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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggatttcttggcaagcgagggctggagtttgctagttttaataaattttccttttgatttcctgacatgttttgaagaccaaaatttatacaaatttgtaagcagctgatagtggtcctattctgatttctgcatatactgactgaactgcacataaaacagGGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAATATAACAGCACTCCCAGCGGAGCTG

Basic information

species Zea mays
transcript GRMZM2G015090_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015090_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os02g58030.1 (Oryza sativa), 3'ss of exon 18
gtaaggatttcttggcaagcgagggctggagtttgctagttt--taataaattttccttttgatttcctgacatgttttgaagaccaaaatttatacaaatttgtaagcagctgatagtg-gtcctattctgatttctgcatatactgactgaactgcacataaaacagGGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAATATAACAGCACTCCCAGCGGAGCTG
                  |  |   || | |||  ||| ||    ||||   ||| |      ||||   | ||| |||  | |     |  |  |    || | |||      || |   || |     |  | | ||| ||| |  | |    ||||| || | ||||| |||||  |||| ||| |  | ||||||||||||||||| ||||||||||||||| |||||||| | ||||||
------------------gtaaacacttg-gttctctatttaaggaatatgattttccccctctttctataaatgcttttcacattcccaggtgcat---ttagaaagttttgaatggcacgtgcgccctttttatttgcttatgcaaaatccgttgcacttaca-cagGGTATCAAAGATTTAACTTCTTTGATTGAGCTTGATCTGTCGGACAACAATATAACAACACTCCCACCTGAGCTG
















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|32937582|gb|CF042401.1|CF042401
EST:     TGCTTAGGATTCTTGACCTGAGTCAGAATCACCTTACAACTGTGCCGGAG                         GGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAAT
genomic: TGCTTAGGATTCTTGACCTGAGTCAGAATCACCTTACAACTGTGCCGGAGgtaaggattt ... cataaaacagGGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAAT
EST: gi|74243286|gb|DT651200.1|DT651200
EST:     TGCTTAGGATTCTTGACCTGAGTCAGAATCACCTTACAACTGTGCCGGAG                         GGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAAT
genomic: TGCTTAGGATTCTTGACCTGAGTCAGAATCACCTTACAACTGTGCCGGAGgtaaggattt ... cataaaacagGGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAAT
EST: gi|32930496|gb|CF035308.1|CF035308
EST:     TGCTTAGGATTCTTGACCTGAGTCAGAATCACCTTACAACTGTGCCGGAG                         GGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAAT
genomic: TGCTTAGGATTCTTGACCTGAGTCAGAATCACCTTACAACTGTGCCGGAGgtaaggattt ... cataaaacagGGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAAT
EST: gi|88751761|gb|DY535902.1|DY535902
EST:     TGCTTAGGATTCTTGACCTGAGTCAGAATCACCTTACAACTGTGCCGGAG                         GGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAAT
genomic: TGCTTAGGATTCTTGACCTGAGTCAGAATCACCTTACAACTGTGCCGGAGgtaaggattt ... cataaaacagGGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAAT
EST: gi|211519285|gb|FL432530.1|FL432530
EST:     TGCTTAGGATTCTTGACCTGAGTCAGAATCACCTTACAACTGTGCCGGAG                         GGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAAT
genomic: TGCTTAGGATTCTTGACCTGAGTCAGAATCACCTTACAACTGTGCCGGAGgtaaggattt ... cataaaacagGGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAAT
EST: gi|78109030|gb|DV527447.1|DV527447
EST:     TGCTTAGGATTCTTGACCTGAGTCAGAATCACCTTACAACTGTGCCGGAG                         GGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAAT
genomic: TGCTTAGGATTCTTGACCTGAGTCAGAATCACCTTACAACTGTGCCGGAGgtaaggattt ... cataaaacagGGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAAT
EST: gi|14204018|gb|BG837695.1|BG837695
EST:     TGCTTAGGATTCTTGACCTGAGTCAGAATCACCTTACAACTGTGCCGGAG                         GGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAAT
genomic: TGCTTAGGATTCTTGACCTGAGTCAGAATCACCTTACAACTGTGCCGGAGgtaaggattt ... cataaaacagGGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAAT
EST: gi|32935775|gb|CF040587.1|CF040587
EST:     TGCTTAGGATTCTTGACCTGAGTCAGAATCACCTTACAACTGTGCCGGAG                         GGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAAT
genomic: TGCTTAGGATTCTTGACCTGAGTCAGAATCACCTTACAACTGTGCCGGAGgtaaggattt ... cataaaacagGGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAAT
EST: gi|37399457|gb|CF637057.1|CF637057
EST:     TGCTTAGGATTCTTGACCTGAGTCAGAATCACCTTACAACTGTGCCGGAG                         GGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAATAAT
genomic: TGCTTAGGATTCTTGACCTGAGTCAGAATCACCTTACAACTGTGCCGGAGgtaaggattt ... cataaaacagGGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAAT
EST: gi|60397260|gb|DN230076.1|DN230076
EST:     TGCTTAGGATTCTTGACCTGAGTCAGAATCACCTTACAACTGTGCCGGAG                         GGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAAT
genomic: TGCTTAGGATTCTTGACCTGAGTCAGAATCACCTTACAACTGTGCCGGAGgtaaggattt ... cataaaacagGGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAAT

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: 44 (upstream exon), 49 (downstream exon)
Score: 140

ACGAATGAAACTCCATGAATTTCCTAATGGTTTGCTGGGCCTAAAACTGCTTAGGATTCTTGACCTGAGTCAGAATCACCTTACAACTGTGCCGGAGgtaaggattt ... cataaaacagGGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAATATAACAGCACTCCCAGCGGAGCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 194

ACGAATGAAACTCCATGAATTTCCTAATGGTTTGCTGGGCCTAAAACTGCTTAGGATTCTTGACCTGAGTCAGAATCACCTTACAACTGTGCCGGAGgtaaggattt ... cataaaacagGGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAATATAACAGCACTCCCAGCGGAGCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 140

ACGAATGAAACTCCATGAATTTCCTAATGGTTTGCTGGGCCTAAAACTGCTTAGGATTCTTGACCTGAGTCAGAATCACCTTACAACTGTGCCGGAGgtaaggattt ... cataaaacagGGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAATATAACAGCACTCCCAGCGGAGCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 128

ACGAATGAAACTCCATGAATTTCCTAATGGTTTGCTGGGCCTAAAACTGCTTAGGATTCTTGACCTGAGTCAGAATCACCTTACAACTGTGCCGGAGgtaaggattt ... cataaaacagGGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAATATAACAGCACTCCCAGCGGAGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatagtggtcctattctgatttctgcatatactgactgaactgcacataaaacagGGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAATATAACAGCACTCCCAGCGGAGCTG
                             tactgac  putative branch site (score: 128)
                                            acataaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggatttcttggcaagcgagggctggagtttgctagttttaataaattttccttttgatttcctgacatgttttgaagaccaaaatttatacaaatttgtaagcagctgatagtggtcctattctgatttctgcatatactgactgaactgcacataaaacagGGCATCAAGAATTTCACTGCACTCATTGAGCTTGATCTGTCTGACAACAATATAACAGCACTCCCAGCGGAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT