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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagactattgtcctatgtgattactgttccccatatggttttttcatgcacattatttttatgattattttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAAGGCGCTTGGATGGGAAGCCTTCCAAAGATAAAGATGTGCTAGCCTCTTC

Basic information

species Zea mays
transcript GRMZM2G037185_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037185_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g08480.1 (Oryza sativa), 3'ss of exon 8
gtaagactattgtcctatgtgattactgttc----------cccatatggttttttcatgcacattatttttatgattat---tttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAAGGCGCTTGGATGGGAAGCCTTCCAAAGATAAAGATGTGCTAGCCTCTTC
|||    | |  |  |      ||| || ||          |||  |   | | ||  ||  ||||| ||| |   ||||   |||| |||| |   ||||||||||||||||||||||||||||||| |||||  | || |||||  ||||||||||| || | |||||||| |||||   ||| || ||
gtagatttctctttatgccccgttattgatcttgatctcttccctcagattctcttgctgttcattactttaagatttattcgttttgcagAAGAGGCAGCTGAAGAAGAACCAAAGTTCATCCCCTTTACTGGACCTGGGAGGCGTCTGGATGGGAAGGCTCCTAAAGATAAGGATGTATCAGCTTCATC
















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|29543953|gb|CB604333.1|CB604333
EST:     ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCG                         ACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
genomic: ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
EST: gi|71332942|gb|DR803495.1|DR803495
EST:     ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCG                         ACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
genomic: ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
EST: gi|211433047|gb|FL005816.1|FL005816
EST:     ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCG                         ACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
genomic: ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
EST: gi|93281779|gb|EB674043.1|EB674043
EST:     CCTGAGCCAGTAAAACCTGCTGTTCCCTGCA-GCACGGAGCCTGGTACCG                         ACGTTTCAGCTGAAGAAGA-CCAAAGTTCATCCCCT-CACTGGTTCAGGAA
genomic: CCTGAGCCAGTAAAACCTGCTGTTCC-TGCAAGCACGGAGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
EST: gi|23357513|gb|BU645162.1|BU645162
EST:     ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCG                         ACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
genomic: ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
EST: gi|148985612|gb|EE029713.2|EE029713
EST:     ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCG                         ACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
genomic: ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
EST: gi|4826177|gb|AI667805.1|AI667805
EST:     CGGAGCCTGGTACCG                         ACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
genomic: CGGAGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
EST: gi|93281778|gb|EB674042.1|EB674042
EST:     ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCG                         ACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
genomic: ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
EST: gi|40334979|gb|CK369049.1|CK369049
EST:     ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCG                         ACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
genomic: ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
EST: gi|50332346|gb|CO527472.1|CO527472
EST:     GCAAGCACGGAGCCTGGTACCG                         ACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
genomic: GCAAGCACGGAGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
EST: gi|149106744|gb|EE188640.2|EE188640
EST:     ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCG                         ACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
genomic: ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
EST: gi|37382129|gb|CF627990.1|CF627990
EST:     ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCG                         ACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
genomic: ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
EST: gi|116817619|gb|EC860494.1|EC860494
EST:     ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCG                         ACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
genomic: ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
EST: gi|7227799|gb|AW566440.1|AW566440
EST:     ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCG                         ACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
genomic: ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
EST: gi|4775894|gb|AI664897.1|AI664897
EST:     AGCCTGGTACCG                         ACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
genomic: AGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
EST: gi|13515728|gb|BG518004.1|BG518004
EST:     GTTCCTGCAAGCACGGAGCCT-GTACCG                         ACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
genomic: GTTCCTGCAAGCACGGAGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
EST: gi|71766016|gb|DR963953.1|DR963953
EST:     ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCG                         ACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
genomic: ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
EST: gi|60355659|gb|DN222632.1|DN222632
EST:     ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCG                         ACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
genomic: ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
EST: gi|37401441|gb|CF638084.1|CF638084
EST:     ACCTGAGCCAGTAAAACCTGCTGTCCCTGCAAGCACGGAGCCTGGTACCG                         ACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
genomic: ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
EST: gi|30306883|gb|CD001556.1|CD001556
EST:     ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCG                         ACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
genomic: ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
EST: gi|31361823|gb|CD446180.1|CD446180
EST:     ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCG                         ACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA
genomic: ACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAA

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: 98

ATTGAGACCGATTGTGAGGTTGACTTTGCTCCACCACTTGACTACAAAGAACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAAGGCGCTTGGATGGGAAGCCTTCCAAAGATAAAGATGTGCTAGCCTCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

ATTGAGACCGATTGTGAGGTTGACTTTGCTCCACCACTTGACTACAAAGAACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAAGGCGCTTGGATGGGAAGCCTTCCAAAGATAAAGATGTGCTAGCCTCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

ATTGAGACCGATTGTGAGGTTGACTTTGCTCCACCACTTGACTACAAAGAACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAAGGCGCTTGGATGGGAAGCCTTCCAAAGATAAAGATGTGCTAGCCTCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 146

ATTGAGACCGATTGTGAGGTTGACTTTGCTCCACCACTTGACTACAAAGAACCTGAGCCAGTAAAACCTGCTGTTCCTGCAAGCACGGAGCCTGGTACCGgtaagactat ... attttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAAGGCGCTTGGATGGGAAGCCTTCCAAAGATAAAGATGTGCTAGCCTCTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactgttccccatatggttttttcatgcacattatttttatgattattttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAAGGCGCTTGGATGGGAAGCCTTCCAAAGATAAAGATGTGCTAGCCTCTTC
                                           ttattttttc  CT-rich tract
                 ttttttcatgcacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagactattgtcctatgtgattactgttccccatatggttttttcatgcacattatttttatgattattttttcagACGTTCCAGCTGAAGAAGAACCAAAGTTCATCCCCTTCACTGGTTCAGGAAGGCGCTTGGATGGGAAGCCTTCCAAAGATAAAGATGTGCTAGCCTCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG