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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGCGGGGGCGGAGGACGCGACGCAGCTCTCCATCTCCATCCCCGCGGCTTCGCCCTCCTCTGACCACGCTGCCTCTGCCGCCGCGCGATGCCACAACGgtgagccagcgagccaaagactcgatttttgttggttgttttgtttctcacgtacaatcagtttgctgatcagtgctgccgtttgattgattcacacag

Basic information

species Zea mays
transcript GRMZM2G067743_T03
intron # 3
splice site 5'
intron type U2

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|94477840|gb|EB706798.1|EB706798
EST:     TTCGCCCTCCTCTGACCACGCTGCCTCTGCCGCCGCGCGATGCCACAACG                         ATGGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCTGCAA
genomic: TTCGCCCTCCTCTGACCACGCTGCCTCTGCCGCCGCGCGATGCCACAACGgtgagccagc ... attcacacagATGGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCTGCAA
EST: gi|50330472|gb|CO525598.1|CO525598
EST:     ATGCCACAACG                         ATGGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCTGCAA
genomic: ATGCCACAACGgtgagccagc ... attcacacagATGGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCTGCAA
EST: gi|50339440|gb|CO534566.1|CO534566
EST:     TTCGCCCTCCTCTGACCACGCTGCCTCTGCCGCCGCGCGATGCCACAACG                         ATGGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCTGCAA
genomic: TTCGCCCTCCTCTGACCACGCTGCCTCTGCCGCCGCGCGATGCCACAACGgtgagccagc ... attcacacagATGGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCTGCAA
EST: gi|110494971|gb|EE014539.1|EE014539
EST:     CGCCGCGGGATGCCACAACG                         ATGGGGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCGGC
genomic: CGCCGCGCGATGCCACAACGgtgagccagc ... attcacacagAT--GGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCTGC
EST: gi|91053354|gb|EB163772.1|EB163772
EST:     TTCGCCCTCCTCTGACCACGCTGCCTCTGCCGCCGCGCGATGCCACAACG                         ATGGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCTGCAA
genomic: TTCGCCCTCCTCTGACCACGCTGCCTCTGCCGCCGCGCGATGCCACAACGgtgagccagc ... attcacacagATGGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCTGCAA
EST: gi|78111983|gb|DV530379.1|DV530379
EST:     TTCGCCCTCCTCTGACCACGCTGCCTCTGCCGCCGCGCGATGCCACAACG                         ATGGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCTGCAA
genomic: TTCGCCCTCCTCTGACCACGCTGCCTCTGCCGCCGCGCGATGCCACAACGgtgagccagc ... attcacacagATGGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCTGCAA
EST: gi|91050949|gb|EB161367.1|EB161367
EST:     TTTGCCCTCCTCTGACCACGCTGCCTCTGCCGCCGCGCGATGCCACAACG                         ATGGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCTGCAA
genomic: TTCGCCCTCCTCTGACCACGCTGCCTCTGCCGCCGCGCGATGCCACAACGgtgagccagc ... attcacacagATGGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCTGCAA
EST: gi|78112351|gb|DV530745.1|DV530745
EST:     TTCGCCCTCCTCTGACCACGCTGCCTCTGCCGCCGCGCGATGCCACAACG                         ATGGGAGTGATCGGTGCATTTCCTAGCTGCAACTGCAATGCAAGCCTGCAA
genomic: TTCGCCCTCCTCTGACCACGCTGCCTCTGCCGCCGCGCGATGCCACAACGgtgagccagc ... attcacacagATGGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCTGCAA
EST: gi|21331565|gb|BQ486946.1|BQ486946
EST:     TTCGCCCTCCTCTGACCACGCTGCCTCTGCCGCCGCGCGATGCCACAACG                         ATGGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCTGCAA
genomic: TTCGCCCTCCTCTGACCACGCTGCCTCTGCCGCCGCGCGATGCCACAACGgtgagccagc ... attcacacagATGGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCTGCAA
EST: gi|78083100|gb|DV511493.1|DV511493
EST:     TTCGCCCTCCTCTGACCACGCTGCCTCTGCCGCCGCGCGATGCCACAACG                         ATGGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCTGCAA
genomic: TTCGCCCTCCTCTGACCACGCTGCCTCTGCCGCCGCGCGATGCCACAACGgtgagccagc ... attcacacagATGGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCTGCAA
EST: gi|78081101|gb|DV509513.1|DV509513
EST:     TTCGCCCTCCTCTGACCACGCTGCCTCTGCCGCCGCGCGATGCCACAACG                         ATGGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCTGCAA
genomic: TTCGCCCTCCTCTGACCACGCTGCCTCTGCCGCCGCGCGATGCCACAACGgtgagccagc ... attcacacagATGGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCTGCAA
EST: gi|71425367|gb|DR806631.1|DR806631
EST:     TTCGCCCTCCTCTGACCACGCTGCCTCTGCCGCCGCGCGATGCCACAACG                         ATGGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCTGCAA
genomic: TTCGCCCTCCTCTGACCACGCTGCCTCTGCCGCCGCGCGATGCCACAACGgtgagccagc ... attcacacagATGGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCTGCAA

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 2 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 18

TGGGCGGGGGCGGAGGACGCGACGCAGCTCTCCATCTCCATCCCCGCGGCTTCGCCCTCCTCTGACCACGCTGCCTCTGCCGCCGCGCGATGCCACAACGgtgagccagc ... attcacacagATGGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCTGCAACCGCGTGGATTGTTGTTGATTGGTGTAGTTTCCTAGCTGCAATTCAAGC


Block sizes: 35 (upstream exon), 49 (downstream exon)
Score: 10

TGGGCGGGGGCGGAGGACGCGACGCAGCTCTCCATCTCCATCCCCGCGGCTTCGCCCTCCTCTGACCACGCTGCCTCTGCCGCCGCGCGATGCCACAACGgtgagccagc ... attcacacagATGGGAGTGATCGGTGCATCTCCTAGCTGCAACTGCAATGCAAGCCTGCAACCGCGTGGATTGTTGTTGATTGGTGTAGTTTCCTAGCTGCAATTCAAGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGCGGGGGCGGAGGACGCGACGCAGCTCTCCATCTCCATCCCCGCGGCTTCGCCCTCCTCTGACCACGCTGCCTCTGCCGCCGCGCGATGCCACAACGgtgagccagcgagccaaagactcgatttttgttggttgttttgtttctcacgtacaatcagtttgctgatcagtgctgccgtttgattgattcacacag

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