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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatctacctcatcagtgattaatgtaagcagcatgtgtgctataattgttcatcctttccctctgatttcacatgttatatttgtatggtttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG

Basic information

species Zea mays
transcript GRMZM5G824831_T04
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G824831_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 7
---------------------------------------tatctacctcatcagtgatta-atgtaagcagcatgtgtgctataattgttcatcctttccc------tctgatttcacatgttatatt----------tgtatggtttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG
                                       | | | |||||    |||| | |  |||   | || |||  ||  |   |   | ||||||       | ||| | ||| |||  | ||          | ||||   |||||  |||||||||||||| ||||||||||||||||||||||| ||||| ||||||||| ||||||||||
gtacatagcataccactaatattgtattgtactacactctgttttcctcaatc-tgatcagaaataaagtggatttgt-ttacgaggatatcttctttccaaagttgtatgactgcacttgtactgttgttcaacctctttatgtcctcatttcagATACACAGAAGACATGGAGCTTGATGATGCCATCCATACTGCCATTTTGACTCTGAAAGAAGG

upper sequence: GRMZM5G824831_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA08G17810.3 (Glycine max), 3'ss of exon 9
tatctacctcatcagtgattaatgtaagcagcatgtgtgctat-aattgttcatcctttccctctgatttcacatgttatatttgtatggtttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG
  | |   || |  | ||| | ||| |  |   || ||   || | ||   | || ||| |||     ||   ||| |  | ||| || ||    ||  || |||||||| ||||||||||||||||||||  ||||||| ||||| |||||| |||| |||||
actttctttctttggagataattgtgattatgttgagtttcattagttacacctcattttccttatcatttctatggttgacttg-attgtccacttacagGTACACAGATGATATGGAGCTTGATGATGCAGTCCACACAGCAATATTGACTCTGAAGGAAGG

upper sequence: GRMZM5G824831_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA03G16660.1 (Glycine max), 3'ss of exon 9
----tatctacctcatcagtgattaatgtaagcagcatgtgtgctataattgttcatcctttccctctgatttcacatgttatatttgtatggtttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG
    ||| |      ||  ||| | || | ||  ||||  ||  ||      |||||  ||||||| | |||||  ||| |  | ||  || ||    ||  || |||||||| |||||||||||||||||| |  ||||||| ||||| |||||| |||| |||||
tgattatattatatttctttgaatgatttgagttgcattagttttacctcatttcat--tttccctatcatttc-tatggttgactta-attgtccacttacagGTACACAGATGATATGGAGCTTGATGATTCAGTCCACACAGCAATATTGACTCTGAAGGAAGG

upper sequence: GRMZM5G824831_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA03G16660.2 (Glycine max), 3'ss of exon 9
tatctacctcatcagtgattaatgtaagcagcatgtgtgctataattgttcatcctttccctctgatttcacatgttatatttgtatggtttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG
    ||  |  ||  ||| | || | ||  ||||  ||  ||      |||||  ||||||| | |||||  ||| |  | ||  || ||    ||  || |||||||| |||||||||||||||||| |  ||||||| ||||| |||||| |||| |||||
---ttatatt-tctttgaatgatttgagttgcattagttttacctcatttcat--tttccctatcatttc-tatggttgactta-attgtccacttacaggtacacagATGATATGGAGCTTGATGATTCAGTCCACACAGCAATATTGACTCTGAAGGAAGG

upper sequence: GRMZM5G824831_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA15G41330.1 (Glycine max), 3'ss of exon 9
----------tatctacctcatcagtgattaatgtaagcagcatgtgtgctataattgttcatcctttccctctgatttcacatgttatatttgtatggtttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG
          |   ||  |  ||  ||| | || | ||   ||| |||  ||       ||||  ||||||  | |||||  ||| |  | ||| || ||    ||  || |||||||| ||||||||||||||||||||  ||||||| ||||| |||||| |||| |||||
aagataattgtgattatgtt-tccctgagtgatttgagattcatttgttatac-----ctcat--tttccccatcatttc-tatggttgacttg-attgtccacttacagGTACACAGATGATATGGAGCTTGATGATGCAGTCCACACAGCAATGTTGACTCTGAAGGAAGG

upper sequence: GRMZM5G824831_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA01G25940.2 (Glycine max), 3'ss of exon 8
----tatctacctcatcagtgattaatgtaagcagcatgtgtgctataattgttcatcctttccctctgatttcacatgttatatttgtatggtttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG
    ||| ||     ||  ||| | || | ||  ||||  ||  ||      |||||  ||||||| | |||||  ||| |  | ||| || ||    ||  || |||||||| ||||||||||||||||||||  |||||||  |||| ||||||||||| |||||
tgattatataatatttctttgagtgatttgagttgcattagttttacttcatttcat--tttccctatcatttc-tatggttgacttg-attgtccacttacagGTACACAGATGATATGGAGCTTGATGATGCAGTCCACACATCAATATTGACTTTGAAGGAAGG

upper sequence: GRMZM5G824831_T03 (Zea mays), 3'ss of exon 9
lower sequence: AT1G16470.1 (Arabidopsis thaliana), 3'ss of exon 9
-----------------------------------------------------------------tatctacctcatcagtgattaatgtaagcagcatgtgtgctataattgttcatcctttccctctgattt-cacatgttatatttgtatggtttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG
                                                                 | | |  ||  |||    |  ||   |   ||   |||  ||  | | |  | ||  ||    |   |  || |  |||      || | |||| ||| || ||||||||||| ||||| ||||| |||||||| ||||| || ||  |||| |||||||||||
gtaatactgtttacaatttgttgatatccaaagatatataaccagtatactgattttgaaaattttcttttactactcaaatttcgataatataggctcctgtcataacaatatgaaaccactcttcgtcgctgacaaaccttaaccaattacgatttccttgcagGTACACAGAAGACATGGAACTTGACGATGCCATTCACACAGCGATACTGACATTGAAAGAAGG

upper sequence: GRMZM5G824831_T03 (Zea mays), 3'ss of exon 9
lower sequence: AT1G79210.3 (Arabidopsis thaliana), 3'ss of exon 9
tatctacctcatcagtgattaatgtaagcagcatgtgtgctataattgttcatcctttccctctgatttcacatgttatatttgtatggtttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG
                      ||  |  |   |      | |  |  |   |   |   ||  ||     ||||| || |     | || |      || ||||||||||||||||| |||||||||||||| ||||| ||||| ||||| ||||| |||||
---------------------gtgataataatttaccatttgtggtgatgagtttatgatcttggaa---gcatgtcatttcatcttagtctttgatcagGTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGACATTGAAGGAAGG

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|18181390|gb|BM382600.1|BM382600
EST:     TCAGCCATGGNNNNNNNTGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|211252215|gb|FK953396.1|FK953396
EST:     TCAGCCATGGGAAAAAATGTGTCCTATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGGAGCTTGATGATGCCATCCACACTGCAATTTTGA
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGG-AGCTTGATGATGCCATCCACACTGCAATTTTGA
EST: gi|211269953|gb|FL444406.1|FL444406
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|6952542|gb|AW424610.1|AW424610
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACCGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|148973074|gb|EE024136.2|EE024136
EST:     TCAGCCATGGNNNNNNNTGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|78112696|gb|DV531090.1|DV531090
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGATGATGCCATCCCCCCTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|5268558|gb|AI770522.1|AI770522
EST:     TCAGCCATGGTAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAATATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|149076954|gb|EE165611.2|EE165611
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|211149323|gb|FL312581.1|FL312581
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|32830197|gb|CD969875.1|CD969875
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|71447361|gb|DR828411.1|DR828411
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAAAATATGGAGCTTGATGAT
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGA-TATGGAGCTTGATGAT
EST: gi|78112697|gb|DV531091.1|DV531091
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACT
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACT
EST: gi|6194486|gb|AW146590.1|AW146590
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|211153309|gb|FL164197.1|FL164197
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCT
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCT
EST: gi|67024880|gb|CO453629.1|CO453629
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|32795340|gb|CD947576.1|CD947576
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGGTGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
EST: gi|211321302|gb|FL273340.1|FL273340
EST:     TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAG                         ATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC
genomic: TCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGAC

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), 49 (downstream exon)
Score: 485

GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 241

GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 192

GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 311

GTTGATCCCTCAGGATCATACTTCTCCTGGAAGGCATCAGCCATGGGAAAAAATGTGTCCAATGCAAAGACGTTTCTTGAAAAGAGgtacagcctc ... ttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttcatcctttccctctgatttcacatgttatatttgtatggtttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG
               ctctgat  putative branch site (score: 311)
                                            tttcatt  putative PPT
                           atgttatatttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatctacctcatcagtgattaatgtaagcagcatgtgtgctataattgttcatcctttccctctgatttcacatgttatatttgtatggtttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG