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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactatgctagtcaatttgaagatataattgcaatgaaaagactgcatttacaagtgttgtctggtccatgaactaattgggtcttgttttgtggaacagACATGGACACAAAGGTTAAAGCAATGATCAAACTTATCAATGAAGATGCTGATTCTTTTGCAAGGAGAGCAGAGATGTACTACAAGAAACGTCCAGAGCT

Basic information

species Zea mays
transcript GRMZM2G012030_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G012030_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g28610.1 (Oryza sativa), 3'ss of exon 1
aactatgctagtcaatttgaagat-ataattgca-atgaaaagactgcatttacaagtgttgtctggtccatgaactaattgggtcttgttttgtggaacagACATGGACACAAAGGTTAAAGCAATGATCAAACTTATCAATGAAGATGCTGATTCTTTTGCAAGGAGAGCAGAGATGTACTACAAGAAACGTCCAGAGCT
   | ||    | ||||| |   | ||   |||| ||  |   |   ||||||  |            ||| |    ||     ||||||||| || ||||||||||||  ||||||||||||| |||||||||||| |||||||||||||||||||||||||| | |||||||||||||||||||||||||| ||||||||
--ttttgtagttgaatttcagtttgatgcctgcatattcactcatatcatttagcaacaagtcaataaccaaggttgaagctaatcttgttttatgcaacagACATGGATTCAAAGGTTAAAGCTATGATCAAACTTCTCAATGAAGATGCTGATTCTTTTGCACGAAGAGCAGAGATGTACTACAAGAAACGCCCAGAGCT

upper sequence: GRMZM2G012030_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA01G44680.1 (Glycine max), 3'ss of exon 1
aactatgctagtcaatttgaagatataattgcaatgaaaa--gact---gcatttacaagtgttgtctggtccatgaactaattgggtcttgt-tttgtggaacagACATGGACACAAAGGTTAAAGCAATGATCAAACTTATCAATGAAGATGCTGATTCTTTTGCAAGGAGAGCAGAGATGTACTACAAGAAACGTCCAGAGCT
   |||  ||  ||| |   ||  || |  | |||||     || |   |  | | |   ||||   |  ||||  |||| |   | | || | ||| ||   ||||||| || || || ||||||||||||||||| || ||  |||| || || ||||| ||||||||||| ||||| |||||||| ||||| ||||| |||||
---tataatatacaagtgcgagtaattaaggaaatgatggttgattcgggtctatgcttatgttacttaatccaataactgaagtgatgttatgtttatg---cagACATAGATACCAAAGTTAAAGCAATGATCAAGCTGATTGATGAGGAAGCAGATTCATTTGCAAGGAGGGCAGAAATGTACTATAAGAAGCGTCCGGAGCT

upper sequence: GRMZM2G012030_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G39070.1 (Glycine max), 3'ss of exon 1
------aactatgctagtcaatttgaagatataattgcaatgaaaagactgcatttacaagtgttgtctggtccatgaactaattgggtcttgttttgtggaacagACATGGACACAAAGGTTAAAGCAATGATCAAACTTATCAATGAAGATGCTGATTCTTTTGCAAGGAGAGCAGAGATGTACTACAAGAAACGTCCAGAGCT
      || |||  |     ||||  |    |||    | | | || | | |||    | ||  | | | |    ||   | |||  || ||  |   |    ||||||||||  | || || |||||||||||||| |||||  | || ||||| || || |||||||| || |||||||||||||| ||||| || ||||| ||
tcatcaaaatatagtgacatatttacac---taaaaaaattcataaaaatccatggttaggtaatctttag---gtggtgttattaagtgtttatactttatgcagACATGGATGCCAAAGTAAAAGCAATGATCAAGCTTATTGAAGAGGATGCAGACTCATTTGCAAGAAGGGCAGAGATGTACTATAAGAAGCGGCCAGAACT

upper sequence: GRMZM2G012030_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G03450.1 (Glycine max), 3'ss of exon 1
-aactatgctagtcaatttgaagatataattgcaatgaaaagactgcatttacaagtgttgtctggtccatgaactaattg---ggtcttgttttgtggaacagACATGGACACAAAGGTTAAAGCAATGATCAAACTTATCAATGAAGATGCTGATTCTTTTGCAAGGAGAGCAGAGATGTACTACAAGAAACGTCCAGAGCT
 |  | ||  | |  |||| |   |    ||   ||  |     |||  ||     | |   |  ||   |||||| ||     ||   | |  | | | ||||| |||||  | ||||| ||   |||||| || |||||  | |||||||| ||||| ||||| ||||||||||| ||||| || || ||||| ||||||||
gagatgtgacaat--atttaatttttctgttatcatccatttggtgccgtttgtgttttaagcacgtt--tgaacttatcacaaggatatttcctcttgcacagATATGGATGCCAAGGTGAAGCAAATGATTAAGCTTATTGAAGAAGATGCAGATTCCTTTGCCAGGAGAGCAGAAATGTATTATAAAAAACGCCCAGAGCT

upper sequence: GRMZM2G012030_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA11G00910.1 (Glycine max), 3'ss of exon 1
aactatgctagtcaatttgaagatataat-tgcaatgaaaag--actgcatttacaagtgttgtctggtccatgaac-taattgggtcttgttttgtggaacagACATGGACACAAAGGTTAAAGCAATGATCAAACTTATCAATGAAGATGCTGATTCTTTTGCAAGGAGAGCAGAGATGTACTACAAGAAACGTCCAGAGCT
 | |  |  |   |   |  |  |||||| | |||     ||  | |      |  || ||||  || | | ||  | |  ||  ||  |||||       ||||||| || || || || ||||||||||| || || ||  |||| || || ||||| ||||||||||| ||||| |||||||| ||||| ||||| |||||
taatgcgtcaaagatgctataactataatatacaagtgcgagtaattaaggaaatgagggttgattgattcgtgtccatgcttctgttatgttt----atgcagACATAGATACCAAAGTCAAAGCAATGATAAAGCTCATTGATGAGGAAGCAGATTCATTTGCAAGGAGGGCAGAAATGTACTATAAGAAGCGTCCGGAGCT

upper sequence: GRMZM2G012030_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA20G28750.1 (Glycine max), 3'ss of exon 1
aactatgctagtcaatttgaagatataattgcaatgaaaagactgcatttacaagtgttgtctggt--ccatgaacta-----attgggtcttgttttgtggaacagACATGGACACAAAGGTTAAAGCAATGATCAAACTTATCAATGAAGATGCTGATTCTTTTGCAAGGAGAGCAGAGATGTACTACAAGAAACGTCCAGAGCT
    ||  |  ||||  |  ||  ||  || || | | || | | |||  | |    | ||   ||   | | || |      |||  || ||  |   |    ||||||||||  | || || |||||||||||||| |||||  | || ||||| || || ||||||||||| |||||||||||||| ||||| || ||||| ||
----attttcatcaaaatacagtgat--ttacactaacaaaatt-cataaaaatccatggttcagtaatctttaagtggtgttattaagtgtttatactttatgcagACATGGATGCCAAAGTAAAAGCAATGATCAAGCTTATTGAAGAGGATGCAGACTCATTTGCAAGGAGGGCAGAGATGTACTATAAGAAGCGGCCAGAACT

upper sequence: GRMZM2G012030_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G16380.1 (Glycine max), 3'ss of exon 1
-aactatgctagtcaatttgaagatataattgcaatgaaaagactgcatttacaagtgttgtctggtc-catgaactaattg---ggtcttgttttgtggaacagACATGGACACAAAGGTTAAAGCAATGATCAAACTTATCAATGAAGATGCTGATTCTTTTGCAAGGAGAGCAGAGATGTACTACAAGAAACGTCCAGAGCT
 |  | ||  | |  ||||    || |   ||  || |      ||    |    ||||| |     |   |||||| ||     ||   |    | | | ||||| |||||  | ||||| ||   |||||| || |||||  | |||||||| ||||| ||||| ||||||||||| ||||| || || ||||| ||||||||
gagatgtgacaat--attt---aatttttctgttatcatccatttggtactgtctgtgttttaaaaacgtttgaacttatcacaaggatattccctcttgcacagATATGGATGCCAAGGTGAAGCAAATGATTAAGCTTATTGAAGAAGATGCAGATTCCTTTGCCAGGAGAGCAGAAATGTATTATAAAAAACGCCCAGAGCT

upper sequence: GRMZM2G012030_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT3G22790.1 (Arabidopsis thaliana), 3'ss of exon 2
aactatgctagtcaatttgaagatataattgcaatgaaaagactgcatttacaagtgttgt-ctggtccatga-actaattgggtcttgttttgtggaacagACATGGACACAAAGGTTAAAGCAATGATCAAACTTATCAATGAAGATGCTGATTCTTTTGCAAGGAGAGCAGAGATGTACTACAAGAAACGTCCAGAGCT
                     |      || |  |  |    ||  | |   ||||||| |  |  |   |   | |  ||  |  |  |||  ||    ||| |||||  | || || || |||||||| ||||| ||| | |||||||| |||||||||||||| || ||||||||||| ||||||||||||||||||||
---------------------gtgcctctttctctctatgttctaaagtgttaagtgttttgttcctttgtattattgcttacggttattttcttgatgtagATATGGATTCCAAAGTGAAGGCAATGATTAAACTCATCGAAGAAGATGCAGATTCTTTTGCAAGAAGGGCAGAGATGTATTACAAGAAACGTCCAGAGCT

upper sequence: GRMZM2G012030_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT4G14760.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------------aactatgctagtcaatt-tgaagatataattgcaatgaaaagactgcatttacaagtgttgtctggtccatgaactaatt------gggtcttgttttgtg---gaacagACATGGACACAAAGGTTAAAGCAATGATCAAACTTATCAATGAAGATGCTGATTCTTTTGCAAGGAGAGCAGAGATGTACTACAAGAAACGTCCAGAGCT
                                        |  |  || |  |||| ||    ||||||     |||   |  ||  |  | |  | |||| |  |     |   ||||         | ||  ||||||    ||||||||||||  | || || ||  ||||||| || || ||| | |  ||||| ||||| |||||||| || ||||| ||||||| ||||||||||||||||||
gtattctataatctttcttgacttctccttggtgttttttatgagtcttgaaaattgtggcattataatgcttttgatttgtatgtttaaagatattttgtttcttttggaagtcaatttaaaggaaatatttgtttgtgttgaaacagACATGGATTCCAAAGTCAAGACAATGATAAAGCTCATCGAAGCTGATGCAGATTCGTTTGCAAGAAGGGCAGACATGTACTTCAAGAAACGTCCAGAGCT

upper sequence: GRMZM2G012030_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT4G02710.1 (Arabidopsis thaliana), 3'ss of exon 2
-aactatgctagtcaatttgaagatataa-ttgcaatgaaaagactgcatttacaagtgttgtctggtccatgaactaattgggtcttgttttgtggaacagACATGGACACAAAGGTTAAAGCAATGATCAAACTTATCAATGAAGATGCTGATTCTTTTGCAAGGAGAGCAGAGATGTACTACAAGAAACGTCCAGAGCT
  |   | ||| |     || |  | ||  ||||  |           ||     |   | ||   |   ||||  |  ||   | || || | | |  |||| ||||| |  || || ||    ||||| ||  || |  | |||||||| ||||||||||| ||| ||||||||||||| |||   |||||||| |||||
gtatgtttctacttctagtgtatctttagcttgctcttttgttggcctatgatatatcatcgttaagctgatgatttgtttttttattattcttttgg-cagATATGGATAGTAATGTGAAGCAGATGATTAAGGTTCTTGAAGAAGATGCAGATTCTTTTGCCAGGCGAGCAGAGATGTATTACCGTAAACGTCCTGAGCT

upper sequence: GRMZM2G012030_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv07s0151g00430.t01 (Vitis vinifera), 3'ss of exon 3
--aactatgctagtcaatttgaagatataattgcaatgaaaagactgcatttacaagtgttgtctggtccatgaactaattgggtcttgttttgtggaacagACATGGACACAAAGGTTAAAGCAATGATCAAACTTATCAATGAAGATGCTGATTCTTTTGCAAGGAGAGCAGAGATGTACTACAAGAAACGTCCAGAGCT
  |  | ||        |||     ||| |||     ||      | |     ||||     | || |  |  |   ||      ||| |||  |  |||||| |||||  | || || |||  ||||||||| |||||  | |||||||| ||||| ||||||||||| |||||||||||||| ||||||||||| |||||
ttagttctgtgccatgtttttcttttatcattat--cgatcgcctttctcccccaagacacatgtgattgactatgaaaaccctccttatttgcttaaacagATATGGATGCCAAAGTCAAACAAATGATCAAGCTTATTGAGGAAGATGCAGATTCCTTTGCAAGGAGGGCAGAGATGTACTATAAGAAACGTCCTGAGCT

upper sequence: GRMZM2G012030_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv05s0020g03890.t01 (Vitis vinifera), 3'ss of exon 4
aactatgctagtcaatttgaagatataattg-caatgaaaagactgcatttacaagtgttgtctggtccatgaactaattgggtcttgttttgtggaacagACATGGACACAAAGGTTAAAGCAATGATCAAACTTATCAATGAAGATGCTGATTCTTTTGCAAGGAGAGCAGAGATGTACTACAAGAAACGTCCAGAGCT
|| | |  | ||   |||   |||   ||||    |        |   ||| |||  |        | ||   |     |  || || | |  | ||| ||| |||||    || || |||||||||||||| || ||  | |||||||| ||||| |||||| |||| ||||| |||||||||||||| |||||||| ||
aattgttttggttg-tttattgatcagattgattttttcctcttttttttttcaacagccactgtattcactgatcctatatgtattatctctttgaatagATATGGATGTCAAAGTGAAAGCAATGATCAAGCTCATTGAAGAAGATGCAGATTCCTTTGCACGGAGGGCAGAAATGTACTACAAGAAGCGTCCAGAACT

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: 235

ATGGCGACTTTGGTTCGTCATGATTCAAGGCAGTACTCTTGGTGGTGGGTTAGCCATATCAGCCCCAAGAACTCGAAATGGCTCCAGGAAAATCTCAGCGgtgagttcgt ... tgtggaacagACATGGACACAAAGGTTAAAGCAATGATCAAACTTATCAATGAAGATGCTGATTCTTTTGCAAGGAGAGCAGAGATGTACTACAAGAAACGTCCAGAGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 329

ATGGCGACTTTGGTTCGTCATGATTCAAGGCAGTACTCTTGGTGGTGGGTTAGCCATATCAGCCCCAAGAACTCGAAATGGCTCCAGGAAAATCTCAGCGgtgagttcgt ... tgtggaacagACATGGACACAAAGGTTAAAGCAATGATCAAACTTATCAATGAAGATGCTGATTCTTTTGCAAGGAGAGCAGAGATGTACTACAAGAAACGTCCAGAGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 455

ATGGCGACTTTGGTTCGTCATGATTCAAGGCAGTACTCTTGGTGGTGGGTTAGCCATATCAGCCCCAAGAACTCGAAATGGCTCCAGGAAAATCTCAGCGgtgagttcgt ... tgtggaacagACATGGACACAAAGGTTAAAGCAATGATCAAACTTATCAATGAAGATGCTGATTCTTTTGCAAGGAGAGCAGAGATGTACTACAAGAAACGTCCAGAGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 331

ATGGCGACTTTGGTTCGTCATGATTCAAGGCAGTACTCTTGGTGGTGGGTTAGCCATATCAGCCCCAAGAACTCGAAATGGCTCCAGGAAAATCTCAGCGgtgagttcgt ... tgtggaacagACATGGACACAAAGGTTAAAGCAATGATCAAACTTATCAATGAAGATGCTGATTCTTTTGCAAGGAGAGCAGAGATGTACTACAAGAAACGTCCAGAGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttacaagtgttgtctggtccatgaactaattgggtcttgttttgtggaacagACATGGACACAAAGGTTAAAGCAATGATCAAACTTATCAATGAAGATGCTGATTCTTTTGCAAGGAGAGCAGAGATGTACTACAAGAAACGTCCAGAGCT
                          aactaat  putative branch site (score: 331)
                                     tcttgtttt  putative PPT
                          aactaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactatgctagtcaatttgaagatataattgcaatgaaaagactgcatttacaagtgttgtctggtccatgaactaattgggtcttgttttgtggaacagACATGGACACAAAGGTTAAAGCAATGATCAAACTTATCAATGAAGATGCTGATTCTTTTGCAAGGAGAGCAGAGATGTACTACAAGAAACGTCCAGAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT