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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatagtctagactaccaatataatctagattataacccagattatataatctataagctgaaacaaacatgcccttaactcctgtgatgcctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCGGCACCCATTGCAGCTGCTTCGCCTTTCTCAAGATGAGATGAGATGTAGC

Basic information

species Zea mays
transcript GRMZM2G044137_T01
intron # 4
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|76013092|gb|DT940262.1|DT940262
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|211065202|gb|FL140848.1|FL140848
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|31406277|gb|CD485009.1|CD485009
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCC
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACT-CGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCC
EST: gi|91049094|gb|EB159512.1|EB159512
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|60394375|gb|DN227245.1|DN227245
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|60355557|gb|DN222530.1|DN222530
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|67023955|gb|CO452704.1|CO452704
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|149089950|gb|EE179239.2|EE179239
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|32914523|gb|CF019335.1|CF019335
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCC
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCC
EST: gi|32865422|gb|CF005104.1|CF005104
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|60338522|gb|DN205495.1|DN205495
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|15100298|gb|BI396089.1|BI396089
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATTATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|9824981|gb|BE575183.1|BE575183
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCA
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCA
EST: gi|211067924|gb|FL140850.1|FL140850
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|89251915|gb|DY623701.1|DY623701
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|27575973|gb|CA998667.1|CA998667
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|31441073|gb|CD510504.1|CD510504
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|60357629|gb|DN224602.1|DN224602
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATTATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|211065201|gb|FL140847.1|FL140847
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|71299866|gb|DR785955.1|DR785955
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|60341097|gb|DN208070.1|DN208070
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
EST: gi|60347030|gb|DN214003.1|DN214003
EST:     TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG                         GTGACTCGGACATTATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG
genomic: TGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCG

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: 1105

ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCGGCACCCATTGCAGCTGCTTCGCCTTTCTCAAGATGAGATGAGATGTAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 803

ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCGGCACCCATTGCAGCTGCTTCGCCTTTCTCAAGATGAGATGAGATGTAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 730

ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCGGCACCCATTGCAGCTGCTTCGCCTTTCTCAAGATGAGATGAGATGTAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 596

ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAGgttcgttcct ... cctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCGGCACCCATTGCAGCTGCTTCGCCTTTCTCAAGATGAGATGAGATGTAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataatctataagctgaaacaaacatgcccttaactcctgtgatgcctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCGGCACCCATTGCAGCTGCTTCGCCTTTCTCAAGATGAGATGAGATGTAGC
                            ccttaac  putative branch site (score: 596)
                                             cctgctcc  putative PPT
     tctataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagtctagactaccaatataatctagattataacccagattatataatctataagctgaaacaaacatgcccttaactcctgtgatgcctgctccagGTGACTCGGACATCATCAGTACCACCCCTGGCACCCAGTGAGCCAGCCCCGGCACCCATTGCAGCTGCTTCGCCTTTCTCAAGATGAGATGAGATGTAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG