gb|EB820599.1|EB820599
EST:     GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTG                       
genomic: GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATA---Ggtggttcgtg ... aaatcttc
EST: gi|211006670|gb|FL081507.1|FL081507
EST:     GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAG                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGgtggttcgtg ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|50325237|gb|CO520363.1|CO520363
EST:     GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAG                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGgtggttcgtg ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
EST: gi|50323498|gb|CO518624.1|CO518624
EST:     GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGGTG                       
genomic: GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATA---Ggtggttcgtg ... aaatcttc
EST: gi|71309481|gb|DR791027.1|DR791027
EST:     GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAG                         GATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC
genomic: GCCTGCCATGGCCGCCGCCGGCCCCCCTACCGCGCATGGAGACTCAATAGgtggttcgtg ... aaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgactgtatttattccaagcacatttttttaatgattgcgttcaaaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGCACGTGAAGATCAACCTTGATGGCACTGGTGTCGCCGAGTGTAGCACAGG
                                                tcttc  CT-rich tract
                     acatttttttaatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggttcgtgtgtttcatactggaattttttgctctctgtgcagcttcgtgtttgatttgttcctcagctgtgcccagcacttcatatttcatatttgttcttctttacggtagctatttcgactgactgtatttattccaagcacatttttttaatgattgcgttcaaaatcttcagGATCTTCTAGGATTGGAGAGGTTAAGAGGGTGACCAAAGAGACAAATGTGCACGTGAAGATCAACCTTGATGGCACTGGTGTCGCCGAGTGTAGCACAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA