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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCTGACGGAAAGAAGATTCGTCCTGGTATCAACCCTGTCATGATTGATGAACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAGgtatgtgttgtgttccatattcattgttaaattaaaaggtaaaatatggtcaaacattcattgtggtagactggtagctgtactttataaaaaactgaat...

Basic information

species Zea mays
transcript GRMZM2G037698_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037698_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os10g32880.1 (Oryza sativa), 5'ss of exon 5
CCCTGACGGAAAGAAGATTCGTCCTGGTATCAACCCTGTCATGATTGATGAACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAGgtatgtgttgtgttccatattcattgttaaattaaaaggtaaaatatggtcaaacattcattgtggtagactggtagctgtactttataaaaaactgaat-------------------------------------------------------------------------------------------
|| ||||| ||||||||||||||||||||||||||||| |||||||||||||| |||||||||||||||||||| || || || ||||||||| |||||||| | | | |||| | || | || || ||||| ||| || || | | | | || || | | | || || |
ACCAGACGGGAAGAAGATTCGTCCTGGTATCAACCCTGTGATGATTGATGAACTAACAGAGTGTAATACCATGCTCTCTGCGCATCGTAAGAAACGACAGgtacatatctgtattcatagttatgctacaaacaaggtctaaaacatgcattaatgtt---tttatccaatagttaagattatctca-agaatgctagctcatctcgccaggacattatttctcagtgtttgttgccatctttacaccttacttttgaaatgagataacagttctctacattttctcacag
















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|31350321|gb|CD434678.1|CD434678
EST:     AACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAG                         GTTCCTCCAACTCTGGCACCATTAGATGCACTCGAGAGATACACTCCAATC
genomic: AACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAGgtatgtgttg ... tttctctcagGTTCCTCCAACTCTGGCACCATTAGATGCACTCGAGAGATACACTCAAATC
EST: gi|148956938|gb|EC902874.2|EC902874
EST:     AACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAG                         GTTCCTCCAACTCTGGCACCATTAGATGCACTCGAGAGATACACTCAAATC
genomic: AACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAGgtatgtgttg ... tttctctcagGTTCCTCCAACTCTGGCACCATTAGATGCACTCGAGAGATACACTCAAATC
EST: gi|148987120|gb|EE030948.2|EE030948
EST:     AACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAA                         GTTCCCTC-AACTCTGGGCAC-ATTAGATGCA
genomic: AACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAGgtatgtgttg ... tttctctcagGTTCC-TCCAACTCTGG-CACCATTAGATGCA
EST: gi|60397274|gb|DN230090.1|DN230090
EST:     AACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAG                         GTTCCTCCAACTCTGGCACCATTAGA
genomic: AACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAGgtatgtgttg ... tttctctcagGTTCCTCCAACTCTGGCACCATTAGA
EST: gi|148940045|gb|EC884788.2|EC884788
EST:     AACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAG                         GTTCCTCCAACTCTGGCACCATTAGATGCACTCGAGAGATACACTCAAATC
genomic: AACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAGgtatgtgttg ... tttctctcagGTTCCTCCAACTCTGGCACCATTAGATGCACTCGAGAGATACACTCAAATC
EST: gi|31355564|gb|CD439921.1|CD439921
EST:     AACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAG                         GTTCCTCCAACTCTGGCACCATTAGATGCACTCGAGAGATACACTCAAATC
genomic: AACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAGgtatgtgttg ... tttctctcagGTTCCTCCAACTCTGGCACCATTAGATGCACTCGAGAGATACACTCAAATC
EST: gi|211125238|gb|FL005611.1|FL005611
EST:     AACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAG                         GTTCCTCCAACTCTGGCACCATTAGATGCACTCGAGAGATACACTCAAATC
genomic: AACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAGgtatgtgttg ... tttctctcagGTTCCTCCAACTCTGGCACCATTAGATGCACTCGAGAGATACACTCAAATC
EST: gi|31354887|gb|CD439244.1|CD439244
EST:     AACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAG                         GTTCCTCCAACTCTGGCCCCATTAGATGCACTCGAGAGATACACTCAAATC
genomic: AACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAGgtatgtgttg ... tttctctcagGTTCCTCCAACTCTGGCACCATTAGATGCACTCGAGAGATACACTCAAATC
EST: gi|149095787|gb|EE181433.2|EE181433
EST:     AACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGATAAGACAG                         GTTCCTCCCACTCTGGCACCATTAGATGCACTCGAGAGATACACTCAAATC
genomic: AACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAGgtatgtgttg ... tttctctcagGTTCCTCCAACTCTGGCACCATTAGATGCACTCGAGAGATACACTCAAATC
EST: gi|148958621|gb|EC904872.2|EC904872
EST:     AACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAG                         GTTCCCTCCA-CTCTGGCACCATTAGATGCACTCGAGAGATACACTCAAAT
genomic: AACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAGgtatgtgttg ... tttctctcagGTTCC-TCCAACTCTGGCACCATTAGATGCACTCGAGAGATACACTCAAAT

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: 339

CCCTGACGGAAAGAAGATTCGTCCTGGTATCAACCCTGTCATGATTGATGAACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAGgtatgtgttg ... tttctctcagGTTCCTCCAACTCTGGCACCATTAGATGCACTCGAGAGATACACTCAAATCTCCAGCCATCCCCTTCATAAGACAAACAAACCAGGCATTTTGTCCATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 159

CCCTGACGGAAAGAAGATTCGTCCTGGTATCAACCCTGTCATGATTGATGAACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAGgtatgtgttg ... tttctctcagGTTCCTCCAACTCTGGCACCATTAGATGCACTCGAGAGATACACTCAAATCTCCAGCCATCCCCTTCATAAGACAAACAAACCAGGCATTTTGTCCATGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 98

CCCTGACGGAAAGAAGATTCGTCCTGGTATCAACCCTGTCATGATTGATGAACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAGgtatgtgttg ... tttctctcagGTTCCTCCAACTCTGGCACCATTAGATGCACTCGAGAGATACACTCAAATCTCCAGCCATCCCCTTCATAAGACAAACAAACCAGGCATTTTGTCCATGG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 141

CCCTGACGGAAAGAAGATTCGTCCTGGTATCAACCCTGTCATGATTGATGAACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAGgtatgtgttg ... tttctctcagGTTCCTCCAACTCTGGCACCATTAGATGCACTCGAGAGATACACTCAAATCTCCAGCCATCCCCTTCATAAGACAAACAAACCAGGCATTTTGTCCATGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCTGACGGAAAGAAGATTCGTCCTGGTATCAACCCTGTCATGATTGATGAACTTACAGAGTGTAATACCATGCTTTCAGCACAGCGTAAGAAAAGACAGgtatgtgttgtgttccatattcattgttaaattaaaaggtaaaatatggtcaaacattcattgtggtagactggtagctgtactttataaaaaactgaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaggtaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaaaaa