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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggacaggaatttgattacttaatttaataacagattatgcagaattgcaactgcataaatgcacctttttctctaaactttattttaatttgcaatgaagGTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAATCTAGTGCTATCAAGCTGATTGATTTTGGGAGTACAACTTTCGAGAGCC

Basic information

species Zea mays
transcript GRMZM2G386991_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G386991_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g62080.1 (Oryza sativa), 3'ss of exon 9
--------------------------------------ggacaggaatttgattacttaat--------ttaataacagattatgcagaattgcaactgcataaatgcacctttttctctaaactttattttaatttgcaatgaagGTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAATCTAGTGCTATCAAGCTGATTGATTTTGGGAGTACAACTTTCGAGAGCC
                                           | ||||| ||   ||||         ||   |  | ||||||   | | | |   ||||| ||  |  |||||  || |  ||||| ||  ||| || | |||||| | ||||| || |||||||||||||| || |||||||| |||||||||||||||||||||||||||||||||||||| |||||||| |||||   ||
gtggcttcaatactaaattttgtcattcgaactataatcttttgcaattttatccgttaacacttgtggttgccattacattatgtcaattagtacgagcatacattta--ttttttactgatttttatattgttttcca-taaagGTTACAATACGGCCCCCAAAGGATGGTTCCTTTTTTAAGAATCTTCCAAAATCTAGTGCTATCAAGCTGATTGATTTTGGAAGTACAACATTCGAACACC
















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|211512137|gb|FL430403.1|FL430403
EST:     AGAACATTCTCCTTGTTTCATCAGAGTCTATCAGGGTGCCTGATTATAAG                         GTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAA
genomic: AAAACATTCTCCTTGTTTCATCAGAGTCTATCAGGGTGCCTGATTATAAGgttgttactg ... tgcaatgaagGTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAA
EST: gi|32866970|gb|CF006652.1|CF006652
EST:     AGAACATTCTCCTTGTTTCATCAGAGTCTATCAGGGTGCCTGATTATAAG                         GTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAA
genomic: AAAACATTCTCCTTGTTTCATCAGAGTCTATCAGGGTGCCTGATTATAAGgttgttactg ... tgcaatgaagGTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAA
EST: gi|211073306|gb|FL473576.1|FL473576
EST:     GCCTGATTATAAG                         GTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAA
genomic: GCCTGATTATAAGgttgttactg ... tgcaatgaagGTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAA
EST: gi|211122243|gb|FL474055.1|FL474055
EST:     GACCATTCTCCCTTGTTTCATCAGAGTCTATCAGGGTCCCTGATTATAAG                         TTTTCTATACGACCACCAAAGGGAT-GTTCTTTCTTTAAGAACCTTCCAAA
genomic: AAACATTCT-CCTTGTTTCATCAGAGTCTATCAGGGTGCCTGATTATAAGgttgttactg ... tgcaatgaagGTTTCTATACGACCACCAAA-GGATGGTTCTTTCTTTAAGAACCTTCCAAA
EST: gi|211212596|gb|FL411382.1|FL411382
EST:     AAAACATTCTCCTTGTTTCATCAGAGTCTATCAGGGTGCCTGATTATAAG                         GTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAA
genomic: AAAACATTCTCCTTGTTTCATCAGAGTCTATCAGGGTGCCTGATTATAAGgttgttactg ... tgcaatgaagGTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAA
EST: gi|149089547|gb|EE178794.2|EE178794
EST:     AAAACATTCTCCTTGTTTCATCAGAGTCTATCAGGGTGCCTGATTATAAG                         GTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAA
genomic: AAAACATTCTCCTTGTTTCATCAGAGTCTATCAGGGTGCCTGATTATAAGgttgttactg ... tgcaatgaagGTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAA
EST: gi|60343108|gb|DN210081.1|DN210081
EST:     CATTCTCCTTGTTTCATCAGAGTCTATCAGGGTGCCTGATTATAAG                         GTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAA
genomic: CATTCTCCTTGTTTCATCAGAGTCTATCAGGGTGCCTGATTATAAGgttgttactg ... tgcaatgaagGTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAA
EST: gi|60354602|gb|DN221575.1|DN221575
EST:     TTCATCAGAGTCTATCAGGGTGCCTGATTATAAG                         GTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAA
genomic: TTCATCAGAGTCTATCAGGGTGCCTGATTATAAGgttgttactg ... tgcaatgaagGTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAA
EST: gi|6095292|gb|AW119959.1|AW119959
EST:     AAAACATTCTCCTTGTTTCATCAGAGTCTATCAGGGTGCCTGATTATAAG                         GTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAA
genomic: AAAACATTCTCCTTGTTTCATCAGAGTCTATCAGGGTGCCTGATTATAAGgttgttactg ... tgcaatgaagGTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAA
EST: gi|6695913|gb|AW289021.1|AW289021
EST:     AAAACATTCTCCTTGTTTCATCAGAGTCTATCAGGGTGCCTGATTATAAG                         GTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAA
genomic: AAAACATTCTCCTTGTTTCATCAGAGTCTATCAGGGTGCCTGATTATAAGgttgttactg ... tgcaatgaagGTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAA

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: 186

TTATGCATGACTTGCGACTTATTCACACGGATCTGAAGCCAGAAAACATTCTCCTTGTTTCATCAGAGTCTATCAGGGTGCCTGATTATAAGgttgttactg ... tgcaatgaagGTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAATCTAGTGCTATCAAGCTGATTGATTTTGGGAGTACAACTTTCGAGAGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

TTATGCATGACTTGCGACTTATTCACACGGATCTGAAGCCAGAAAACATTCTCCTTGTTTCATCAGAGTCTATCAGGGTGCCTGATTATAAGgttgttactg ... tgcaatgaagGTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAATCTAGTGCTATCAAGCTGATTGATTTTGGGAGTACAACTTTCGAGAGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 255

TTATGCATGACTTGCGACTTATTCACACGGATCTGAAGCCAGAAAACATTCTCCTTGTTTCATCAGAGTCTATCAGGGTGCCTGATTATAAGgttgttactg ... tgcaatgaagGTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAATCTAGTGCTATCAAGCTGATTGATTTTGGGAGTACAACTTTCGAGAGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 241

TTATGCATGACTTGCGACTTATTCACACGGATCTGAAGCCAGAAAACATTCTCCTTGTTTCATCAGAGTCTATCAGGGTGCCTGATTATAAGgttgttactg ... tgcaatgaagGTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAATCTAGTGCTATCAAGCTGATTGATTTTGGGAGTACAACTTTCGAGAGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaactgcataaatgcacctttttctctaaactttattttaatttgcaatgaagGTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAATCTAGTGCTATCAAGCTGATTGATTTTGGGAGTACAACTTTCGAGAGCC
                                     ttttaat  putative branch site (score: 241)
                    tttttctctaaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggacaggaatttgattacttaatttaataacagattatgcagaattgcaactgcataaatgcacctttttctctaaactttattttaatttgcaatgaagGTTTCTATACGACCACCAAAGGATGGTTCTTTCTTTAAGAACCTTCCAAAATCTAGTGCTATCAAGCTGATTGATTTTGGGAGTACAACTTTCGAGAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - -aataaca
- - - - - - - - - - - - - - - - - ttatgca
- - - - - - - - - - - - - - - - - - - - - - - gcaactg