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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgcttactttgtgtatggcctatagttgtagttattttgctttatggttgtccactaaatctgacttttcgctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTTGCTGATCTGCTCTGCCTGAGTTTGCAG

Basic information

species Zea mays
transcript GRMZM2G013750_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013750_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g63430.1 (Oryza sativa), 3'ss of exon 9
gtactgcttactttg-tgtatggcctatagttgtagttattttgctttatggttgtccactaaat-ctgacttttcgctct-gcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTTGCTGATCTGCTCTGCCTGAGTTTGCAG
||| |||||||||   | ||| |  | |   | | | |   ||||||| |  |||||   | | | |    | || ||| | | | |||||||||||||||| || ||||||||||| ||| ||||| | |||||||| || ||||| || ||| |||| ||||||
gtattgcttacttgactttatcgtatttctcttttggttccttgctttgtatttgtcagttgatttccagttctttgcttttgttcagAATATCTTGGTTGTTTCGAAGTACTATTCAAGGATTACCCTGAAGAGGCTCGCAGATCTTCTTTGCTTGAGCTTGCAG
















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|110953365|gb|EE173417.1|EE173417
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|9743007|gb|BE519155.1|BE519155
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTGAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|60354046|gb|DN221019.1|DN221019
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|37387451|gb|CF630919.1|CF630919
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTGAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|60342669|gb|DN209642.1|DN209642
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACAT                         AATATTTTGGTTGTGTTTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|4630552|gb|AI621426.1|AI621426
EST:     GAAGCTAAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: GAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|6031286|gb|AW076143.1|AW076143
EST:     CTNTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTGAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|78545102|gb|DV622600.1|DV622600
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTGAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|60394675|gb|DN227545.1|DN227545
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|14243980|gb|BG841694.2|BG841694
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|37377438|gb|CF625322.1|CF625322
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTGAGAA-AATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|60345832|gb|DN212805.1|DN212805
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|60396663|gb|DN229531.1|DN229531
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|149074395|gb|EE162783.2|EE162783
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|67021450|gb|CO450199.1|CO450199
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|31909273|gb|CD650836.1|CD650836
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACGATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|37400251|gb|CF637475.1|CF637475
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTGAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|37374825|gb|CF623804.1|CF623804
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTGAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|13381714|gb|BG458269.1|BG458269
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|60349290|gb|DN216263.1|DN216263
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACAT                         AATATCTTGGTTGTGT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGT
EST: gi|6563654|gb|AW231381.1|AW231381
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|8930022|gb|BE224860.1|BE224860
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTGAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCCT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|60358924|gb|DN225897.1|DN225897
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|211414360|gb|FL328790.1|FL328790
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTGAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|5055399|gb|AI734286.1|AI734286
EST:     AGATTTGAAGCTGAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: AGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|4966662|gb|AI691518.1|AI691518
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTGAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|78023300|gb|DV491687.1|DV491687
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTGAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|33095588|gb|CF055582.1|CF055582
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGT
EST: gi|5871332|gb|AW017803.1|AW017803
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTGAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|211279038|gb|FL066029.1|FL066029
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTGAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|40335770|gb|CK369840.1|CK369840
EST:     CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTGAGAATAATTGAACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
genomic: CTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|13557647|gb|BG549003.1|BG549003
EST:     TGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGGACAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCCT
genomic: TGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT
EST: gi|5804749|gb|AI979719.1|AI979719
EST:     GAATAATTGACCAT                         AATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTCCCATAAAGAGGCTT
genomic: GAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTT

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: 47 (upstream exon), 49 (downstream exon)
Score: 254

GGAATTCTCTAAGCACGAATTTGAAAACGAGAAGAATCTGCTAGGAGGAGCTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTTGCTGATCTGCTCTGCCTGAGTTTGCAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 187

GGAATTCTCTAAGCACGAATTTGAAAACGAGAAGAATCTGCTAGGAGGAGCTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTTGCTGATCTGCTCTGCCTGAGTTTGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

GGAATTCTCTAAGCACGAATTTGAAAACGAGAAGAATCTGCTAGGAGGAGCTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTTGCTGATCTGCTCTGCCTGAGTTTGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 242

GGAATTCTCTAAGCACGAATTTGAAAACGAGAAGAATCTGCTAGGAGGAGCTTTGGGTGCCAAAGCTGCAGAAGATTTGAAGCTAAGAATAATTGAACATgtactgctta ... ctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTTGCTGATCTGCTCTGCCTGAGTTTGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtagttattttgctttatggttgtccactaaatctgacttttcgctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTTGCTGATCTGCTCTGCCTGAGTTTGCAG
                                      cttttcgctctgctt  CT-rich tract
     ttattttgctttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgcttactttgtgtatggcctatagttgtagttattttgctttatggttgtccactaaatctgacttttcgctctgcttagAATATCTTGGTTGTGTCTAAGTACTATTCGAGGGTTACCATAAAGAGGCTTGCTGATCTGCTCTGCCTGAGTTTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT