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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaacgcactggaccacgacgtaagtctacattcctgactactccaattcagtgctactttagttctgaatctaaactaatgtattttaagcttgtatagCTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAGCTAAACCATCATTGTCACCAGTCCTTCAAAGCTTAAATTATGTTCTTGA

Basic information

species Zea mays
transcript GRMZM5G891056_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G891056_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g19870.1 (Oryza sativa), 3'ss of exon 2
aaaacgcactggaccacgacgtaagtctacattcctgactactccaattcagtgctactttagttctgaatctaaactaatgtattttaagcttgtatagCTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAGCTAAACCATCATTGTCACCAGTCCTTCAAAGCTTAAATTATGTTCTTGA
                    |||||| ||   |  |||||| |  ||||||| | |||   ||| ||  |    ||||    ||||||   | | | |||| ||||| ||||||||| |||| |||||||| || |||||| |||  |||| |  |||||||   ||||||||||||| ||||||||||||| |   || 
--------------------gtaagtttatcattttgactaattaaattcagagttacagaagtgcttcaatctaactgtaatattttgtacatttgtagCATGTCCTGTTTGTTATGTGCCTGTTGAGCAGGCCCTGGCATTGATGCCAGGTGCACCATCAGCATCACCAGTCCTTCGAAGCTTAAATTATTTGTCTGG
















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|211516010|gb|FL160576.1|FL160576
EST:     TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGAC                         CTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAG
genomic: TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctac ... gcttgtatagCTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAG
EST: gi|211516008|gb|FL160574.1|FL160574
EST:     TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGAC                         CTTTGTC-AGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCA
genomic: TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctac ... gcttgtatagCTT-GTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCA
EST: gi|211516009|gb|FL160575.1|FL160575
EST:     TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGAC                         CTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAG
genomic: TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctac ... gcttgtatagCTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAG
EST: gi|211516003|gb|FL160569.1|FL160569
EST:     TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGAC                         CTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAG
genomic: TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctac ... gcttgtatagCTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAG
EST: gi|211516006|gb|FL160572.1|FL160572
EST:     TTGGACATCGTCAGGCAGACCAGCTGATAGAAAACGCACTGGACCACGAC                         CTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAG
genomic: TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctac ... gcttgtatagCTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAG
EST: gi|211516004|gb|FL160570.1|FL160570
EST:     TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGAC                         CTTGTCCAGTTTTGT-ATTTGCCAGTTGAGCAAGCACTGGGACTGAGACCA
genomic: TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctac ... gcttgtatagCTTGTCCAGTTT-GTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCA
EST: gi|211516012|gb|FL160578.1|FL160578
EST:     TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGAC                         CTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAG
genomic: TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctac ... gcttgtatagCTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAG
EST: gi|211516002|gb|FL160568.1|FL160568
EST:     TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGAC                         CTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAG
genomic: TTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctac ... gcttgtatagCTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAG

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: 21 (upstream exon), 48 (downstream exon)
Score: 26

GAGACCATGCTTGTGTTTTCTGATCATGTCCGGAGCTTTGTGAACCCTGTTTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctac ... gcttgtatagCTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAGCTAAACCATCATTGTCACCAGTCCTTCAAAGCTTAAATTATGTTCTTGA


Block sizes: 31 (upstream exon), 46 (downstream exon)
Score: 11

GAGACCATGCTTGTGTTTTCTGATCATGTCCGGAGCTTTGTGAACCCTGTTTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctac ... gcttgtatagCTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAGCTAAACCATCATTGTCACCAGTCCTTCAAAGCTTAAATTATGTTCTTGA


Block sizes: 26 (upstream exon), 46 (downstream exon)
Score: 10

GAGACCATGCTTGTGTTTTCTGATCATGTCCGGAGCTTTGTGAACCCTGTTTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctac ... gcttgtatagCTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAGCTAAACCATCATTGTCACCAGTCCTTCAAAGCTTAAATTATGTTCTTGA


Block sizes: 26 (upstream exon), 48 (downstream exon)
Score: 8

GAGACCATGCTTGTGTTTTCTGATCATGTCCGGAGCTTTGTGAACCCTGTTTGGACATCGTCAGGCAGACCAGTTGATAGAAAACGCACTGGACCACGACgtaagtctac ... gcttgtatagCTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAGCTAAACCATCATTGTCACCAGTCCTTCAAAGCTTAAATTATGTTCTTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattcagtgctactttagttctgaatctaaactaatgtattttaagcttgtatagCTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAGCTAAACCATCATTGTCACCAGTCCTTCAAAGCTTAAATTATGTTCTTGA
                             aactaat  putative branch site (score: 8)
                       aatctaaactaatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaacgcactggaccacgacgtaagtctacattcctgactactccaattcagtgctactttagttctgaatctaaactaatgtattttaagcttgtatagCTTGTCCAGTTTGTTATTTGCCAGTTGAGCAAGCACTGGCACTGAGACCAGCTAAACCATCATTGTCACCAGTCCTTCAAAGCTTAAATTATGTTCTTGA

- - -gcactgg
- - - - - - -ccacgac
- - - - - - - - - - - - - - -cattcct
- - - - - - - - - - - - - - - - - - - ctactcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtattt