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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaaataaaggattcaaaagattttttttcttaatgatgatattatttgacttccatgaaaacatatcacatacccctactactcttaacagga...

Basic information

species Zea mays
transcript GRMZM2G177001_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177001_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g30980.1 (Oryza sativa), 5'ss of exon 5
CTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaaat-aaaggatt-caaaagattttttttcttaatgatgatattatttgacttccatgaaaac-atatcacatacccctactactcttaacagga
| || ||||||||| | || ||||||||||||||||||||  |||| ||||| |||||||||||||| | |||||||||||||||| || |||||  ||||||   | || |||||||||  | ||  ||   ||||    ||  | || |||| ||| ||  |    |  ||| | | |  ||  
CCGGCTGTGCCTTTTTGAAGTATGAAACAAAAGAGCAAGCGCTGGCAGCTATCGAAGCTCTAAATGGGAAACACAAAATAGAGgtttgtggaaattgaaggatgatacaatattttttttgctgatt-tgtgtttatagatctctcctgcaaacgatagcaacttaggcatctattgt-actagc-

upper sequence: GRMZM2G177001_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S12_239V6.1 (Physcomitrella patens), 5'ss of exon 7
CTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagta--------------gaaataaaggattcaaaagattttttttcttaatgatgatattatttgacttccatgaa-aacatatcacatacccc-tactactcttaacagga--------------------------------------------------------------------------
   | || || ||| ||||||||||||| || || |||||| | |||||||| |||||||| ||||||   |||| ||| |||||   |               ||    ||||||  |  |  | | ||||     |    | |||  |||   | | ||   |   |   |  ||     |||| |  |  | |||                                                                           
---GATGCGCTTTTTTAAAATATGAAACTAAGGAACAAGCTATTGCTGCTATTGAAGCTCTTAATGGAGTCCACAGAATGGAGgtatatgctttctctatctttgattctaaggatagagtacgtctgttttacggctttcaacattcattgttgttcttggttagtcttctaggtaggaagtactgcgttctaaagggttgtgaaatgcgttcttggaacaaataagtgccgcagtggttcatactgagcactgacgacttatgttttgtag

upper sequence: GRMZM2G177001_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S175_12V6.1 (Physcomitrella patens), 5'ss of exon 6
CTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaaataaaggattcaaaagattttttttcttaatgatgatattatttgacttccatgaaaacatatcacatacccctactac--tcttaacagga
   | || || ||| ||||||||||||| ||||| ||||| || |||||||| |||||| | ||||||  ||||||||| |||||    |    |     ||   | |  || | |     |  | || || ||  |   ||  ||     ||| ||    ||      |||  ||||   | | 
---GATGCGCTTTTTTAAAATATGAAACTAAAGAACAAGCCGTTGCTGCTATTGAAGCTTTGAATGGAGTACACAAAATGGAGgtatacatttgttctatatctgatactttgtatgcacaagagttggtactacgtaggttttatacttgcat-tcgtcgacttaatttaccctcttggtaag-

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|149108797|gb|EE189842.2|EE189842
EST:     AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAG                         GGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG
genomic: AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaa ... tttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG
EST: gi|60400937|gb|DN233744.1|DN233744
EST:     AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAG                         GGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG
genomic: AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaa ... tttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG
EST: gi|149098711|gb|EE184722.2|EE184722
EST:     AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAG                         GGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG
genomic: AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaa ... tttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG
EST: gi|71438922|gb|DR819972.1|DR819972
EST:     AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAG                         GGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG
genomic: AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaa ... tttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG
EST: gi|211051931|gb|FL422541.1|FL422541
EST:     AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAG                         GGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG
genomic: AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaa ... tttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG
EST: gi|89761503|gb|DY689493.1|DY689493
EST:     AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAG                         GGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG
genomic: AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaa ... tttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG
EST: gi|60396221|gb|DN229090.1|DN229090
EST:     AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAG                         GGTTCAAGTGTTCCCTTGGTTGTCA
genomic: AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaa ... tttttgttagGGTTCAAGTGTTCCCTTGGTTGTCA
EST: gi|6020453|gb|AW065381.1|AW065381
EST:     AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAG                         GGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG
genomic: AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaa ... tttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGG
EST: gi|6564129|gb|AW231751.1|AW231751
EST:     AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAG                         GGTTCAAGTGTTCCCTT
genomic: AGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaa ... tttttgttagGGTTCAAGTGTTCCCTT

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), 46 (downstream exon)
Score: 67

CTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaa ... tttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAGGCTCGAAAAGCACAAAAAGCTCAATTCCAGTCTTCTAACATGTTGA


Block sizes: 49 (upstream exon), 35 (downstream exon)
Score: 33

CTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaa ... tttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAGGCTCGAAAAGCACAAAAAGCTCAATTCCAGTCTTCTAACATGTTGA


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 17

CTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaa ... tttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAGGCTCGAAAAGCACAAAAAGCTCAATTCCAGTCTTCTAACATGTTGA


Block sizes: 45 (upstream exon), 39 (downstream exon)
Score: 14

CTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaa ... tttttgttagGGTTCAAGTGTTCCCTTGGTTGTCAAATGGGCTGACACTGAAAAGGAAAGGCAGGCTCGAAAAGCACAAAAAGCTCAATTCCAGTCTTCTAACATGTTGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGGTTGTGCCTTTCTAAAATATGAAACAAAAGAGCAAGCTGTGGCTGCTATAGAAGCTCTAAATGGAACACACAAAATAGAGgttagtagaaataaaggattcaaaagattttttttcttaatgatgatattatttgacttccatgaaaacatatcacatacccctactactcttaacagga

- - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaaagat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccctact