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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattatcaagaacaaacaaacaatcaaacaaaaaagaagaagaactttaccttagttatttaaaactgtttcttcactgggcacctggcctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG

Basic information

species Zea mays
transcript GRMZM2G146463_T03
intron # 7
splice site 3'
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:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|78108215|gb|DV526633.1|DV526633
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|71428787|gb|DR809837.1|DR809837
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|50334852|gb|CO529978.1|CO529978
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|71443418|gb|DR824468.1|DR824468
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|148973153|gb|EE024223.2|EE024223
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|26560002|gb|CA832237.1|CA832237
EST:     TGGATCTCTGGGCTACGAAGAGAAGGATGCTAAAAAGGTTGGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: TGGATCTCTGGGCTACGAGGAGAGGGATGCT-AAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|91875282|gb|EB405239.1|EB405239
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|91054335|gb|EB164753.1|EB164753
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|87157241|gb|DY402030.1|DY402030
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|89763957|gb|DY690934.1|DY690934
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAN
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|29947680|gb|CB816781.1|CB816781
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|71443280|gb|DR824330.1|DR824330
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|74238712|gb|DT646626.1|DT646626
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|149009677|gb|EE041609.2|EE041609
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|78113279|gb|DV531671.1|DV531671
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|148940241|gb|EC885013.2|EC885013
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|23199550|gb|BU582115.1|BU582115
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|78075209|gb|DV503643.1|DV503643
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|89250668|gb|DY622454.1|DY622454
EST:     TGGATCTCTGGGCTACCAGGAAGAGG-ATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTCCCTGAAGTATGACAACTGC
genomic: TGGATCTCTGGGCTACGAGGA-GAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGC
EST: gi|71318127|gb|DR795825.1|DR795825
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|76011884|gb|DT939054.1|DT939054
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|71442888|gb|DR823938.1|DR823938
EST:     TGGATCCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCCTGAAGTAGGACAACTGC-ACAGAGACGGCACCGCCTG
genomic: TGGATC-TCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACC-TGAAGTATGACAACTGCTACAGAGACGGCAC-GCCTG
EST: gi|26559550|gb|CA831785.1|CA831785
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|78088431|gb|DV516824.1|DV516824
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|149013904|gb|EE043402.2|EE043402
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|78110547|gb|DV528957.1|DV528957
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|87156914|gb|DY401703.1|DY401703
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|71431665|gb|DR812715.1|DR812715
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|149055656|gb|EE156361.2|EE156361
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|71442889|gb|DR823939.1|DR823939
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAN
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
EST: gi|76930345|gb|DV172346.1|DV172346
EST:     CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGG                         GGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA
genomic: CTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAA

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 3 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 31

GACAAGAACTTGCAGCAACAGGATGCCTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG


Block sizes: 48 (upstream exon), 27 (downstream exon)
Score: 13

GACAAGAACTTGCAGCAACAGGATGCCTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG


Block sizes: 47 (upstream exon), 32 (downstream exon)
Score: 7

GACAAGAACTTGCAGCAACAGGATGCCTGGATCTCTGGGCTACGAGGAGAGGGATGCTAAGATGTTTGCGTCATGGgtacatacta ... ctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttaccttagttatttaaaactgtttcttcactgggcacctggcctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG
                                            cctgtct  CT-rich tract
       ttagttatttaaaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttattatcaagaacaaacaaacaatcaaacaaaaaagaagaagaactttaccttagttatttaaaactgtttcttcactgggcacctggcctgtctgcagGGCGTTGACTACCTGAAGTATGACAACTGCTACAGAGACGGCACGCCTGAAACCGTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG