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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatataccatttgtatttggatgtcctgtgctatttaaatttctgtattaccaaaaatgtaattttcttctgattgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCA

Basic information

species Zea mays
transcript GRMZM2G139894_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139894_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os11g29380.1 (Oryza sativa), 3'ss of exon 11
--gtatgatataccatttgtatt-tggatgtcctgtgctatttaaatttctgtattaccaaaaatgtaattttcttctgattgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCA
   | ||  |||||||||| ||  ||  ||   |     |||||  ||    |||| ||  ||  |  || ||  ||| ||||||||||||| ||||||||||| || ||||||||||| ||||||||||||||||| || ||||| |||||||| ||||||||| | ||||||||||||||||| |||
gtatgtgtaataccatttggataatgtgtgcttttaagcatttatgttc---tattgccctaa--gatatctttctcttattgtttcagGGTGAGTATTCATGAGGCCATGGAGCAACAAAGTATCAGTATATCAAAGGCCGGAATTGTCACATCCCTTCAAGCTCGGTGCAGTGTTATTGCTGCAGCA

upper sequence: GRMZM2G139894_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA07G36680.1 (Glycine max), 3'ss of exon 10
gtatgatataccat-ttgtatttggatgtcctgtgctatttaaatttctgtatt--accaaaaatgtaattttcttctgattgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCA
||| || |    |  |||||  |   ||   | |  || ||| |||  | |  |  | ||  ||| ||  ||| |  |  |  |  |||||| || || |||||||| |||||||| |||||||| || ||||||||||| ||||| || ||||||||||| ||  | ||   ||||||||||||||||
gtaagaaaattgaccttgtaaatccttgagttttcttaattacattattatccttgatcattaatttatatttatatttttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGTTCTGTTATTGCTGCGGCA

upper sequence: GRMZM2G139894_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA17G03920.1 (Glycine max), 3'ss of exon 10
gtatgatataccat-ttgtatttggatgtcctgtgctatttaaatttctgtattac----------------caaaaa-tgtaattttcttctgatt---gttt-------cagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCA
||| || |  | || ||||| ||   ||   | | ||| ||| |||  |  | |||                |||||| | |  ||  |   | |||    |||       |||||| ||||| |||||||| |||||||| |||||||| || ||||||||||| ||||| || ||||||||||| ||  | |||  |||||||||||| |||
gtaagaaaatcaatcttgtaattatttgaattttcctaattacattgttaaactacaccttcacatgatatacaaaaactatccttgaccattaatttatatttttgttaccagGGTGAGTATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGCTCTGTTATTGCTGCTGCA

upper sequence: GRMZM2G139894_T02 (Zea mays), 3'ss of exon 11
lower sequence: AT1G44900.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatgatataccatttgtatttggatgtcctgtgctatttaaatttctgtattaccaaaaatgtaattttcttctgattgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCA
      || || |  || |  |  |||     | || ||   |      |  | |  |  || ||| ||| || | |      |||||| ||||| |||||||| ||||| ||||||||||| |||||||| || |||||||| || || |||||||||||| | |||  |||||||||||| || 
-----gta-acaaaatgcaacta-atgatagttacttttctgaaggaaatggtgctgacgatataagttt-ttgtaac-----cagGGTGAGTATCCATGAAGCCATGGAACAACAGAGTATTAGTATATCGAAGGCAGGAATAGTTACTTCTCTTCAAGCTCGTTGCTCTGTTATTGCTGCAGCT

upper sequence: GRMZM2G139894_T02 (Zea mays), 3'ss of exon 11
lower sequence: PP1S28_266V6.1 (Physcomitrella patens), 3'ss of exon 10
------------------------------------------------------gtatgatataccatttgtatttggatgtcctgtgctatttaaatttctgtattacc--aaaaatgtaattttcttctgattgt-ttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCA
                                                        |   |  |          || ||    |  | ||   |    | || | | | |  || | | |   |    |  |||| | || ||||| ||||||||||| |||||||| || ||||| ||||||||||| || ||||| || || || ||  | |||||  | |||  |||||||||||| |||
gtgcagtccctttctggagatgcatttttcataaccatttgtatacagttcttgaaactctcaattgccaagccttagaaaaacgctccttgatgtgctgctatttcatctgaagactttgtgtgaaattcgattttgtttagGGTGAGTATTCATGAGGCTATGGAACAGCAGAGCATCAGTATATCTAAGGCAGGCATTGTGACTTCGTTGCAAGCCCGGTGCGCTGTTATTGCTGCAGCA

upper sequence: GRMZM2G139894_T02 (Zea mays), 3'ss of exon 11
lower sequence: EFJ17122 (Selaginella moellendorffii), 3'ss of exon 9
gtatgatataccatttgtatttggatgtcctgtgctatttaaatttctgtattaccaaaaatgtaattttcttctg-attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCA
                                 |   ||||||     |  ||||    | |||  |  ||    | ||| ||||||||||||||| |||||||| |||||||| || |||||||| || |||||||| || || || |||||  | |||||| | |||  ||| || ||||| |||
---------------------------------gtattttaaacgcagggcttac----attgtcttactcgggagtattttttcagGGTAAGTATACATGAAGCCATGGAGCAGCAAAGTATCAGCATCTCAAAAGCTGGTATAGTAACATCATTGCAAGCTCGTTGCTCTGTGATCGCTGCCGCA

upper sequence: GRMZM2G139894_T02 (Zea mays), 3'ss of exon 11
lower sequence: EFJ31227 (Selaginella moellendorffii), 3'ss of exon 7
gtatgatataccatttgtatttggatgtcctgtgctatttaaatttctgtattaccaaaaatgtaattttcttctg-attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCA
                                 |   ||||||     |  ||||    |||||  |  ||    | ||| ||||||||||||||| |||||||| |||||||| || |||||||| || |||||||| || || || |||||  | |||||| | |||  ||| || ||||| |||
---------------------------------gtattttaaacgcagggcttac----aatgtcttactcgggagtattttttcagGGTAAGTATACATGAAGCCATGGAGCAGCAAAGTATCAGCATCTCAAAAGCTGGTATAGTAACATCATTGCAAGCTCGTTGCTCTGTGATCGCTGCCGCA

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|211351173|gb|FL066633.1|FL066633
EST:     AGGGGCATTTGCCTCATTGACGAGTTTGACMAGATGAATGATCAAGATAG                         GGTAAGTATTCATGAAGCTATGGAGCAACAAAGTATCAGTATATCAAAAGC
genomic: AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
EST: gi|211174125|gb|FL130962.1|FL130962
EST:     AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAG                         GGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
genomic: AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
EST: gi|32932509|gb|CF037321.1|CF037321
EST:     AGGGGCATTTGCCTCATTGACGAGTTTGACAAGATGAATGATCAAGATAG                         GGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
genomic: AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
EST: gi|211172448|gb|FL130949.1|FL130949
EST:     AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAG                         GGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
genomic: AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
EST: gi|211174123|gb|FL130960.1|FL130960
EST:     AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAG                         GGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
genomic: AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
EST: gi|211174124|gb|FL130961.1|FL130961
EST:     AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAG                         GGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
genomic: AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
EST: gi|211172450|gb|FL130951.1|FL130951
EST:     AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAG                         GGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
genomic: AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
EST: gi|32943927|gb|CF048746.1|CF048746
EST:     GAATGATCAAGATAG                         GGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
genomic: GAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
EST: gi|30306555|gb|CD001228.1|CD001228
EST:     AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAG                         GGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
genomic: AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
EST: gi|29544563|gb|CB604943.1|CB604943
EST:     AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAG                         GGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
genomic: AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
EST: gi|211174122|gb|FL130959.1|FL130959
EST:     AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAG                         GGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
genomic: AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
EST: gi|29544433|gb|CB604813.1|CB604813
EST:     AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAG                         GGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
genomic: AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC

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: 48 (upstream exon), 48 (downstream exon)
Score: 432

CAGTAACACGAGAATGGACACTTGAGGGAGGTGCACTAGTTCTTGCTGATAGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 57

CAGTAACACGAGAATGGACACTTGAGGGAGGTGCACTAGTTCTTGCTGATAGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCA


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 41

CAGTAACACGAGAATGGACACTTGAGGGAGGTGCACTAGTTCTTGCTGATAGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 69

CAGTAACACGAGAATGGACACTTGAGGGAGGTGCACTAGTTCTTGCTGATAGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgctatttaaatttctgtattaccaaaaatgtaattttcttctgattgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCA
                                        ttctgat  putative branch site (score: 69)
                                              ttgtttc  CT-rich tract
     atttaaatttctgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatataccatttgtatttggatgtcctgtgctatttaaatttctgtattaccaaaaatgtaattttcttctgattgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC