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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACACCTTGTGCTCTCTTTGACGTTCTTTCTCCACCATACTCCGCTGAGGATGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggagatcttgaaacataagtttaaacttacagatgtttctgccgagctttctaacttaggttaaaatttctgcctaccag

Basic information

species Zea mays
transcript GRMZM2G162175_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G162175_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os04g06790.2 (Oryza sativa), 5'ss of exon 6
ACACCTTGTGCTCTCTTTGACGTTCTTTCTCCACCATACTCCGCTGAGGATGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAG---CCACCTGgtaagtggagatcttgaaacataagtttaaacttacagatgtttctgccgagctttctaacttaggttaaaatttctgcctaccag--------
   ||||||||||||||||| || |||||||| || || || |||||| | ||| |  |||||||||||||||| ||||||    | |   |    |||||||||| || ||||||||  ||| | |  ||    |||||     | |||       ||||||||   |         | | |    |         
---CCTTGTGCTCTCTTTGATGTCCTTTCTCCTCCTTATTCTGCTGAGAAGGGGAGGGACTGTTCATACTTCCGGAAGTCTTCAGTAAGGGAAACACCACCTGgtatgtagagatcttataacttgaacttgttattacac-cactgctgagcgctgttctaactcccgccccccaccccgtccgatattcctccag
















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|110954112|gb|EE174164.1|EE174164
EST:     ATCAGCCACCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
genomic: ATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
EST: gi|50329440|gb|CO524566.1|CO524566
EST:     TTCATACTTCCGAAAGTTTCAGATGAATCAGCCCCCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTTTCAGGTAGTTTGGTTGGAGGAGT
genomic: TTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
EST: gi|149096943|gb|EE182742.2|EE182742
EST:     TTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
genomic: TTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
EST: gi|101382864|gb|EB813486.1|EB813486
EST:     TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
genomic: TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
EST: gi|113809067|gb|DW930297.1|DW930297
EST:     TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGG
genomic: TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGG
EST: gi|78119800|gb|DV538184.1|DV538184
EST:     TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
genomic: TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
EST: gi|149078130|gb|EE166879.2|EE166879
EST:     TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
genomic: TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
EST: gi|76919420|gb|DV167706.1|DV167706
EST:     TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGG
genomic: TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGG
EST: gi|149013589|gb|EE043058.2|EE043058
EST:     TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
genomic: TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
EST: gi|166447313|gb|EG142167.1|EG142167
EST:     TGGGCGACACTGTTCATACTTCCGAAAATCTCAGATGAATCAGCCACCTG                         TTGTTTTGCCTGC
genomic: TGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGC
EST: gi|4681159|gb|AI629829.1|AI629829
EST:     TGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTG                         TTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT
genomic: TGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGT

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), 48 (downstream exon)
Score: 107

ACACCTTGTGCTCTCTTTGACGTTCTTTCTCCACCATACTCCGCTGAGGATGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGTTGGAGGACCATCAGCCCCCAGAAGGCTTTGTTGTTGCAAGAGGTCTGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 40

ACACCTTGTGCTCTCTTTGACGTTCTTTCTCCACCATACTCCGCTGAGGATGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGTTGGAGGACCATCAGCCCCCAGAAGGCTTTGTTGTTGCAAGAGGTCTGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 70

ACACCTTGTGCTCTCTTTGACGTTCTTTCTCCACCATACTCCGCTGAGGATGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGTTGGAGGACCATCAGCCCCCAGAAGGCTTTGTTGTTGCAAGAGGTCTGTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 67

ACACCTTGTGCTCTCTTTGACGTTCTTTCTCCACCATACTCCGCTGAGGATGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggag ... tgcctaccagTTGTTTTGCCTGCTGAGATAGATAGCTCTCAGGTAGTTTGGTTGGAGGAGTTGGAGGACCATCAGCCCCCAGAAGGCTTTGTTGTTGCAAGAGGTCTGTA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACACCTTGTGCTCTCTTTGACGTTCTTTCTCCACCATACTCCGCTGAGGATGGGCGACACTGTTCATACTTCCGAAAGTCTCAGATGAATCAGCCACCTGgtaagtggagatcttgaaacataagtttaaacttacagatgtttctgccgagctttctaacttaggttaaaatttctgcctaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG