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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCCAGCGGTGTCATTCTAACCGCTGTCTCTACAAGCTGGCTTCCTTTCAACCATCAGAAGGTCTTCGAGCTTCTTGCCGATGAACAACAGCGTTGTCAGgtactacctatatttacgatttcaaacatgcatcgcatcgttttggttctttgtttctgttgcaacaagcttgagattagtagtgtcttcatggatgttttaattttgcag

Basic information

species Zea mays
transcript GRMZM2G123140_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G123140_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os10g42490.1 (Oryza sativa), 5'ss of exon 10
GCCCAGCGGTGTCATTCTAACCGCTGTCTCTACAAGCTGGCTTCCTTTCAACCATCAGAAGGTCTTCGAGCTTCTTGCCGATGAACAACAGCGTTGTCAGgtactacctatatttacgatttcaaacatgcatcgcatcgttttggttctttgtttctgttgcaacaagcttgagattagtagtg-tcttcatggatgttttaa-ttttgcag
||||||||||||||| || ||||||||||| ||||||||||||||||| | ||||||| |||| || ||||||||||| |||||||||||||| || ||||||| |   | |    | || | | | |  ||   |||  |     ||    |||  ||||      | |||   ||| || ||| || |  | | |  |||   ||||||||
GCCCAGCGGTGTCATCCTCACCGCTGTCTCCACAAGCTGGCTTCCTTTTACCCATCAGCAGGTGTTTGAGCTTCTTGCAGATGAACAACAGCGCTGCCAGgtacaatgaaga---gccatataatatactcagtccatactgaaaatt----gttgttgttc-----accttataattcgttgtggtcatgtttgttaatttgccttttgcag
















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|31910760|gb|CD651585.1|CD651585
EST:     GAGCTTCTTGCCGATG-ACAACAGCGTTGTCAG                         CTTGAGATTATGTCAAGCGGGGGCTCACTTCACGAAGTGGCACATATTGCA
genomic: GAGCTTCTTGCCGATGAACAACAGCGTTGTCAGgtactaccta ... aattttgcagCTTGAGATTATGTCAAGCGGGGGCTCACTTCACGAAGTGGCACATATTGCA
EST: gi|71321764|gb|DR797569.1|DR797569
EST:     ACCATCAGAAGGTCTTCGAGCTTCTTGCCGATGAACAACAGCGTTGTCAG                         CTTGAGATTATGTCAAGCGGGGGCTCACTTCACGAAGTGGCACATATTGCA
genomic: ACCATCAGAAGGTCTTCGAGCTTCTTGCCGATGAACAACAGCGTTGTCAGgtactaccta ... aattttgcagCTTGAGATTATGTCAAGCGGGGGCTCACTTCACGAAGTGGCACATATTGCA
EST: gi|22819056|gb|BU499146.1|BU499146
EST:     ACCATCAGAAGGTCTTCGAGCTTCTTGCCGATGAACAACAGCGTTGTCAG                         CTTGAGATTATGTCAAGCGGGGGCTCACTTCACGAAGTGGCACATATTGCA
genomic: ACCATCAGAAGGTCTTCGAGCTTCTTGCCGATGAACAACAGCGTTGTCAGgtactaccta ... aattttgcagCTTGAGATTATGTCAAGCGGGGGCTCACTTCACGAAGTGGCACATATTGCA
EST: gi|5555586|gb|AI881537.1|AI881537
EST:     ACCATCAGAAGGTCTTCGAGCTTCTTGCCGATGAACAACAGCGTTGTCAG                         CTTGAGATTATGTCAAGCGGGGGCTCACTTCACGAAGTGGCACATATTGCA
genomic: ACCATCAGAAGGTCTTCGAGCTTCTTGCCGATGAACAACAGCGTTGTCAGgtactaccta ... aattttgcagCTTGAGATTATGTCAAGCGGGGGCTCACTTCACGAAGTGGCACATATTGCA
EST: gi|71329968|gb|DR801717.1|DR801717
EST:     ACCATCAGAAGGTCTTCGAGCTTCTTGCCGATGAACAACAGCGTTGTCAG                         CTTGAGATTATGTCAAGCGGGGGCTCACTTCACGAAGTGGCACATATTGCA
genomic: ACCATCAGAAGGTCTTCGAGCTTCTTGCCGATGAACAACAGCGTTGTCAGgtactaccta ... aattttgcagCTTGAGATTATGTCAAGCGGGGGCTCACTTCACGAAGTGGCACATATTGCA
EST: gi|87157207|gb|DY401996.1|DY401996
EST:     ACCATCAGAAGGTCTTCGAGCTTCTTGCCGATGAACAACAGCGTTGTCAG                         CTTGAGATTATGTCAAGCGGGGGCTCACTTCACGAAGTGGCACATATTGCA
genomic: ACCATCAGAAGGTCTTCGAGCTTCTTGCCGATGAACAACAGCGTTGTCAGgtactaccta ... aattttgcagCTTGAGATTATGTCAAGCGGGGGCTCACTTCACGAAGTGGCACATATTGCA
EST: gi|30306491|gb|CD001164.1|CD001164
EST:     GAGCTTCTTGCCGATGAACAACAGCGTTGTCAG                         CTTGAGATTATGTCAAGCGGGGGCTCACTTCACGAAGTGGCACATATTGCA
genomic: GAGCTTCTTGCCGATGAACAACAGCGTTGTCAGgtactaccta ... aattttgcagCTTGAGATTATGTCAAGCGGGGGCTCACTTCACGAAGTGGCACATATTGCA
EST: gi|26559801|gb|CA832036.1|CA832036
EST:     ACCATCAGAAGGTCTTCGAGCTTCTTGCCGATGAACAACAGCGTTGTCAG                         CTTGAGATTATGTCAAGCGGGGGCTCACTTCACGAAGTGGCACATATTGCA
genomic: ACCATCAGAAGGTCTTCGAGCTTCTTGCCGATGAACAACAGCGTTGTCAGgtactaccta ... aattttgcagCTTGAGATTATGTCAAGCGGGGGCTCACTTCACGAAGTGGCACATATTGCA

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 80

GCCCAGCGGTGTCATTCTAACCGCTGTCTCTACAAGCTGGCTTCCTTTCAACCATCAGAAGGTCTTCGAGCTTCTTGCCGATGAACAACAGCGTTGTCAGgtactaccta ... aattttgcagCTTGAGATTATGTCAAGCGGGGGCTCACTTCACGAAGTGGCACATATTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAAT


Block sizes: 49 (upstream exon), 19 (downstream exon)
Score: 2

GCCCAGCGGTGTCATTCTAACCGCTGTCTCTACAAGCTGGCTTCCTTTCAACCATCAGAAGGTCTTCGAGCTTCTTGCCGATGAACAACAGCGTTGTCAGgtactaccta ... aattttgcagCTTGAGATTATGTCAAGCGGGGGCTCACTTCACGAAGTGGCACATATTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAAT


Block sizes: 18 (upstream exon), 32 (downstream exon)
Score: 1

GCCCAGCGGTGTCATTCTAACCGCTGTCTCTACAAGCTGGCTTCCTTTCAACCATCAGAAGGTCTTCGAGCTTCTTGCCGATGAACAACAGCGTTGTCAGgtactaccta ... aattttgcagCTTGAGATTATGTCAAGCGGGGGCTCACTTCACGAAGTGGCACATATTGCAAATGGATCACACCCAAAGAATTGCATTTCTCTTCTTAGAATCAAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCCAGCGGTGTCATTCTAACCGCTGTCTCTACAAGCTGGCTTCCTTTCAACCATCAGAAGGTCTTCGAGCTTCTTGCCGATGAACAACAGCGTTGTCAGgtactacctatatttacgatttcaaacatgcatcgcatcgttttggttctttgtttctgttgcaacaagcttgagattagtagtgtcttcatggatgttttaattttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT