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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtagcgcaccgactaaaggccgtgtttttcgctgatcggcgtgtctcaattggcgtgtgctaattttgcagCCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCACGAACCCAAGGTGCTGCTCGACAAGATCGCCTATTGGACCGTCAAATTAC

Basic information

species Zea mays
transcript AC233960.1_FGT002
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC233960.1_FGT002 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g47200.1 (Oryza sativa), 3'ss of exon 1
--------------------------------------------------gtgagtagcgcaccgactaaaggccgtgtttttcgctgatcggcgtgtctcaattggcgtg--tgctaattttgcagCCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCACGAACCCAAGGTGCTGCTCGACAAGATCGCCTATTGGACCGTCAAATTAC
                                                   |   |         |||||      |    || |   | | ||||   | ||||   |||  ||||||||| ||||||||||||| |||||  ||||||||| |||||||| || || |  |||||||| || |||||||||||||||||| ||||||| |||||||||||    |
gtaagaatcgatttatccatgatcctgcttaaagatcgcttcctctcttttttgctgttaatttaactaatctgaattcaatttgtgtaactgcgtcgatgaattaatgtgtttgctaattt-gcagCCATGGGAGACGTACTCGCCGGACACGACGATCGACCTGAAGAAGCACCACGAGCCGAAGGTGCTGCTCGACAAGGTCGCCTACTGGACCGTCAAGGCGC
















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|78107637|gb|DV526055.1|DV526055
EST:     CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGG                         CCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
genomic: CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGGgtgagtagcg ... aattttgcagCCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
EST: gi|78116560|gb|DV534947.1|DV534947
EST:     CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGG                         CCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
genomic: CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGGgtgagtagcg ... aattttgcagCCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
EST: gi|149099036|gb|EE185054.2|EE185054
EST:     CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGG                         CCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
genomic: CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGGgtgagtagcg ... aattttgcagCCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
EST: gi|71422715|gb|DR805803.1|DR805803
EST:     CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGG                         CCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
genomic: CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGGgtgagtagcg ... aattttgcagCCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
EST: gi|71764916|gb|DR962853.1|DR962853
EST:     CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGG                         CCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
genomic: CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGGgtgagtagcg ... aattttgcagCCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
EST: gi|71764059|gb|DR961996.1|DR961996
EST:     CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGG                         CCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCTACAGACACCAC
genomic: CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGGgtgagtagcg ... aattttgcagCCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
EST: gi|149095769|gb|EE181412.2|EE181412
EST:     CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGG                         CCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
genomic: CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGGgtgagtagcg ... aattttgcagCCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
EST: gi|148937945|gb|EC882176.2|EC882176
EST:     CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGG                         CCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
genomic: CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGGgtgagtagcg ... aattttgcagCCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
EST: gi|149096470|gb|EE182212.2|EE182212
EST:     CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGG                         CCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
genomic: CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGGgtgagtagcg ... aattttgcagCCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
EST: gi|89249421|gb|DY621207.1|DY621207
EST:     CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGG                         CCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
genomic: CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGGgtgagtagcg ... aattttgcagCCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
EST: gi|76015230|gb|DT942400.1|DT942400
EST:     CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGG                         CCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
genomic: CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGGgtgagtagcg ... aattttgcagCCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
EST: gi|76017432|gb|DT944602.1|DT944602
EST:     CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGG                         CCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
genomic: CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGGgtgagtagcg ... aattttgcagCCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
EST: gi|78107664|gb|DV526082.1|DV526082
EST:     CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGG                         CCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
genomic: CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGGgtgagtagcg ... aattttgcagCCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
EST: gi|149078562|gb|EE167345.2|EE167345
EST:     CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGG                         CCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC
genomic: CGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGGgtgagtagcg ... aattttgcagCCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCAC

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: 36 (upstream exon), 47 (downstream exon)
Score: 9

TGACGGAAAGAGAGACAAAGTGGTGAGCAGCTACTGGGGCGTCGCGCCGTCGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGGgtgagtagcg ... aattttgcagCCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCACGAACCCAAGGTGCTGCTCGACAAGATCGCCTATTGGACCGTCAAATTAC


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

TGACGGAAAGAGAGACAAAGTGGTGAGCAGCTACTGGGGCGTCGCGCCGTCGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGGgtgagtagcg ... aattttgcagCCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCACGAACCCAAGGTGCTGCTCGACAAGATCGCCTATTGGACCGTCAAATTAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 102

TGACGGAAAGAGAGACAAAGTGGTGAGCAGCTACTGGGGCGTCGCGCCGTCGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGGgtgagtagcg ... aattttgcagCCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCACGAACCCAAGGTGCTGCTCGACAAGATCGCCTATTGGACCGTCAAATTAC


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 21

TGACGGAAAGAGAGACAAAGTGGTGAGCAGCTACTGGGGCGTCGCGCCGTCGAAGCTGATGAACAAGGACGGCGCCGAGTGGAGGTGGTCTTGCTTCAGGgtgagtagcg ... aattttgcagCCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCACGAACCCAAGGTGCTGCTCGACAAGATCGCCTATTGGACCGTCAAATTAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggccgtgtttttcgctgatcggcgtgtctcaattggcgtgtgctaattttgcagCCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCACGAACCCAAGGTGCTGCTCGACAAGATCGCCTATTGGACCGTCAAATTAC
                                         tgctaat  putative branch site (score: 21)
                                            taatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtagcgcaccgactaaaggccgtgtttttcgctgatcggcgtgtctcaattggcgtgtgctaattttgcagCCATGGGAGGCGTACAAGCCGGACACCACGATCGATCTCAACAGACACCACGAACCCAAGGTGCTGCTCGACAAGATCGCCTATTGGACCGTCAAATTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT