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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttatattcttacaaataagctgtctggtctaacttctaagcaccactagtgatgctgctccagggattaatcattattttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATACGGGAGCTTGCCTTTCTAAATCCTGAG

Basic information

species Zea mays
transcript GRMZM2G111014_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111014_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g16290.1 (Oryza sativa), 3'ss of exon 7
gtaagcttatattcttacaaataagctgtctggtctaacttctaagcaccactagtgatgctgctccagggattaatcattattttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATACGGGAGCTTGCCTTTCTAAATCCTGAG
||| |||| | |  ||||| ||    | | | |    ||       ||  |||| | ||| | | |||  |  |||| ||| || |  ||||||| ||||||||||| || || |||||||||||||| ||  |  ||||||| ||||| |||||||||||||||||||||
gtatgcttctgtctttacatat---ttttttagctgtac-------cattactacttatgtt-ccccaatgtgtaattattgttcttgatgtagTTTTTACCACCACAATGGACTTTGACTTCAATACGATAGCTGGTCGCATCCGGGAACTTGCCTTTCTAAATCCTGAG
















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|32924684|gb|CF029496.1|CF029496
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32926908|gb|CF031720.1|CF031720
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGAT
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGAT
EST: gi|31612357|gb|CD568979.1|CD568979
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32925623|gb|CF030435.1|CF030435
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCT
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCT
EST: gi|32925026|gb|CF029838.1|CF029838
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32925749|gb|CF030561.1|CF030561
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32925384|gb|CF030196.1|CF030196
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32925421|gb|CF030233.1|CF030233
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32925219|gb|CF030031.1|CF030031
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATC
EST: gi|32925064|gb|CF029876.1|CF029876
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCGGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|5268379|gb|AI770343.1|AI770343
EST:     AACAAACTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32925570|gb|CF030382.1|CF030382
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATA
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATA
EST: gi|32925143|gb|CF029955.1|CF029955
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGGCTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32925327|gb|CF030139.1|CF030139
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32925179|gb|CF029991.1|CF029991
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32924802|gb|CF029614.1|CF029614
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32925639|gb|CF030451.1|CF030451
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32925015|gb|CF029827.1|CF029827
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32924772|gb|CF029584.1|CF029584
EST:     AACAAACTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32925454|gb|CF030266.1|CF030266
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32926646|gb|CF031458.1|CF031458
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32926273|gb|CF031085.1|CF031085
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32926591|gb|CF031403.1|CF031403
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCATGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32925737|gb|CF030549.1|CF030549
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32925461|gb|CF030273.1|CF030273
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCCGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32925062|gb|CF029874.1|CF029874
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32925309|gb|CF030121.1|CF030121
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32926568|gb|CF031380.1|CF031380
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCCGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32925900|gb|CF030712.1|CF030712
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32925339|gb|CF030151.1|CF030151
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATG                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
EST: gi|32925242|gb|CF030054.1|CF030054
EST:     AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATA                         TATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC
genomic: AACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATAC

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), 45 (downstream exon)
Score: 120

TCGCGGGGGAAACCAACCACTAGGCTAACTAGTAGCACACTGACTGGTGAAACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATACGGGAGCTTGCCTTTCTAAATCCTGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 46

TCGCGGGGGAAACCAACCACTAGGCTAACTAGTAGCACACTGACTGGTGAAACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATACGGGAGCTTGCCTTTCTAAATCCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 25

TCGCGGGGGAAACCAACCACTAGGCTAACTAGTAGCACACTGACTGGTGAAACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATACGGGAGCTTGCCTTTCTAAATCCTGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 21

TCGCGGGGGAAACCAACCACTAGGCTAACTAGTAGCACACTGACTGGTGAAACAAGCTCTCGTCAAGGGACGCGCATCAGATTTTGGCCTGATAAAGATAgtaagcttat ... ttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATACGGGAGCTTGCCTTTCTAAATCCTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctaagcaccactagtgatgctgctccagggattaatcattattttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATACGGGAGCTTGCCTTTCTAAATCCTGAG
                               gattaat  putative branch site (score: 21)
                                        ttatttt  putative PPT
                                attaatcattattttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttatattcttacaaataagctgtctggtctaacttctaagcaccactagtgatgctgctccagggattaatcattattttgaatgtagTATTTACCACCACGATCGATTTTGACTTCAATACAATCTCCAGTCGCATACGGGAGCTTGCCTTTCTAAATCCTGAG

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