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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCTAGAGACTCTAAGCAAAAATTGTGGGGATATTGTTCATCAACAGATTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgatgataatacctgtttgatgtactgttttttctgcattcatgtgcttctatgtttgatatttgtttctacttttcag

Basic information

species Zea mays
transcript GRMZM2G151050_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151050_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os11g09329.2 (Oryza sativa), 5'ss of exon 4
GTGCTAGAGACTCTAAGCAAAAATTGTGGGGATATTGTTCATCAACAGATTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgatgataatacctg--tttgatgtactgttttttctgcattcatgtgc-ttctatgtttgatatttgtttctacttttcag-----------------
||||||||||||||||||||||| ||||||||| ||||| | || || ||  ||||||| |||||||| |||||||||||||||||||||||||||||||||| ||| ||||     ||   ||  |   | || ||    |  |     ||  |  ||  ||  ||  |   | |    ||                 
GTGCTAGAGACTCTAAGCAAAAACTGTGGGGATGTTGTTTACCAGCAAATCATTGAGCGAGACATATTAAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgaggattatactcacattcagtggccaactattgctttcctagttcctgttagaacttcaatggttactctcattgagaagaggatggcactcggagt

upper sequence: GRMZM2G151050_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA06G12570.1 (Glycine max), 5'ss of exon 4
GTGCTAGAGACTCTAAGCAAAAATTGTGGGGATATTGTTCATCAACAGATTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgatgataatacctgt---ttgatgtactgttttt--tctgcattca-----tgtgcttctatgtttgatatttgtttctacttttcag------------------------
|| || ||||| || || ||||||||||| || | |||   ||| ||||| |||||||| || || ||   |||||||||||||||||||||||| |||||  | ||      ||    || || |    |||||  ||| | |||      |||  ||  | ||   | | ||  || | | || | |                        
GTACTGGAGACCCTTAGTAAAAATTGTGGTGAAAGTGTATTTCAGCAGATCGTTGAGCGAGATATCTTACATGAAATGGTTAAGATAGTAAAGAAGAAGgtatttattggttttgccactttatatttcatttttaatcttccttctgtaactgtatttggaagtggaagactttcttatccattgctgccttcttttgatctgattgtacag
















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|148954553|gb|EC899991.2|EC899991
EST:     TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAG                         CCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
genomic: TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgatgataa ... tacttttcagCCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
EST: gi|149100088|gb|EE186140.2|EE186140
EST:     TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAG                         CCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
genomic: TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgatgataa ... tacttttcagCCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
EST: gi|91871540|gb|EB401497.1|EB401497
EST:     TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAG                         CCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
genomic: TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgatgataa ... tacttttcagCCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
EST: gi|93012296|gb|EB637816.1|EB637816
EST:     TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAG                         CCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
genomic: TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgatgataa ... tacttttcagCCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
EST: gi|89247370|gb|DY619156.1|DY619156
EST:     TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAG                         CCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
genomic: TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgatgataa ... tacttttcagCCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
EST: gi|29168003|gb|CB411263.1|CB411263
EST:     TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAG                         CCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
genomic: TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgatgataa ... tacttttcagCCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
EST: gi|33942576|gb|CF349176.1|CF349176
EST:     TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAG                         CCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATCGACACATGGCAA
genomic: TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgatgataa ... tacttttcagCCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
EST: gi|91876199|gb|EB406156.1|EB406156
EST:     TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAG                         CCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
genomic: TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgatgataa ... tacttttcagCCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
EST: gi|211038878|gb|FL017021.1|FL017021
EST:     TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAG                         C-AGACTTGAGCGTCCGAGAGA-GATATTGAGTTTGATTGACACA
genomic: TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgatgataa ... tacttttcagCCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACA
EST: gi|74233431|gb|DT641345.1|DT641345
EST:     TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAG                         CCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
genomic: TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgatgataa ... tacttttcagCCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
EST: gi|28873357|gb|CB329357.1|CB329357
EST:     TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAG                         CCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
genomic: TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgatgataa ... tacttttcagCCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
EST: gi|93013764|gb|EB639284.1|EB639284
EST:     TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAG                         CCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
genomic: TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgatgataa ... tacttttcagCCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
EST: gi|148962190|gb|EE013005.2|EE013005
EST:     TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAG                         CCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
genomic: TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgatgataa ... tacttttcagCCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
EST: gi|149106511|gb|EE188403.2|EE188403
EST:     TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAG                         CCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
genomic: TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgatgataa ... tacttttcagCCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
EST: gi|31909129|gb|CD650764.1|CD650764
EST:     TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAG                         CCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
genomic: TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgatgataa ... tacttttcagCCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
EST: gi|71449169|gb|DR830219.1|DR830219
EST:     TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAG                         CCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA
genomic: TTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgatgataa ... tacttttcagCCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAA

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: 78

GTGCTAGAGACTCTAAGCAAAAATTGTGGGGATATTGTTCATCAACAGATTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgatgataa ... tacttttcagCCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAAGTGGCTTTTGGAGGTCCATCTGGAAAATATCGACAGTATCATGCGGCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 127

GTGCTAGAGACTCTAAGCAAAAATTGTGGGGATATTGTTCATCAACAGATTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgatgataa ... tacttttcagCCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAAGTGGCTTTTGGAGGTCCATCTGGAAAATATCGACAGTATCATGCGGCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 143

GTGCTAGAGACTCTAAGCAAAAATTGTGGGGATATTGTTCATCAACAGATTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgatgataa ... tacttttcagCCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAAGTGGCTTTTGGAGGTCCATCTGGAAAATATCGACAGTATCATGCGGCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 138

GTGCTAGAGACTCTAAGCAAAAATTGTGGGGATATTGTTCATCAACAGATTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgatgataa ... tacttttcagCCAGACTTGAGCGTCCGAGAGAAGATATTGAGTTTGATTGACACATGGCAAGTGGCTTTTGGAGGTCCATCTGGAAAATATCGACAGTATCATGCGGCTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCTAGAGACTCTAAGCAAAAATTGTGGGGATATTGTTCATCAACAGATTGTTGAGCGCGACATATTGAGTGAAATGGTTAAGATAGTAAAGAAAAAGgtgatgataatacctgtttgatgtactgttttttctgcattcatgtgcttctatgtttgatatttgtttctacttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA