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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgctttctctgctgtgcggtttcattaaacttgtatgcgttgtcttgttagctttacatgctatggtgttagGTCGATGAGAATTTTCTTTTGAGGACATTTGGTCGGTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTAGAACAGAAGAGGAACGCAGAAGGCAAA

Basic information

species Zea mays
transcript GRMZM2G174785_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174785_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g08360.1 (Oryza sativa), 3'ss of exon 7
---------------gttgctttctctgctgtgcggtttcattaaacttgtatg--cgttgtcttgttagctttac-atgctatggtgttagGTCGATGAGAATTTTCTTTTGAGGACATTTGGTCGGTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTAGAACAGAAGAGGAACGCAGAAGGCAAA
                  ||||  | || |      |    ||||  ||  ||     ||  |||| | | |  |  ||  |||  ||  |||| || |||||||||||| |||||||||||||||| |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||
gttggcattctccaatgcgcttgttttgtttatacataaggttaactttacatcatgattaacttgatggttgcattatattata-tgacagGTGGACGAGAATTTTCTTATGAGGACATTTGGTCGTTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTCGAACAGAAGAGGAACGCAGAAGGCAAA

upper sequence: GRMZM2G174785_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA16G15820.1 (Glycine max), 3'ss of exon 3
-------------gttgctttctctgctgtgcggtttcattaaacttgtatgcgttgtcttgttagctttaca-tgctatggtgttagGTCGATGAGAATTTTCTTTTGAGGACATTTGGTCGGTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTAGAACAGAAGAGGAACGCAGAAGGCAAA
              |   |   |   || ||  |||   | | | ||       |  |  | | | | |  || |  | |  |  ||||| ||||| ||||||||| |  | || |||||  | |||||||||||||||||||| |||||||||||||| |||||||| |||||  | ||  ||||||
gtcagagtgtcccctcaatagatggactttgttgttctttgagaattaaggagatgttagtctcatcatcgcagttttgtaattgtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGAACAGAGGAGGAGAGAAGGCGGCAAA

upper sequence: GRMZM2G174785_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA08G34030.2 (Glycine max), 3'ss of exon 7
-------------gttgctttctctgctgtgcggtttcattaaacttgtatgcgttgtcttgttagctttaca-tgctatggtgttagGTCGATGAGAATTTTCTTTTGAGGACATTTGGTCGGTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTAGAACAGAAGAGGAACGCAGAAGGCAAA
              |   |   |  ||| ||  |||   |   | ||     | |  |  | | | |||  || |  | |  |  ||||| ||||| ||||||||| |  | || |||||  | |||||||||||||||||||| |||||||||||||| || ||||| |||||  | ||  ||||||
gttagagtgtcccctcaataaatgggctttgttgttctttgggaattaaggacatgttagtctcaccttggcagttttttaattgtagGTTGATGAAAATTTTCTTCTCCGTACTTTTGGAAGATTTGGACCTATTGCTAGTGTGAAGATTATGTGGCCAAGGACAGAGGAGGAGAGAAGGCGGCAAA

upper sequence: GRMZM2G174785_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT5G25060.1 (Arabidopsis thaliana), 3'ss of exon 6
----------gttgctttctctgct---gtgcggtttcattaaac--ttgtatgcgttgtcttgttagctttacatgctatggtgt--tagGTCGATGAGAATTTTCTTTTGAGGACATTTGGTCGGTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTAGAACAGAAGAGGAACGCAGAAGGCAAA
           || ||| ||  | |    ||  ||||  |    |  |||||| | |  | ||  ||   |   ||  |||| |    ||||| ||||||||||| ||| || | || || ||  | ||||| || || ||||||||||||||||||||||| |||||||| |||||    ||  | ||||
gtgttttttcttttcttacttggatcatatgttgttttctctcgccattgtattcttaatattcataaggtataattttatgctcacgtagGTTGATGAGAATTTCCTTCTGCGCACTTTCGGAAGATTTGGGCCCATAGCTAGTGTCAAGATTATGTGGCCAAGAACAGATGAGGAGAAGAGGCGACAAA

upper sequence: GRMZM2G174785_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT5G10800.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------------gttgctttctctgctgtgcggtttcattaaacttgtatgcgttgtcttgttagctttac---atgctatggtgttagGTCGATGAGAATTTTCTTTTGAGGACATTTGGTCGGTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTAGAACAGAAGAGGAACGCAGAAGGCAAA
                          ||| || | | |  |     |  || | | || | | |  |  | |   |  |||     ||  | |  | |||||| ||||| ||||||||| || |||| |||||  | ||||| || || |||||||| || ||||||||||| |||||||| |||||    ||  |  |||
gtttgttctcatccaacttaaatacctgcgttgttttccatagctatatatcataattttcttcccttgcctaaaacttttgtggtattgtctttttttagGTTGATGAAAATTTTCTTCTGCGGACTTTTGGAAGATTTGGGCCAATAGCTAGTGTTAAAATTATGTGGCCAAGAACAGAGGAGGAGAAAAGGCGAGAAA

upper sequence: GRMZM2G174785_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv04s0008g06810.t01 (Vitis vinifera), 3'ss of exon 6
----------------------------------gttgctttctctgctgtgcggt-ttcattaaacttgtatgcgttgtcttgttagctttacatgctatggtgttagGTCGATGAGAATTTTCTTTTGAGGACATTTGGTCGGTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTAGAACAGAAGAGGAACGCAGAAGGCAAA
                                  |||  | | | | || |    |  || ||  || || |  |       | | | || |   |  | |  |  ||||| ||||||||||| |||||| | || |||||  | ||||| ||||| |||||||| || || ||||||||||| |||||||||||||| ||  | ||||
gttgcattcctaatttttggatgctcaattctctgttattcttt-tactctttaatgctctttggacctgaaaccaacaaaatataatctgtttttatttt--ttatagGTGGATGAGAATTTCCTTTTGCGTACTTTTGGAAGATTTGGTCCTATCGCTAGTGTGAAAATAATGTGGCCTAGGACAGAAGAGGAACGGAGGCGACAAA

upper sequence: GRMZM2G174785_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S137_118V6.1 (Physcomitrella patens), 3'ss of exon 6
----------------------gttgctttctctgctgtgcggtttcattaaacttgtatgcgttgtcttgttagctttacatgctatggtgt----tagGTCGATGAGAATTTTCTTTTGAGGACATTTGGTCGGTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTAGAACAGAAGAGGAACGCAGAAGGCAAA
                      || |   | |    |  |     |    | |  |||    |||||| |  |    | | |   |||   ||     |||| |||||||| ||||| ||||| || ||||| || ||||| |||||||| ||||| || ||||||||||| || ||||| || || |||||  ||||  
tcctctagttatacattttttggtagtagtttggtttaaggaaaatgtccacatctgtcacggttgtcgtacttttctcagagcatatatcgtaatgcagGTTGATGAGAACTTTCTGTTGAGAACTTTTGGGCGATTTGGGCCTATTGCCAGTGTAAAAATTATGTGGCCGAGGACAGATGAAGAGCGCAGGCGGCAGC

upper sequence: GRMZM2G174785_T01 (Zea mays), 3'ss of exon 7
lower sequence: EFJ32251 (Selaginella moellendorffii), 3'ss of exon 5
gttgctttctctgctgtgcggtttcattaaacttgtatgcgttgtcttgttagctttacatgctatggtgttagGTCGATGAGAATTTTCTTTTGAGGACATTTGGTCGGTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTAGAACAGAAGAGGAACGCAGAAGGCAAA
     |    || || ||   | || ||   ||       | | | |   ||  | || ||||  |||| | |||||||||| || || ||  ||||||| || ||||| |||||||| ||||| || |||||||||||||||||  |||||||||||||| | ||||||||  
----gtaaagcttctatgttttctcgtt---ctctctcttgatatatatatatatatatatgcactggtttcagGTCGATGAAAACTTCCTGCTGAGGACGTTCGGTCGTTTTGGACCAATTGCCAGCGTCAAGATTATGTGGCCACGAACAGAAGAGGAAAGAAGAAGGCAGC

upper sequence: GRMZM2G174785_T01 (Zea mays), 3'ss of exon 7
lower sequence: EFJ16538 (Selaginella moellendorffii), 3'ss of exon 5
gttgctttctctgctgtgcggtttcattaaacttgtatgcgttgtcttgttagctttacat--gctatggtgttagGTCGATGAGAATTTTCTTTTGAGGACATTTGGTCGGTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTAGAACAGAAGAGGAACGCAGAAGGCAAA
               ||   | |||  |    |    | |  | ||||| ||  | || ||  ||  |||| | ||||||| || || || ||  ||||||| || ||||| |||||||| ||||| || |||||||||||||||||  |||||||||||||| | ||||||||  
---------------gtaaagcttctatgttttctcgttctctctcttgatatatatatatatgcactggtttcagGTCGACGAAAACTTCCTGCTGAGGACGTTCGGTCGTTTTGGACCAATTGCCAGCGTCAAGATTATGTGGCCACGAACAGAAGAGGAAAGAAGAAGGCAGC

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), 48 (downstream exon)
Score: 103

ACTACCAGATGAATTTGATCCGACTGGGAGATTTCCAGGATCATTTGATGATGGTGATCCTCAAACCACCAACTTATATGTTGGCAATCTATCTCCCAAGgttgctttct ... atggtgttagGTCGATGAGAATTTTCTTTTGAGGACATTTGGTCGGTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTAGAACAGAAGAGGAACGCAGAAGGCAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 56

ACTACCAGATGAATTTGATCCGACTGGGAGATTTCCAGGATCATTTGATGATGGTGATCCTCAAACCACCAACTTATATGTTGGCAATCTATCTCCCAAGgttgctttct ... atggtgttagGTCGATGAGAATTTTCTTTTGAGGACATTTGGTCGGTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTAGAACAGAAGAGGAACGCAGAAGGCAAA


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 41

ACTACCAGATGAATTTGATCCGACTGGGAGATTTCCAGGATCATTTGATGATGGTGATCCTCAAACCACCAACTTATATGTTGGCAATCTATCTCCCAAGgttgctttct ... atggtgttagGTCGATGAGAATTTTCTTTTGAGGACATTTGGTCGGTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTAGAACAGAAGAGGAACGCAGAAGGCAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 42

ACTACCAGATGAATTTGATCCGACTGGGAGATTTCCAGGATCATTTGATGATGGTGATCCTCAAACCACCAACTTATATGTTGGCAATCTATCTCCCAAGgttgctttct ... atggtgttagGTCGATGAGAATTTTCTTTTGAGGACATTTGGTCGGTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTAGAACAGAAGAGGAACGCAGAAGGCAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttcattaaacttgtatgcgttgtcttgttagctttacatgctatggtgttagGTCGATGAGAATTTTCTTTTGAGGACATTTGGTCGGTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTAGAACAGAAGAGGAACGCAGAAGGCAAA
      attaaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgctttctctgctgtgcggtttcattaaacttgtatgcgttgtcttgttagctttacatgctatggtgttagGTCGATGAGAATTTTCTTTTGAGGACATTTGGTCGGTTTGGACCTATTGCTAGTGTCAAGATTATGTGGCCTAGAACAGAAGAGGAACGCAGAAGGCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA