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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttctgttcacctgcacattcagttcgtgtagcatttcttcttgtttccatgtaccagccgtcgattgtgatgcag

Basic information

species Zea mays
transcript GRMZM2G146463_T03
intron # 8
splice site 5'
intron type U2

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|22935898|gb|BU572173.1|BU572173
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|78108215|gb|DV526633.1|DV526633
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|71428787|gb|DR809837.1|DR809837
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCCATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|50334852|gb|CO529978.1|CO529978
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|22472587|gb|BU037067.1|BU037067
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|71443418|gb|DR824468.1|DR824468
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|148973153|gb|EE024223.2|EE024223
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|26560002|gb|CA832237.1|CA832237
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|91875282|gb|EB405239.1|EB405239
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|60357458|gb|DN224431.1|DN224431
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|91054335|gb|EB164753.1|EB164753
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|87157241|gb|DY402030.1|DY402030
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|89763957|gb|DY690934.1|DY690934
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGANACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|71443280|gb|DR824330.1|DR824330
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|74238712|gb|DT646626.1|DT646626
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCCGCC-AATCTTCT
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCC-GCCCAATCTTCT
EST: gi|149009677|gb|EE041609.2|EE041609
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|78113279|gb|DV531671.1|DV531671
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|148940241|gb|EC885013.2|EC885013
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|23199550|gb|BU582115.1|BU582115
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|78075209|gb|DV503643.1|DV503643
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|71318127|gb|DR795825.1|DR795825
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|76011884|gb|DT939054.1|DT939054
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|26559550|gb|CA831785.1|CA831785
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|78088431|gb|DV516824.1|DV516824
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|149013904|gb|EE043402.2|EE043402
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|78110547|gb|DV528957.1|DV528957
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|87156914|gb|DY401703.1|DY401703
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|71431665|gb|DR812715.1|DR812715
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|149055656|gb|EE156361.2|EE156361
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|71442889|gb|DR823939.1|DR823939
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGANACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
EST: gi|76930345|gb|DV172346.1|DV172346
EST:     TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG                         GTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA
genomic: TACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTA

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: 37 (upstream exon), 47 (downstream exon)
Score: 23

GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 18

GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG


Block sizes: 46 (upstream exon), 32 (downstream exon)
Score: 7

GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG


Block sizes: 25 (upstream exon), 31 (downstream exon)
Score: 2

GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttc ... tgtgatgcagGTTTGGGCGCATGTCCCGAGCGCTGGTGAACTCTGGCCGCCCAATCTTCTACTCGCTTTGCGAATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAGgtgcggtttctgttcacctgcacattcagttcgtgtagcatttcttcttgtttccatgtaccagccgtcgattgtgatgcag

- - - - - - CTGAAG