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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggctgctaacgctgtgttttgacctttcaatataaggctgattgtgaatataacattgcgttggttgtttcttttttctgcttattcacaagcaaatcaaaattatgatttcaaattatgaacttgctccatagGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGGGGATCTGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCT

Basic information

species Zea mays
transcript GRMZM2G059151_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 5
gttggctgctaacgctgtgttttgacctttcaatataaggctgattgtgaatataacattgcgttggttgtttcttttttctgcttattcacaagcaaatcaaaattatgatttcaaattatgaacttgctccatagGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGGGGATCTGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCT
                        |   | ||| |||  |   | | |  |||| |   |     | | ||||  ||       |||   | | ||   |  | |   ||| |    ||| |    |  ||   ||||   | |||||||||||| ||||| |||||||||||||||||||| ||||| ||||||||||| ||||||||||| ||||||||||| ||||| || |||
-----------------------aattctgcaacatagag---aatctagatattattct----cgatagttttattggcaatattaactatatgcttgttgacaa-gtgagt---gattgt---ttaactttgtagGGGGAAGAACATGAAAACTCGTGTCATTGGTTGCCCAAAGACTATTGATGGAGATCTGAAATGCAAGGAGGTTCCAACAAGCTTTGGGTTTGACACTGCT

upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 3
gttggctgctaacgctgtgttttgacct-ttcaatataaggctgattgtgaatataacattgcgttggttgtttcttttttctgcttattcacaagcaaatcaaaattatgatttcaaattatgaacttgctccatagGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGGGGATCTGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCT
                      | |  | ||    |||    |||  |  || || || || | |   |       |||| ||| ||  | |          |  ||| |   ||||| ||          |  | |||   |  || |||||||| ||||| ||||| ||||| || || || ||||| ||| ||||||| || || ||||| ||||| ||||| ||||||||||| 
----------------------taatttgtttggcatatacatgagagaaaaaattacctttcataaatatacaacttttcctgtttcctta----------actattgtttgttcaatttgga------ttatacagGAGTAAAAATATGAAAACTCGTGTGATTGGGTGCCCTAAAACCATTGATGGTGATTTGAAATGCAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCA

upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G39380.1 (Glycine max), 3'ss of exon 5
----gttggctgctaacgctgtgttttgacctttcaatataaggctgattgtgaatataacattgcgttggttgtttcttttttctgcttattcacaagcaaatcaaaattat--gatttcaaattatgaacttg--ctccatagGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGGGGATCTGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCT
      ||   |  ||   |   |||  | || |  || |   |   | | ||  |   | |   | |  |       ||   | |  | | |    |||   ||    || |   | |     |  | || |||   |  | |||   |  || |||||||| ||||| ||||| ||||| || || || ||||| ||| ||||||| || || ||||| ||||| ||||| ||||||||||| 
gttctatgaagggaaaaattacctttccatctgttcatctgttgtataatttgtttggcatac-acatgagagaaaaattacctttcataaatatgcagctgttcctgtttctttaactatttctgtttaatttggattatacagGAGTAAAAATATGAAAACTCGTGTGATTGGGTGCCCTAAAACCATTGATGGTGATTTGAAATGCAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCA

upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 5
----------gttggctgctaacgctg-tgtt-ttgacctttcaatataaggctgattgtgaa--tataacattgcgttggttgtttcttt-------------tttctgcttattcacaagcaaatcaaaattatgatttcaa-attatgaacttgctccat--agGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGGGGATCTGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCT
          | ||  |  ||   ||| |||  |  |  | | |  |      ||||  ||||   ||    |   ||||||| ||  |||             ||||   ||||  | | ||| |   |   | |   |||||   | | |  | | | |||  |||   |  ||  | |||||  |||| ||||| ||||| || || || ||||| ||| |||||||||| || ||||| ||||| ||||| ||||||||||||
gtttgtcttagctgaattttatttctggtgtaatctatgtcttaggaagcttttgatattgaaatcatgttttcatgttggtttttaatttacattcaaggacatttccatttatgaatatgcatagtgatcctgtttgttcaatgctttaatatggattcatgcagGAGCAAAAATTTAAAAACAAGTGTAATTGGATGCCCTAAAACCATTGATGGTGATTTGAAATGTAAAGAAGTTCCCACAAGTTTTGGGTTTGATACAGCT

upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 5
-----gttggctgctaa---cgctgtgttttgacctttcaatataaggctgattgtgaatataacattgcgttggttgtttcttttttctgcttattcacaagcaaatcaaaattatgatttcaaattatgaacttgctccat-agGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGGGGATCTGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCT
       | || | | |    | | ||||   || | |  || | |||| ||  ||   | |  | |   | |   |||  |     |||  ||| |        | |||  ||| ||| ||   |||||  |||||    || |||   | |||| |||||||||| || ||||| ||||| ||||| || ||||| ||| ||||||| || |||||||| || || ||||| ||||||||||||
gtaaaccttgcagttgaatctgttatgttgaaacttatttatcttaggc-gaaagtagttgtt-cttgaagatccatgtgaccagaatct--ttaatatttgctgattcagcatt-tgactt---attatctacttgtataattagGAGTAAGAACTTGAAAACCCGAGTCATTGGGTGCCCCAAGACCATTGATGGTGATTTGAAATGCAAAGAGGTTCCTACTAGTTTTGGGTTTGATACAGCT

upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 5
gttggctgctaacgctgtgttttgacctttcaatataaggctgattgtgaatataacattgcgttggttgtttcttttttctgcttattcacaagcaaatcaaaattatgatttcaaattatgaacttgctccat-agGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGGGGATCTGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCT
                                      |    |||  |||    ||  || | |  |      |     |||  | || |  |   | | |    | | | || |  | ||  |  ||    || |||   |  || |||||| | || || ||||| ||||||||||| || ||||| ||| ||||||| ||||||||||| ||||| |||||||||||||| || 
-------------------------------------tgttaaattcagaaatctactatgtgatcatcagaa-taagaactgactctttagtaatcagtgatttgtttaactttatttgatctatctgacaaatcagGGGTAAAAATATGAAAGCTCGGGTGATTGGATGCCCAAAGACCATTGATGGTGATTTGAAATGCAAGGAGGTTCCCACAAGTTTTGGATTTGATACTGCA

upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ13842 (Selaginella moellendorffii), 3'ss of exon 5
gttggctgctaacgctgtgttttgacctttcaatataaggctgattgtgaatataacattgcgttggttgtttcttttttctgcttattcacaagcaaatcaaaattatgatttcaaattatgaacttgctccatagGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGGGGATCTGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCT
                                                                  ||| |    || |  |  ||||  | ||  |||      || |||  |   ||        ||      ||  |||||||| ||||||| | |||||| || |||||||||||||| ||||| ||||| ||  | ||||| || ||||  || || ||||| || ||||| 
------------------------------------------------------------------gttatagtattctctt--ttatctagaaaaaaaaagtgtttttgacgttcgatcgctt-tctgtcatccagAGCAAGGAACCTGAAAACTCATGTTATCGGATGCCCAAAGACTATTGATGGTGATCTTAAGAGCAAGGAAGTGCCGATTAGTTTCGGATTCGACACAGCC

upper sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 5
lower sequence: EFJ12684 (Selaginella moellendorffii), 3'ss of exon 5
gttggctgctaacgctgtgttttgacctttcaatataaggctgattgtgaatataacattgcgttggttgtttcttttttctgcttattcacaagcaaatcaaaattatgatttcaaattatgaacttgctccatagGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGGGGATCTGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCT
                                                                     |||    | ||||  ||  ||   |  |||      || |||| |   ||        ||      ||  |||||||| ||||||| | |||||| || |||||||||||||| ||||| ||||| ||  | ||||| || ||||  || || ||||| || ||||| 
---------------------------------------------------------------------gttatagtattctcttttatctagaaaaaaaagtgtttttgatgttcgatcgctt-tctgtcatccagAGCAAGGAACCTGAAAACTCATGTTATCGGATGCCCAAAGACTATTGATGGTGATCTTAAGAGCAAGGAAGTGCCGATTAGTTTCGGATTCGACACAGCC

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|29167975|gb|CB411235.1|CB411235
EST:     GGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAATACTTTAG                         GTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGG
genomic: GGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAATACTTTAGgttggctgct ... tgctccatagGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGG
EST: gi|211458486|gb|FL255599.1|FL255599
EST:     GGTGGTGATGATTCAA-CACCAATGCCTGCCTCCTTGGTGAATACTTTAG                         GTTCA-GGA-CATTGAAA-CCCGCTGTTAT-GGTTTGCCCAA-GACTATC
genomic: GGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAATACTTTAGgttggctgct ... tgctccatagGT-CAAGGAACAT-GAAAACCCG-TGTTATTGGTT-GCCCAAAGACTATC
EST: gi|148953762|gb|EC899129.2|EC899129
EST:     GGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAATACTTTAG                         GTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGG
genomic: GGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAATACTTTAGgttggctgct ... tgctccatagGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGG
EST: gi|211458479|gb|FL255592.1|FL255592
EST:     GTGGTGATGATTCAAACACCAATGCCCTGCCTCCNTGGTGAATACTTTAG                         GTCA-GGAACATGNANNACCCGTGTTATTGGTTGCCCAAA-ACTATTCGAT
genomic: -TGGTGATGATTCAAACACCAATGCC-TGCCTCCTTGGTGAATACTTTAGgttggctgct ... tgctccatagGTCAAGGAACATGAAA-ACCCGTGTTATTGGTTGCCCAAAGACTAT-CGAT
EST: gi|211458477|gb|FL255590.1|FL255590
EST:     TGGTGATGATTCAAACACCNATGCCTGCCCTC-TTNGTGAAATACTT-AG                         GTCAAGGA-CATGAAAACCCGTGTTATTGGTTGCC-AAAGACTATCGATG
genomic: TGGTGATGATTCAAACACCAATGCCTGCC-TCCTTGGTGAA-TACTTTAGgttggctgct ... tgctccatagGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATG
EST: gi|211462254|gb|FL324872.1|FL324872
EST:     GGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGA-TACTTTAG                         GTCAAGGAACATGAAAACC-GTGNTATTGGTTGCCCAA-GACTATCGATGG
genomic: GGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAATACTTTAGgttggctgct ... tgctccatagGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGG
EST: gi|31348678|gb|CD433035.1|CD433035
EST:     GGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAATACTTTCC                         GTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGG
genomic: GGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAATACTTTAGgttggctgct ... tgctccatagGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGG
EST: gi|211179440|gb|FL364368.1|FL364368
EST:     GGTGGTGATGATTCAAACAC-AATGCCTGCCTCCTTGGTGAATACTTTAG                         GTCAAGGA-CATGAAAACC
genomic: GGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAATACTTTAGgttggctgct ... tgctccatagGTCAAGGAACATGAAAACC
EST: gi|211540563|gb|FL329390.1|FL329390
EST:     GGTGGTGATGATTCAAACACCAATGNCTGCCTCCTTGGTGAATACTTTAN                         GTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGG
genomic: GGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAATACTTTAGgttggctgct ... tgctccatagGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGG
EST: gi|149103124|gb|EE288493.2|EE288493
EST:     GGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAATACTTTAG                         GTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGG
genomic: GGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAATACTTTAGgttggctgct ... tgctccatagGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGG
EST: gi|31354738|gb|CD439095.1|CD439095
EST:     GGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAATACTTTAG                         GTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGG
genomic: GGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAATACTTTAGgttggctgct ... tgctccatagGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGG
EST: gi|211334009|gb|FL255568.1|FL255568
EST:     GTGGTGATGATTCAAACACCAATGCCTGCCTTCCT-GGTGAATACTTTAG                         GTCAAG-AACATGAAAACCCGTGTTTTTTGGTTGCCCAAAGACTTTCGATG
genomic: GTGGTGATGATTCAAACACCAATGCCTGCCT-CCTTGGTGAATACTTTAGgttggctgct ... tgctccatagGTCAAGGAACATGAAAACCCGTGTTATT-GGTTGCCCAAAGACTATCGATG

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: 236

AAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTTGTCATTGGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAATACTTTAGgttggctgct ... tgctccatagGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGGGGATCTGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 298

AAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTTGTCATTGGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAATACTTTAGgttggctgct ... tgctccatagGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGGGGATCTGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 296

AAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTTGTCATTGGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAATACTTTAGgttggctgct ... tgctccatagGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGGGGATCTGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 333

AAGCTGAAGACACGGCCAACAAGCTTGATTTGGATGGACTTGTTGTCATTGGTGGTGATGATTCAAACACCAATGCCTGCCTCCTTGGTGAATACTTTAGgttggctgct ... tgctccatagGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGGGGATCTGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttattcacaagcaaatcaaaattatgatttcaaattatgaacttgctccatagGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGGGGATCTGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCT
                                           cttgctcc  CT-rich tract
              aaatcaaaattatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggctgctaacgctgtgttttgacctttcaatataaggctgattgtgaatataacattgcgttggttgtttcttttttctgcttattcacaagcaaatcaaaattatgatttcaaattatgaacttgctccatagGTCAAGGAACATGAAAACCCGTGTTATTGGTTGCCCAAAGACTATCGATGGGGATCTGAAATGTAAGGAGGTTCCGACAAGCTTTGGATTTGATACAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT