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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcctcctccactgccttcctgtttttaaacagggagaggggtggccctccgctagccgcacggatcctctccatcctcaccgtttcttcctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAG

Basic information

species Zea mays
transcript GRMZM2G115939_T01
intron # 1
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|211132803|gb|FL366559.1|FL366559
EST:     AAAAACCGTTCCCCTCTGCCGTTTCCGG                         GTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
genomic: AAAAACCGTTCCCCTCTGCCGTTTCCGGgtgagtctac ... ctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
EST: gi|211373002|gb|FL342998.1|FL342998
EST:     CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGG                         GTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
genomic: CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGGgtgagtctac ... ctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
EST: gi|9028438|gb|BE238583.1|BE238583
EST:     CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGG                         GTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
genomic: CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGGgtgagtctac ... ctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
EST: gi|211398788|gb|FL318386.1|FL318386
EST:     CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGG                         GTCTCTTAGTGCAAGCAAGGAAGCCGTTCCACGCTCCTCCAGCGAGCTCCG
genomic: CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGGgtgagtctac ... ctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
EST: gi|32915063|gb|CF019875.1|CF019875
EST:     CTCGTCCTCTCGCCCACCGGCGAAAAACAGTTCCCCTCTGCCGTTTCCGG                         GTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
genomic: CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGGgtgagtctac ... ctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
EST: gi|211259767|gb|FL311710.1|FL311710
EST:     CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGG                         GTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
genomic: CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGGgtgagtctac ... ctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
EST: gi|78077789|gb|DV506218.1|DV506218
EST:     CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGG                         GTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
genomic: CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGGgtgagtctac ... ctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
EST: gi|24462527|gb|BM660058.1|BM660058
EST:     CTCGTCCTCTCGCCCACCGGCGAAAAACAGTTCCCCTCTGCCGTTTCCGG                         GTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
genomic: CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGGgtgagtctac ... ctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
EST: gi|211350032|gb|FL354315.1|FL354315
EST:     CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGG                         GTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
genomic: CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGGgtgagtctac ... ctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
EST: gi|211320075|gb|FL327296.1|FL327296
EST:     TCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGG                         GTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
genomic: TCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGGgtgagtctac ... ctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
EST: gi|211153912|gb|FL325451.1|FL325451
EST:     CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGG                         GTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
genomic: CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGGgtgagtctac ... ctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
EST: gi|50326390|gb|CO521516.1|CO521516
EST:     CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGG                         GTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
genomic: CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGGgtgagtctac ... ctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
EST: gi|211407585|gb|FL360124.1|FL360124
EST:     CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGG                         GTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
genomic: CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGGgtgagtctac ... ctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
EST: gi|211021365|gb|FL343612.1|FL343612
EST:     CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGG                         GTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
genomic: CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGGgtgagtctac ... ctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
EST: gi|211162273|gb|FL345451.1|FL345451
EST:     CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGG                         GTCTCTTAGTGCAAGCAAGGAGGCSGTTCCACGCTCCTCCAGCGAGCTCCG
genomic: CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGGgtgagtctac ... ctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
EST: gi|211505256|gb|FL326165.1|FL326165
EST:     CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGG                         GTCTCTTAGTGCAAGCAAGGAAGCCGTTCCACGCTCCTCCAGCGAGCTCCG
genomic: CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGGgtgagtctac ... ctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
EST: gi|211472923|gb|FL342170.1|FL342170
EST:     CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGG                         GTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
genomic: CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGGgtgagtctac ... ctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
EST: gi|211118985|gb|FL350356.1|FL350356
EST:     CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGG                         GTMTCTTAGTGCAAGNAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
genomic: CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGGgtgagtctac ... ctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
EST: gi|211090799|gb|FL312054.1|FL312054
EST:     CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGG                         GTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG
genomic: CTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGGgtgagtctac ... ctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCG

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: 48 (upstream exon), 42 (downstream exon)
Score: 127

GACCGACGCACGCGGACGCCTCCGTTCGTACTCCCGCCGCCTGTAGAGGCCTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGGgtgagtctac ... ctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 92

GACCGACGCACGCGGACGCCTCCGTTCGTACTCCCGCCGCCTGTAGAGGCCTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGGgtgagtctac ... ctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 93

GACCGACGCACGCGGACGCCTCCGTTCGTACTCCCGCCGCCTGTAGAGGCCTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGGgtgagtctac ... ctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 115

GACCGACGCACGCGGACGCCTCCGTTCGTACTCCCGCCGCCTGTAGAGGCCTCGTCCTCTCGCCCACCGGCGAAAAACCGTTCCCCTCTGCCGTTTCCGGgtgagtctac ... ctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctccgctagccgcacggatcctctccatcctcaccgtttcttcctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAG
                             tcctcac  putative branch site (score: 115)
                    tcctctccatcctcac  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcctcctccactgccttcctgtttttaaacagggagaggggtggccctccgctagccgcacggatcctctccatcctcaccgtttcttcctctctgcagGTCTCTTAGTGCAAGCAAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - -cctccac
- - - - - - tgccttc
- - - - - - - - - -ctgtttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gccgcac