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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctcctcttctatttttaggccatggtactgtagtacttatttgaccttattttaactgtcatttgtagCTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTT

Basic information

species Zea mays
transcript GRMZM2G010085_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 16
gtatgctcctcttctatttttaggccatggtac-tgtagtacttat-ttgaccttattttaactgtcatttgtagCTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTT
||| |   || | || | | |  ||      || | | || || |   |||||| |||||   ||| | |  |||||||||||||||||| |||||||||||||||||||||||||||||||| ||||| |||||||||||| | |||||||||||||||||| |
gtaagtctctat-ctctatgtgtgcatgcacacgtctggtgctcaaactgacctaattttgtttgttactc-tagCTACTCTGAGTCTGAATACTTTAAGCAAGCACTTCGCCAAGGTGCACCTGCAAAACCTAGGGAACCACGAATTCCAAGAATGCCGCACCT

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 13
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 16
gtatgctcctcttctatttttaggccatggtac-tgtagtacttat-ttgaccttattttaactgtcatttgtagCTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTT
|||     || | || | | |  ||      || | | || || |   |||||| |||||   ||| | |  |||||||||||||||||| |||||||||||||||||||||||||||||||| ||||| |||||||||||| | |||||||||||||| ||| |
gtaaatctctat-ctctatgtgtgcatgcacacgtctggtgctgaaactgacctaattttgtttgttactc-tagCTACTCTGAGTCTGAATACTTTAAGCAAGCACTTCGCCAAGGTGCACCTGCAAAACCTAGGGAACCACGAATTCCAAGAATGCCACACCT

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 16
--------------------gtatgctcctcttctatttttaggccatggtactgtagtacttatttgaccttatttt-----aactgtcatttgtagCTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTT
                     ||||  | | ||  ||    ||   ||  || | |  | || ||  |||  | ||||     |  |||   |  |||||||||||||||||| || || |||||||||||||||||||||||||||||||| ||||||||||| || |||||  ||||||| |||||
gtatgctttatataactatgttatgtccatttttaataacgaga--ataatagtctccttctgatcagactatttttttgttaatatgtttctattagCTACTCTGAGTCTGATTATTTCAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAACCTAGGGAACCGAGAATTCCTCGAATGCCACACTT

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 16
----------------------gtatgctcctcttctatttt-taggccatggta-ctgtagtacttatttgaccttattttaactgtc--atttgtagCTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTT
                        ||  | |  | |||||||    | | |  || ||  |  |   ||      || ||||| ||     || |  ||||||||||| ||||| |||||||||||| || | || |||||||| ||||| || ||||  || || || |||||  | ||||| || ||
gtaatgattacttctgtcttatacattgtgcagtcctattttgccagtcttcatatctaaaagaaacatccc-ttttgttttatctactgtatcttcagCTACTCTGAATCTGAGTACTTTAAGCAAACATTGCGGCAAGGTGCTCCAGCTAAACCTAAAGAGCCTAGAATTCCGCGCATGCCCCAGTT

upper sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 16
--------------------gtatgctcctcttctatttttaggc----catggtactgtagtacttatttgaccttattttaactgtcatttgtagCTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTT
                    |    ||  | || || ||||| |     |||  |  | ||  || | |||  | || | ||  |  | |   |||| ||||| |||||||| |||||||||||| || | || |||||||| |||||||| |  || || || || || ||  | ||||| ||  |
gtaattgtgaattttcagttgccaacttatgttataattttatgtttttcattatcatttaagacatgtttc-cattttcttgtcctttaa--gtagTTACTCAGAGTCTGAATACTTTAAGCAAACAATGCGGCAAGGTGCTCCAGCAAAACAAAGAGAGCCTAGAATACCGCGCATGCCCCAGCT

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|87155727|gb|DY400516.1|DY400516
EST:     CTTGTTAGTGATAACTGGATTGAGCCACCTAGAAGAGAAAGGAAGAGAAA                         CTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGC
genomic: CTTGTTAGTGATAACTGGATTGAGCCACCTAGAAGAGAAAGGAAGAGAAAgtatgctcct ... tcatttgtagCTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGC
EST: gi|32930781|gb|CF035593.1|CF035593
EST:     CTTGTTAGTGATAACTGGATTGAGCCACCTAGAAGAGAAAGGAAGAGAAA                         CTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGC
genomic: CTTGTTAGTGATAACTGGATTGAGCCACCTAGAAGAGAAAGGAAGAGAAAgtatgctcct ... tcatttgtagCTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGC
EST: gi|31351381|gb|CD435738.1|CD435738
EST:     CTTGTTAGTGATAACTGGATTGAGCCACCTAGAAGAGAAAGGAAGAGAAA                         CTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGC
genomic: CTTGTTAGTGATAACTGGATTGAGCCACCTAGAAGAGAAAGGAAGAGAAAgtatgctcct ... tcatttgtagCTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGC
EST: gi|6194488|gb|AW146592.1|AW146592
EST:     CTTGTTAGTGATAACTGGATTGAGCCACCTAGAAGAGAAAGGAAGAGAAA                         CTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGC
genomic: CTTGTTAGTGATAACTGGATTGAGCCACCTAGAAGAGAAAGGAAGAGAAAgtatgctcct ... tcatttgtagCTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGC
EST: gi|32930784|gb|CF035596.1|CF035596
EST:     CTTGTTAGTGATAACTGGATTGAGCCACCTAGAAGAGAAAGGAAGAGAAA                         CTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGC
genomic: CTTGTTAGTGATAACTGGATTGAGCCACCTAGAAGAGAAAGGAAGAGAAAgtatgctcct ... tcatttgtagCTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGC
EST: gi|6194533|gb|AW146637.1|AW146637
EST:     CTTGTTAGTGATAACTGGATTGAGCCACCTAGAAGAGAAAGGAAGAGAAA                         CTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGC
genomic: CTTGTTAGTGATAACTGGATTGAGCCACCTAGAAGAGAAAGGAAGAGAAAgtatgctcct ... tcatttgtagCTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGC
EST: gi|22546162|gb|BU098473.1|BU098473
EST:     CTTGTTAGTGATAACTGGATTGAGCCACCTAGAAGAGAAAGGAAGAGAAA                         CTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGC
genomic: CTTGTTAGTGATAACTGGATTGAGCCACCTAGAAGAGAAAGGAAGAGAAAgtatgctcct ... tcatttgtagCTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGC

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: 369

GATGAAAACAAGGTTGATTTCAAGAAACTTGTTAGTGATAACTGGATTGAGCCACCTAGAAGAGAAAGGAAGAGAAAgtatgctcct ... tcatttgtagCTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 69

GATGAAAACAAGGTTGATTTCAAGAAACTTGTTAGTGATAACTGGATTGAGCCACCTAGAAGAGAAAGGAAGAGAAAgtatgctcct ... tcatttgtagCTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 81

GATGAAAACAAGGTTGATTTCAAGAAACTTGTTAGTGATAACTGGATTGAGCCACCTAGAAGAGAAAGGAAGAGAAAgtatgctcct ... tcatttgtagCTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 71

GATGAAAACAAGGTTGATTTCAAGAAACTTGTTAGTGATAACTGGATTGAGCCACCTAGAAGAGAAAGGAAGAGAAAgtatgctcct ... tcatttgtagCTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaggccatggtactgtagtacttatttgaccttattttaactgtcatttgtagCTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTT
                                    ttttaac  putative branch site (score: 71)
                                 ttattttaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctcctcttctatttttaggccatggtactgtagtacttatttgaccttattttaactgtcatttgtagCTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG