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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatttgttgtcaaaggaaaccatatatttaatgacaggatttttgatgttttcctattaaatttgacttgattcaaaaggtcgtatacatcttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCTACTCAGCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATC

Basic information

species Zea mays
transcript GRMZM2G154890_T03
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|34391377|gb|CF384605.1|CF384605
EST:     GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCA                         ATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
genomic: GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCAgtgagtaact ... cttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
EST: gi|91874746|gb|EB404703.1|EB404703
EST:     GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCA                         ATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
genomic: GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCAgtgagtaact ... cttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
EST: gi|89755818|gb|DY686096.1|DY686096
EST:     GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCA                         ATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
genomic: GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCAgtgagtaact ... cttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
EST: gi|78112616|gb|DV531010.1|DV531010
EST:     GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCA                         ATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
genomic: GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCAgtgagtaact ... cttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
EST: gi|50339681|gb|CO534807.1|CO534807
EST:     GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGA---A                         -TTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
genomic: GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCAgtgagtaact ... cttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
EST: gi|78114767|gb|DV533155.1|DV533155
EST:     GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCA                         ATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
genomic: GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCAgtgagtaact ... cttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
EST: gi|211104769|gb|FL158955.1|FL158955
EST:     GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCA                         ATTTGGTGAATCCCCC-TCCCCTCTCACGCTCCACCACTGATCATGGGGCT
genomic: GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCAgtgagtaact ... cttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
EST: gi|91875540|gb|EB405497.1|EB405497
EST:     GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCA                         ATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
genomic: GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCAgtgagtaact ... cttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
EST: gi|60337602|gb|DN204575.1|DN204575
EST:     GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCA                         ATTTGGTGAAT-CCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
genomic: GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCAgtgagtaact ... cttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
EST: gi|50335743|gb|CO530869.1|CO530869
EST:     GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCA                         ATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
genomic: GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCAgtgagtaact ... cttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
EST: gi|76016499|gb|DT943669.1|DT943669
EST:     GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCA                         ATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
genomic: GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCAgtgagtaact ... cttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
EST: gi|86469538|gb|DY235908.1|DY235908
EST:     GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCA                         ATTTGGAGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCGTGGGGCT
genomic: GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCAgtgagtaact ... cttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
EST: gi|89248462|gb|DY620248.1|DY620248
EST:     GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCA                         ATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
genomic: GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCAgtgagtaact ... cttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
EST: gi|101390933|gb|EB817402.1|EB817402
EST:     GTCGCTCCCAGCTGGCCATCCTCTCCGCCCCCTTGTTGCACAGCGAGTCA                         ATTTGGTGAAT
genomic: GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCAgtgagtaact ... cttttatcagATTTGGTGAAT
EST: gi|76286526|gb|DV026094.1|DV026094
EST:     GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCA                         ATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
genomic: GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCAgtgagtaact ... cttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
EST: gi|211102307|gb|FL158954.1|FL158954
EST:     GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCA                         ATTTGGTGAATCCCCC-TCCCCTCTCACGCTCCACCACTGATCATGGGGGC
genomic: GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCAgtgagtaact ... cttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGG-C
EST: gi|74239326|gb|DT647240.1|DT647240
EST:     GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCA                         ATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
genomic: GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCAgtgagtaact ... cttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
EST: gi|211102303|gb|FL158950.1|FL158950
EST:     GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCA                         ATTTGGTGAATCCCCC-TCCCCTCTCACGCTCCACCACTGATCATGGGGCT
genomic: GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCAgtgagtaact ... cttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
EST: gi|71318964|gb|DR796231.1|DR796231
EST:     GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCA                         ATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
genomic: GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCAgtgagtaact ... cttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
EST: gi|78082479|gb|DV510891.1|DV510891
EST:     GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCA                         ATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT
genomic: GTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCAgtgagtaact ... cttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCT

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: 450

AGGGCTGCTGGTGCCTGCTCTTGTCCTCCGGCACAGCGCAGGGTGTCGGGGTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCAgtgagtaact ... cttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCTACTCAGCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 126

AGGGCTGCTGGTGCCTGCTCTTGTCCTCCGGCACAGCGCAGGGTGTCGGGGTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCAgtgagtaact ... cttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCTACTCAGCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 149

AGGGCTGCTGGTGCCTGCTCTTGTCCTCCGGCACAGCGCAGGGTGTCGGGGTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCAgtgagtaact ... cttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCTACTCAGCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 223

AGGGCTGCTGGTGCCTGCTCTTGTCCTCCGGCACAGCGCAGGGTGTCGGGGTCGCTCCCAGCTGGCCATCCTCTCGGCCCCCTTGTTGCACAGCGAGTCAgtgagtaact ... cttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCTACTCAGCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttttcctattaaatttgacttgattcaaaaggtcgtatacatcttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCTACTCAGCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATC
                                            tcttttatc  CT-rich tract
         tattaaatttgactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatttgttgtcaaaggaaaccatatatttaatgacaggatttttgatgttttcctattaaatttgacttgattcaaaaggtcgtatacatcttttatcagATTTGGTGAATCCCCCCTCCCCTCTCACGCTCCACCACTGATCATGGGGCTACTCAGCATTATCCGCAAGATCAAGCGCAAGGAGAAGGAGATGCGCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG