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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgtatttaagtatttttcttaaagaaatgcattcttcctcaacattgcatgctgcgtatttgacgcttctcctctaacttcctattcaatttatttagTAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGTATTTATGCACCTTTCTTGTTGCCGGCGGTGTGTCCTCCTTTGCGTTGTT

Basic information

species Zea mays
transcript GRMZM2G176029_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G176029_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g39260.1 (Oryza sativa), 3'ss of exon 4
---tatgtatttaagtatttttcttaa-agaaatgcattcttcctcaacattgcatgctgcgtatttgacgcttctcctctaacttcctattcaatttatttagTAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGTATTTATGCACCTTTCTTGTTGCCGGCGGTGTGTCCTCCTTTGCGTTGTT
   |  || || ||| ||   | |||| || |   | ||| |  |  | | |   |   | | || || ||| | || ||| ||     ||| ||| | |  ||||||| ||||||||||| | || |||||||| ||||||||| |||| |||||  | ||||||||||||||||| || ||||| || ||||||||||||||
caatcagtgtt-aagaataacttttaacagtagccctttcatgtttcatagtctgtatagtg-atgtg-cgcatatc-tctgaccaatgatttaatatgtacagTAATGCTGATGGGAACTATACTGTATGGTGTCAAGTACACATTTCCGGAGTACATTTGCACCTTTCTTGTTGCTGGGGGTGTATCATCCTTTGCGTTGTT
















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|78118465|gb|DV536850.1|DV536850
EST:     GTGTTGGCAAAATCTTCTAAGATGATTCCTG                         TAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGT
genomic: GTGTTGGCAAAATCTTCTAAGATGATTCCTGgtaagtttac ... atttatttagTAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGT
EST: gi|148931883|gb|EC877348.2|EC877348
EST:     GTGTTGGCAAAATCTTCTAAGATGATTCCTG                         TAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGT
genomic: GTGTTGGCAAAATCTTCTAAGATGATTCCTGgtaagtttac ... atttatttagTAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGT
EST: gi|149005383|gb|EE039935.2|EE039935
EST:     GTGTTGGCAAAATCTTCTAAGATGATTCCTG                         TAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGT
genomic: GTGTTGGCAAAATCTTCTAAGATGATTCCTGgtaagtttac ... atttatttagTAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGT
EST: gi|148977669|gb|EE026096.2|EE026096
EST:     GTGTTTGGCAAA-TCTTCTAAGATGATTCCTG                         TAATGTTGATGGGAACTCTTCTCTAT
genomic: GTGTT-GGCAAAATCTTCTAAGATGATTCCTGgtaagtttac ... atttatttagTAATGTTGATGGGAACTCTTCTCTAT
EST: gi|78080957|gb|DV509369.1|DV509369
EST:     GTGTTGGCAAAATCTTCTAAGATGATTCCTG                         TAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGT
genomic: GTGTTGGCAAAATCTTCTAAGATGATTCCTGgtaagtttac ... atttatttagTAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGT
EST: gi|148985614|gb|EE029715.2|EE029715
EST:     GTGTTGGCAAAATCTTCTAAGATGATTCCTG                         TAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGT
genomic: GTGTTGGCAAAATCTTCTAAGATGATTCCTGgtaagtttac ... atttatttagTAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGT
EST: gi|94479889|gb|EB708847.1|EB708847
EST:     GTGTTGGCAAAACCTTCTAAGATGATTCCTG                         TAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACCACACTTCCAGAG
genomic: GTGTTGGCAAAATCTTCTAAGATGATTCCTGgtaagtttac ... atttatttagTAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTAC-ACACTTCCAGAG
EST: gi|50324993|gb|CO520119.1|CO520119
EST:     GTGTTGGCAAAATCTTCTAAGATGATTCCTG                         TAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGT
genomic: GTGTTGGCAAAATCTTCTAAGATGATTCCTGgtaagtttac ... atttatttagTAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGT
EST: gi|74234865|gb|DT642779.1|DT642779
EST:     GTGTTGGCAAAATCTTCTAAGATGATTCCTG                         TAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGT
genomic: GTGTTGGCAAAATCTTCTAAGATGATTCCTGgtaagtttac ... atttatttagTAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGT
EST: gi|148953372|gb|EE152866.2|EE152866
EST:     GTGTTGGCAAAATCTTCTAAGATGATTCCTG                         TAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGT
genomic: GTGTTGGCAAAATCTTCTAAGATGATTCCTGgtaagtttac ... atttatttagTAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGT
EST: gi|211523327|gb|FL357648.1|FL357648
EST:     GTGTTGGCAAAATCTTCTAAGATGATTCCTG                         TAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTA
genomic: GTGTTGGCAAAATCTTCTAAGATGATTCCTGgtaagtttac ... atttatttagTAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTA
EST: gi|78107092|gb|DV525510.1|DV525510
EST:     GTGTTGGCAAAATCTTCTAAGATGATTCCTG                         TAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGT
genomic: GTGTTGGCAAAATCTTCTAAGATGATTCCTGgtaagtttac ... atttatttagTAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGT
EST: gi|71318369|gb|DR795946.1|DR795946
EST:     GTGTTGGCAAAATCTTCTAAGATGATTCCTG                         TAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGT
genomic: GTGTTGGCAAAATCTTCTAAGATGATTCCTGgtaagtttac ... atttatttagTAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGT
EST: gi|71440454|gb|DR821504.1|DR821504
EST:     GTGTTGGCAAAATCTTCTAAGATGATTCCTG                         TAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGT
genomic: GTGTTGGCAAAATCTTCTAAGATGATTCCTGgtaagtttac ... atttatttagTAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGT

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: 41 (upstream exon), 48 (downstream exon)
Score: 217

GTGTTGGCAAAATCTTCTAAGATGATTCCTGgtaagtttac ... atttatttagTAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGTATTTATGCACCTTTCTTGTTGCCGGCGGTGTGTCCTCCTTTGCGTTGTT


Block sizes: 31 (upstream exon), 49 (downstream exon)
Score: 196

GTGTTGGCAAAATCTTCTAAGATGATTCCTGgtaagtttac ... atttatttagTAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGTATTTATGCACCTTTCTTGTTGCCGGCGGTGTGTCCTCCTTTGCGTTGTT


Block sizes: 31 (upstream exon), 49 (downstream exon)
Score: 246

GTGTTGGCAAAATCTTCTAAGATGATTCCTGgtaagtttac ... atttatttagTAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGTATTTATGCACCTTTCTTGTTGCCGGCGGTGTGTCCTCCTTTGCGTTGTT


Block sizes: 31 (upstream exon), 49 (downstream exon)
Score: 832

GTGTTGGCAAAATCTTCTAAGATGATTCCTGgtaagtttac ... atttatttagTAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGTATTTATGCACCTTTCTTGTTGCCGGCGGTGTGTCCTCCTTTGCGTTGTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgcatgctgcgtatttgacgcttctcctctaacttcctattcaatttatttagTAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGTATTTATGCACCTTTCTTGTTGCCGGCGGTGTGTCCTCCTTTGCGTTGTT
                            ctctaac  putative branch site (score: 832)
                                              tttattt  putative PPT
                                       tattcaatttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgtatttaagtatttttcttaaagaaatgcattcttcctcaacattgcatgctgcgtatttgacgcttctcctctaacttcctattcaatttatttagTAATGTTGATGGGAACTCTTCTCTATGGTGTGAAGTACACACTTCCAGAGTATTTATGCACCTTTCTTGTTGCCGGCGGTGTGTCCTCCTTTGCGTTGTT

tatgtat
- - - - - - - - - - - aaagaaa
- - - - - - - - - - - - - - -tgcattc
- - - - - - - - - - - - - - - - - - - - - - - - - atgctgc