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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagttctattctatctagactgccttttgtccctttcacattttttttcaaaagtttttcagaaaaaatattatgtagacccactcttaaacgtgtgtattctatcagATGACAAGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGCAATGGATGATCATACCAGAGAATTGAAGAAGCAAAAATCAAATGATCAAG

Basic information

species Zea mays
transcript GRMZM2G052688_T01
intron # 5
splice site 3'
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|76923847|gb|DV169691.1|DV169691
EST:     ATGGCCCTGGAGATTTGGACTGTGACAGCAATGACCTCGAAGGAGAACTG                         ATGACAAGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGGC
genomic: ATGGCCCTGGAGATTTGGACTGTGACAGCAATGACCTCGAAGGAGAACTGgtaaagttct ... attctatcagATGACAAGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATG-C
EST: gi|91872021|gb|EB401978.1|EB401978
EST:     ATGGCCCTGGAGATTTGGACTGTGACAGCAATGACCTCGAAGGAGAACTG                         ATGACAAGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGCA
genomic: ATGGCCCTGGAGATTTGGACTGTGACAGCAATGACCTCGAAGGAGAACTGgtaaagttct ... attctatcagATGACAAGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGCA
EST: gi|60396041|gb|DN228911.1|DN228911
EST:     ATGGCCCTGGAGATTTGGACTGTGACAGCAATGACCTCGAAGGAGAACTG                         ATGACAAGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGCA
genomic: ATGGCCCTGGAGATTTGGACTGTGACAGCAATGACCTCGAAGGAGAACTGgtaaagttct ... attctatcagATGACAAGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGCA
EST: gi|78088729|gb|DV517122.1|DV517122
EST:     ATGGCCCTGGAGATTTGGACTGTGACAGCAATGACCTCGAAGGAGAACTG                         ATGACAAGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGCA
genomic: ATGGCCCTGGAGATTTGGACTGTGACAGCAATGACCTCGAAGGAGAACTGgtaaagttct ... attctatcagATGACAAGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGCA
EST: gi|22935404|gb|BU571679.1|BU571679
EST:     TGGCCCTGGAGATTTGGCACTGTGACAGCAATGACCTCGAAGGAGAACTG                         ATGACAAGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGCA
genomic: TGGCCCTGGAGATTTGG-ACTGTGACAGCAATGACCTCGAAGGAGAACTGgtaaagttct ... attctatcagATGACAAGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGCA
EST: gi|74233407|gb|DT641321.1|DT641321
EST:     ATGGCCCTGGAGATTTGGACTGTGACAGCAATGACCTCGAAGGAGAACTG                         ATGACAAGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGCA
genomic: ATGGCCCTGGAGATTTGGACTGTGACAGCAATGACCTCGAAGGAGAACTGgtaaagttct ... attctatcagATGACAAGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGCA
EST: gi|78073936|gb|DV502370.1|DV502370
EST:     ATGGCCCTGGAGATTTGGACTGTGACAGCAATGACCTCGAAGGAGAACTG                         ATGACCAGCCTATCACCTCTTCCAACTGCATTGAAACGAGAGGCAAATGCA
genomic: ATGGCCCTGGAGATTTGGACTGTGACAGCAATGACCTCGAAGGAGAACTGgtaaagttct ... attctatcagATGACAAGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGCA
EST: gi|87156124|gb|DY400913.1|DY400913
EST:     ATGGCCCTGGAGATTTGGACTGTGACAGCAATGACCTCGAAGGAGAACTG                         ATGACAAGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGCA
genomic: ATGGCCCTGGAGATTTGGACTGTGACAGCAATGACCTCGAAGGAGAACTGgtaaagttct ... attctatcagATGACAAGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGCA

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 4 RNA-Seq libraries.


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

TGCACCAATGGCTTTTGTACGAAAGGGTCATTCTGGGTCACAATCTTCTGATGGCCCTGGAGATTTGGACTGTGACAGCAATGACCTCGAAGGAGAACTGgtaaagttct ... attctatcagATGACAAGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGCAATGGATGATCATACCAGAGAATTGAAGAAGCAAAAATCAAATGATCAAG


Block sizes: 47 (upstream exon), 38 (downstream exon)
Score: 7

TGCACCAATGGCTTTTGTACGAAAGGGTCATTCTGGGTCACAATCTTCTGATGGCCCTGGAGATTTGGACTGTGACAGCAATGACCTCGAAGGAGAACTGgtaaagttct ... attctatcagATGACAAGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGCAATGGATGATCATACCAGAGAATTGAAGAAGCAAAAATCAAATGATCAAG


Block sizes: 44 (upstream exon), 40 (downstream exon)
Score: 4

TGCACCAATGGCTTTTGTACGAAAGGGTCATTCTGGGTCACAATCTTCTGATGGCCCTGGAGATTTGGACTGTGACAGCAATGACCTCGAAGGAGAACTGgtaaagttct ... attctatcagATGACAAGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGCAATGGATGATCATACCAGAGAATTGAAGAAGCAAAAATCAAATGATCAAG


Block sizes: 29 (upstream exon), 34 (downstream exon)
Score: 3

TGCACCAATGGCTTTTGTACGAAAGGGTCATTCTGGGTCACAATCTTCTGATGGCCCTGGAGATTTGGACTGTGACAGCAATGACCTCGAAGGAGAACTGgtaaagttct ... attctatcagATGACAAGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGCAATGGATGATCATACCAGAGAATTGAAGAAGCAAAAATCAAATGATCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttcagaaaaaatattatgtagacccactcttaaacgtgtgtattctatcagATGACAAGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGCAATGGATGATCATACCAGAGAATTGAAGAAGCAAAAATCAAATGATCAAG
                                              ttctatc  CT-rich tract
       agaaaaaatattatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagttctattctatctagactgccttttgtccctttcacattttttttcaaaagtttttcagaaaaaatattatgtagacccactcttaaacgtgtgtattctatcagATGACAAGCCTATCACCTCTTCAAACTGCATTGAAACGAGAGGCAAATGCAATGGATGATCATACCAGAGAATTGAAGAAGCAAAAATCAAATGATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA