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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcaccatttactcagatcacacaaactggcttatctttattgttgcctggctaacatgatatgctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGACACGTATGTCATATTCGGCGAGGCTAAGATCGAGGACCTCAGCTCCCAGC

Basic information

species Zea mays
transcript GRMZM2G000923_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000923_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G27580.2 (Glycine max), 3'ss of exon 3
---gtaattcaccatttactcagatcacacaaactggcttatctttat-tgttgc---ctggctaacat--gatatgctatttcc----------agATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGACACGTATGTCATATTCGGCGAGGCTAAGATCGAGGACCTCAGCTCCCAGC
      |||   ||| || | |  |   | ||  |  | |   || || | || |   || |  || ||   || |  |  | |           |||| || ||||| || || ||||||||||| ||||||||||||| ||| ||||| ||  | ||||||||||| || ||||| || ||| | ||||| ||||
gttagcatttgacatctatttattttgaagaacttttcattgtttcatctatttcgtacttgtcaatattgaatttatttctcctttgtttgtttagATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGACACATACATTATATTCGGCGAAGCCAAGATTGAAGACTTGAGCTCACAGC

upper sequence: GRMZM2G000923_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------------gtaattcaccatttactcagatcacacaaactggcttatctttattgttgcctggctaacatgatat--gctatttc-------cagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGACACGTATGTCATATTCGGCGAGGCTAAGATCGAGGACCTCAGCTCCCAGC
                                                 || | |||| | || |   |       ||   ||     |    |||     ||    | || |  | |||| |       |||||  | |||||||| || ||||||||||| ||||||||||| |  || || || |||||||| || |||||||| ||||| || ||| | ||||| ||||
gttagtttccctctcttttctttgtgtgtatattcccctcttgctccccatgccccatctgcttaatccttttgtcctccttttgtcctccctttgaacttctgttgtaatctcggttattacttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGATACATATGTCATTTTTGGCGAGGCAAAGATTGAAGACTTGAGCTCACAGC

upper sequence: GRMZM2G000923_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0040g00600.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------------------------gtaattcaccatttactcagatcacacaaactggcttatc-tttattgttgcctggctaacatgatatgctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGACACGTATGTCATATTCGGCGAGGCTAAGATCGAGGACCTCAGCTCCCAGC
                                                      |  |   |  |||| |   |     |   ||   |||   | |||||    | |  ||  ||| | |    | | ||||| |||||||||||||| || |||||||||||||||||||| | ||| ||||| ||||| ||||| |||||||| ||||| |||||  | || || || |
gtcagtttctctttgcccactgttgattactttttatttttcatgttgggcctattgtcacctctttaatatcaggtttctttctattttacaatctattgaaagcagtttactatggtttttattattcagATTCTCTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCAACTTCAGACACTTATGTAATATTTGGCGAGGCAAAGATTGAGGATTTGAGTTCACAAC

upper sequence: GRMZM2G000923_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S539_1V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------gtaattcac-catttactcagatcacacaaactggcttatctttattgttgcctggctaacatgat-atgctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGACACGTATGTCATATTCGGCGAGGCTAAGATCGAGGACCTCAGCTCCCAGC
                       | |  ||  |||   ||||||| |   |  || |  |  || | |          |||| | ||  ||| | || ||||| |||||||| ||||| || || |||||||||||||||||    || ||||| || || || ||||||||||| ||||| |||||  | || || ||  
tataccttcaatctttatcgcagattctacatattctttcagatc-cttgagatgtcagaatttcaatagcttgcaagtaacttcatcgtgcaacttgcagATCCTCTTTGTGATCTCGAAGCCTGATGTGTTCAAGAGCCCTGCATCAGACACTTACGTAATCTTCGGCGAGGCAAAGATTGAGGATTTGAGTTCTCAAT

upper sequence: GRMZM2G000923_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 3
gtaattcaccatttactcagatcacacaaactggcttatctttattgttgcctggctaacatgatatgctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGACACGTATGTCATATTCGGCGAGGCTAAGATCGAGGACCTCAGCTCCCAGC
                | || |  |       |    |     || |   |     |  | |     | | |||||||||||| ||||| |||||||| || || |||||||||||||||   ||||||||  |  |||| || |||||||| |||||||||||| | || |||||||
---------------gtaagcttgcgttggtagatcgaagagaatagagactaacttcgctt--ctggttctttccagATACTGTTTGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC

upper sequence: GRMZM2G000923_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ21445 (Selaginella moellendorffii), 3'ss of exon 1
gtaattcaccatttactcagatcacacaaactggcttatctttattgttgcctggctaacatgatatgctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGACACGTATGTCATATTCGGCGAGGCTAAGATCGAGGACCTCAGCTCCCAGC
                | || |  |  |   | | | |     | |   | ||  ||  |      || | |||||||||||| || || |||||||| || || |||||||||||||||   ||||||||  |  |||| || |||||||| |||||||||||| | || |||||||
---------------gtaagcttgcgtag--tagatgaaagagaatagagtctaactt-cgctccttgttctttccagATACTGTTCGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC

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|9028696|gb|BE238736.1|BE238736
EST:     CCGCGTCACTGTAAAGAAAAGCAAGAAT                         ATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
genomic: CCGCGTCACTGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
EST: gi|60352329|gb|DN219302.1|DN219302
EST:     TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAAT                         ATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
genomic: TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
EST: gi|31910389|gb|CD651399.1|CD651399
EST:     TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAAT                         ATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
genomic: TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
EST: gi|37386513|gb|CF630442.1|CF630442
EST:     TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAAT                         ATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
genomic: TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
EST: gi|12971083|gb|BG267306.1|BG267306
EST:     TGTAAAGAAAAGCAAGAAT                         ATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
genomic: TGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
EST: gi|4776550|gb|AI665553.1|AI665553
EST:     TGTAAAGAAAAGCAAGAAT                         ATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
genomic: TGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
EST: gi|5124085|gb|AI745926.1|AI745926
EST:     TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAAT                         ATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
genomic: TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
EST: gi|30087450|gb|CB885656.1|CB885656
EST:     TGTAAAGAAAAGCAAGAAT                         ATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
genomic: TGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
EST: gi|78026202|gb|DV494589.1|DV494589
EST:     TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAAT                         ATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
genomic: TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
EST: gi|47961571|gb|CN844280.1|CN844280
EST:     GTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAAT                         ATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
genomic: GTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
EST: gi|37392534|gb|CF633519.1|CF633519
EST:     TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAAT                         ATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
genomic: TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
EST: gi|60348322|gb|DN215295.1|DN215295
EST:     TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAAT                         ATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
genomic: TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
EST: gi|78025744|gb|DV494131.1|DV494131
EST:     TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAAT                         ATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
genomic: TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
EST: gi|78025838|gb|DV494225.1|DV494225
EST:     TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAAT                         ATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
genomic: TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
EST: gi|24766680|gb|CA401827.1|CA401827
EST:     TGAAGCCCATCACTGGTGTCAGCCGCGTCNCTGTAAAGAAAAGCAAGAAT                         ATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
genomic: TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
EST: gi|60396469|gb|DN229338.1|DN229338
EST:     TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAAT                         ATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
genomic: TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
EST: gi|30088348|gb|CB886553.1|CB886553
EST:     TGAAGCCCATCACTGGGGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAAT                         ATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
genomic: TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
EST: gi|31910387|gb|CD651398.1|CD651398
EST:     TGAAGCCCATCACTGGTGTCAGCCGCGTCNCTGTAAAGAAAAGCAAGAAT                         ATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
genomic: TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
EST: gi|211430625|gb|FL465163.1|FL465163
EST:     CGCGTCACTGTAAAGAAAAGCAAGAAT                         ATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
genomic: CGCGTCACTGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
EST: gi|74240376|gb|DT648290.1|DT648290
EST:     TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAAT                         ACACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
genomic: TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
EST: gi|31910255|gb|CD651332.1|CD651332
EST:     TGAAGCCCATCNCTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAAT                         ATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC
genomic: TGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGAC

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: 418

GCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGACACGTATGTCATATTCGGCGAGGCTAAGATCGAGGACCTCAGCTCCCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 499

GCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGACACGTATGTCATATTCGGCGAGGCTAAGATCGAGGACCTCAGCTCCCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 623

GCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGACACGTATGTCATATTCGGCGAGGCTAAGATCGAGGACCTCAGCTCCCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 356

GCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGTCACTGTAAAGAAAAGCAAGAATgtaattcacc ... ctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGACACGTATGTCATATTCGGCGAGGCTAAGATCGAGGACCTCAGCTCCCAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acacaaactggcttatctttattgttgcctggctaacatgatatgctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGACACGTATGTCATATTCGGCGAGGCTAAGATCGAGGACCTCAGCTCCCAGC
                              ggctaac  putative branch site (score: 356)
                                             ctatttcc  putative PPT
            ttatctttattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattcaccatttactcagatcacacaaactggcttatctttattgttgcctggctaacatgatatgctatttccagATACTCTTTGTCATCTCCAAACCAGATGTGTTCAAGAGCCCGAATTCCGACACGTATGTCATATTCGGCGAGGCTAAGATCGAGGACCTCAGCTCCCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC