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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaaacaagtctctggagccattaaaataaacatcttcgcgcattctgaaatgccattgtttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGCCACGATTGGTGTCTTGCTTGTTATGGAGACCCTGAGTGCATTCCTTCAC

Basic information

species Zea mays
transcript GRMZM2G058910_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os03g14690.1 (Oryza sativa), 3'ss of exon 17
----------------------gtaagcaaacaagtctctggagcc-attaaaataaacatcttc----gcgcattctgaaatgccattgtttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGCCACGATTGGTGTCTTGCTTGTTATGGAGACCCTGAGTGCATTCCTTCAC
                       |  ||   |    || |    || ||  |  ||  |    ||    || |||| | |  ||||     |||||||||||  |||||  || | ||||  ||   |||  |   ||||||||||| ||| ||  |||||||||||||||||||||||||||| |||||||||||||||
gtaagaactaagaagcctccctctccgcctcctctccttttctccctatctatgtagccgctatctggagctcatttttatgtgcc-----ttcttgtagGTACAACAACATTCTTATCCGCATCGCTGGCATTACCATCTTCATCTGTGCGACAGTTGGTGTCTTGCTTGTTATGGAGACCCTAAGTGCATTCCTTCAC
















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|87156017|gb|DY400806.1|DY400806
EST:     TCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGG                         GTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
genomic: TCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGGgtaagcaaac ... tttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
EST: gi|30031854|gb|CB833705.1|CB833705
EST:     TCTGAGTTGTCCCCTGTATTCTACGAGAAAGTACTAATGACGGCATATGG                         GTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
genomic: TCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGGgtaagcaaac ... tttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
EST: gi|71768892|gb|DR966829.1|DR966829
EST:     TCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGG                         GTTTAACAATGTTTTCATCCTTATTATTGGTGTCG
genomic: TCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGGgtaagcaaac ... tttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGGTGTCG
EST: gi|60396043|gb|DN228913.1|DN228913
EST:     TCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGG                         GTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATC
genomic: TCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGGgtaagcaaac ... tttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATC
EST: gi|60351631|gb|DN218604.1|DN218604
EST:     TCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGG                         GTTTAACAATGTTTTCATCCTTATTATTGGGTGTCGTCATCT
genomic: TCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGGgtaagcaaac ... tttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGG-TGTCGTCATCT
EST: gi|32930576|gb|CF035388.1|CF035388
EST:     TACTAATGACGGCATATGG                         GTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
genomic: TACTAATGACGGCATATGGgtaagcaaac ... tttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
EST: gi|16377225|gb|BI991828.1|BI991828
EST:     TCTGAGTTGTCCACTGTATTCTGCGAGAAAGTACTAATGACGGCATATGG                         GTTTAGCAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
genomic: TCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGGgtaagcaaac ... tttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
EST: gi|60352256|gb|DN219229.1|DN219229
EST:     TCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGG                         GGTTTA-CAATGTTTT
genomic: TCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGGgtaagcaaac ... tttcttgtagG-TTTAACAATGTTTT
EST: gi|26559777|gb|CA832012.1|CA832012
EST:     TCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGG                         GTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
genomic: TCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGGgtaagcaaac ... tttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
EST: gi|87157808|gb|DY402597.1|DY402597
EST:     TCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGG                         GTTTAACAATGTTTTCATCCTTATTATTGGTGTCG
genomic: TCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGGgtaagcaaac ... tttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGGTGTCG
EST: gi|166452986|gb|EG188622.1|EG188622
EST:     CTGTATTCTACGAGAAAGTACTAATGACGGCATATGG                         GTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
genomic: CTGTATTCTACGAGAAAGTACTAATGACGGCATATGGgtaagcaaac ... tttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
EST: gi|78116822|gb|DV535209.1|DV535209
EST:     TGACGGCATATGG                         GTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
genomic: TGACGGCATATGGgtaagcaaac ... tttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
EST: gi|84977217|gb|DW475639.1|DW475639
EST:     TCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGG                         GTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
genomic: TCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGGgtaagcaaac ... tttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
EST: gi|24767313|gb|CA402457.1|CA402457
EST:     TCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGG                         GTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
genomic: TCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGGgtaagcaaac ... tttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
EST: gi|31359889|gb|CD444246.1|CD444246
EST:     TCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGG                         GTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
genomic: TCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGGgtaagcaaac ... tttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
EST: gi|166435894|gb|EG322318.1|EG322318
EST:     TGTATTCTACGAGAAAGTACTAATGACGGCATATGG                         GTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
genomic: TGTATTCTACGAGAAAGTACTAATGACGGCATATGGgtaagcaaac ... tttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
EST: gi|32943091|gb|CF047910.1|CF047910
EST:     ACTAATGACGGCATATGG                         GTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
genomic: ACTAATGACGGCATATGGgtaagcaaac ... tttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
EST: gi|22935980|gb|BU572255.1|BU572255
EST:     TCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGG                         GTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC
genomic: TCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGGgtaagcaaac ... tttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGC

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: 106

TCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGGgtaagcaaac ... tttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGCCACGATTGGTGTCTTGCTTGTTATGGAGACCCTGAGTGCATTCCTTCAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 203

TCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGGgtaagcaaac ... tttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGCCACGATTGGTGTCTTGCTTGTTATGGAGACCCTGAGTGCATTCCTTCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 155

TCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGGgtaagcaaac ... tttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGCCACGATTGGTGTCTTGCTTGTTATGGAGACCCTGAGTGCATTCCTTCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 122

TCTTGCACACTCTGAGTTGTCCACTGTATTCTACGAGAAAGTACTAATGACGGCATATGGgtaagcaaac ... tttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGCCACGATTGGTGTCTTGCTTGTTATGGAGACCCTGAGTGCATTCCTTCAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggagccattaaaataaacatcttcgcgcattctgaaatgccattgtttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGCCACGATTGGTGTCTTGCTTGTTATGGAGACCCTGAGTGCATTCCTTCAC
                                          ttgtttctt  CT-rich tract
      attaaaataaacatct  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaaacaagtctctggagccattaaaataaacatcttcgcgcattctgaaatgccattgtttcttgtagGTTTAACAATGTTTTCATCCTTATTATTGGTGTCGTCATCTTCATCTTTGCCACGATTGGTGTCTTGCTTGTTATGGAGACCCTGAGTGCATTCCTTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA