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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAAGTCAATTGCTTATGTTGGCCGTGAGGGAGAAGGAATTATAGGTGCTATTGCTATATCAGATATTTTACGAGAAGATGCAAACTTAACTGTGGAGAGgtaatttctggagtgattatttgcattttaaccgtgttttcttggtacagatccatttctcttatcaaatagggttatcttcagaagcatggtgaaatgc...

Basic information

species Zea mays
transcript GRMZM5G855347_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G855347_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g08070.1 (Oryza sativa), 5'ss of exon 12
CGAAGTCAATTGCTTATGTTGGCCGTGAGGGAGAAGGAATTATAGGTGCTATTGCTATATCAGATATTTTACGAGAAGATGCAAACTTAACTGTGGAGAGgtaatttctggag----tgattatttgcattttaaccgtgt-tttcttggtacagatccatttctcttatcaaatagggttatcttcagaagcatggtgaaatgc
| || ||||||||||||||||||||||||||||||||||| ||||||||||| ||| |||||||| || | || || ||||| ||   ||| ||||| ||||| || ||| ||        | | || || || | || || | || || |  |    |||   ||   ||||| |    |  ||   |   |||  | | |   
CAAAATCAATTGCTTATGTTGGCCGTGAGGGAGAAGGAATAATAGGTGCTATCGCTGTATCAGATGTTCTGCGTGATGATGCCAAAGCAACCGTGGACAGgtatttactgcagataccatctgtctgtatatttatcgagtgtctcctgcttta---tcataattca-gtcaaacatatcttcctaacgggacatattcagaat-
















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|60353203|gb|DN220176.1|DN220176
EST:     ATTGCTATATCAGATATTTTACGAGAAGATGCAAACTTAACTGTGGAGAG                         GTTGCAGCAGGAAAGCATTACAACGTTCCTGCTGTCAGGGGATAGGGGAGA
genomic: ATTGCTATATCAGATATTTTACGAGAAGATGCAAACTTAACTGTGGAGAGgtaatttctg ... taatcatcagGTTGCAGCAGGAAAGCATTACAACGTTCCTGCTGTCAGGGGATAGGGGAGA
EST: gi|166429613|gb|EG299227.1|EG299227
EST:     TTGCTATATCAGATATTTTACGAGAAGATGCAAACTTAACTGTGGAGAG                         GTTGCAGCAGGAAAGCATTACAACGTTCCTGCTGTCAGGGGATAGGGGAG
genomic: TTGCTATATCAGATATTTTACGAGAAGATGCAAACTTAACTGTGGAGAGgtaatttctg ... taatcatcagGTTGCAGCAGGAAAGCATTACAACGTTCCTGCTGTCAGGGGATAGGGGAG
EST: gi|74245969|gb|DT653883.1|DT653883
EST:     ATTGCTATATCAGATATTTTACGAGAAGATGCAAACTTAACTGTGGAGAG                         GTTGCAGCAGGAAAGCATTACAACGTTCCTGCTGTCANGGGATAGGGGAGA
genomic: ATTGCTATATCAGATATTTTACGAGAAGATGCAAACTTAACTGTGGAGAGgtaatttctg ... taatcatcagGTTGCAGCAGGAAAGCATTACAACGTTCCTGCTGTCAGGGGATAGGGGAGA
EST: gi|5847391|gb|AW000470.1|AW000470
EST:     ATTGCTATATCAGATATTTTCCGAGAAGATGCAAACTTAACTGTGGAGAG                         GTTGCAGCAGGAAAGCATTACAACGTTCCTGCTGTCAGGGGATAGGGGAGA
genomic: ATTGCTATATCAGATATTTTACGAGAAGATGCAAACTTAACTGTGGAGAGgtaatttctg ... taatcatcagGTTGCAGCAGGAAAGCATTACAACGTTCCTGCTGTCAGGGGATAGGGGAGA
EST: gi|60336693|gb|DN203666.1|DN203666
EST:     ATTGCTATATCAGATATTTTACGAGAAGATGCAAACTTAACTGTGGAGAG                         GTTGCAGCAGGAAAGCATTACAACGTTCCTGCTGTCAGGGGATAGGGGAGA
genomic: ATTGCTATATCAGATATTTTACGAGAAGATGCAAACTTAACTGTGGAGAGgtaatttctg ... taatcatcagGTTGCAGCAGGAAAGCATTACAACGTTCCTGCTGTCAGGGGATAGGGGAGA
EST: gi|60358034|gb|DN225007.1|DN225007
EST:     ATTGCTATATCAGATATTTTACGAGAAGATGCAAACTTAACTGTGGAGAG                         GTTGCAGCAGGAAAGCATTACAACGTTCCTGCTGTCAGGGGATAGGGGAGA
genomic: ATTGCTATATCAGATATTTTACGAGAAGATGCAAACTTAACTGTGGAGAGgtaatttctg ... taatcatcagGTTGCAGCAGGAAAGCATTACAACGTTCCTGCTGTCAGGGGATAGGGGAGA

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: 48 (upstream exon), 49 (downstream exon)
Score: 672

CGAAGTCAATTGCTTATGTTGGCCGTGAGGGAGAAGGAATTATAGGTGCTATTGCTATATCAGATATTTTACGAGAAGATGCAAACTTAACTGTGGAGAGgtaatttctg ... taatcatcagGTTGCAGCAGGAAAGCATTACAACGTTCCTGCTGTCAGGGGATAGGGGAGAAGCAGTGACAAGCATTGGGAGGACCATTGGAATCAGGAATGAAAACATA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 275

CGAAGTCAATTGCTTATGTTGGCCGTGAGGGAGAAGGAATTATAGGTGCTATTGCTATATCAGATATTTTACGAGAAGATGCAAACTTAACTGTGGAGAGgtaatttctg ... taatcatcagGTTGCAGCAGGAAAGCATTACAACGTTCCTGCTGTCAGGGGATAGGGGAGAAGCAGTGACAAGCATTGGGAGGACCATTGGAATCAGGAATGAAAACATA


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 182

CGAAGTCAATTGCTTATGTTGGCCGTGAGGGAGAAGGAATTATAGGTGCTATTGCTATATCAGATATTTTACGAGAAGATGCAAACTTAACTGTGGAGAGgtaatttctg ... taatcatcagGTTGCAGCAGGAAAGCATTACAACGTTCCTGCTGTCAGGGGATAGGGGAGAAGCAGTGACAAGCATTGGGAGGACCATTGGAATCAGGAATGAAAACATA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 397

CGAAGTCAATTGCTTATGTTGGCCGTGAGGGAGAAGGAATTATAGGTGCTATTGCTATATCAGATATTTTACGAGAAGATGCAAACTTAACTGTGGAGAGgtaatttctg ... taatcatcagGTTGCAGCAGGAAAGCATTACAACGTTCCTGCTGTCAGGGGATAGGGGAGAAGCAGTGACAAGCATTGGGAGGACCATTGGAATCAGGAATGAAAACATA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAAGTCAATTGCTTATGTTGGCCGTGAGGGAGAAGGAATTATAGGTGCTATTGCTATATCAGATATTTTACGAGAAGATGCAAACTTAACTGTGGAGAGgtaatttctggagtgattatttgcattttaaccgtgttttcttggtacagatccatttctcttatcaaatagggttatcttcagaagcatggtgaaatgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA