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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtcataccgtgtttgttgatgcatggatcttactatactttgccaatttacattcacttatgtattggttgtttgctaagtgtgtgcacttttatgtagACTGTGGACAATGATCTTGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACAC

Basic information

species Zea mays
transcript GRMZM2G430947_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 12
----------------------------------------------------------tgtcataccgtgtttgttgatgcatggatcttactatactttgccaatttacattcacttatgtattggttgtttgctaagtgtg-----tgcacttttatgtagACTGTGGACAATGATCTTGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACAC
                                                          |||       |  ||||| |   |    | | |   | |||    ||||| | |    | |  |  |   | | || ||| | ||     |    |    |||||||||||||||||||||||||  | ||||||||||| || || || || || || ||||||||||||||||||||||| || ||||||||||||||||  |
gttgggttgcatttgaaattttgaaaaactctaaactgatctgtttattttttgcgtttgtttctttctaattgtttacctaatagtataatactgcttgttgaatttgcttattatgaaatggtatatttgtgttaattttgattaatatgttccattgtagACTGTGGACAATGATCTTGCTTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC

upper sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 12
-------------tgtcataccgtgtttgttgatgcatggatcttactatactttgccaatttacattcacttatgtattggttgtttgctaagtgt-----gtgcacttttatgtagACTGTGGACAATGATCTTGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACAC
             | | ||   |  |||||| |   |    | |     | |||    ||||| | |    | |  |  |   | | || ||| | |      |    |    ||||||||||||| |||||||||||  | ||||||||||| || || || || || || ||||||||||||||||||||||| || ||||||||||||||||  |
gttgggttgcatttataattttgcttttgtttacctaatagtatactactgcttgttgaatttgcttattatgaaatggtatatttgtgttaatttttattaatatgttccattgtagACTGTGGATAATGATCTTGCCTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTC

upper sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 12
---------------------------------------------------tgtcataccgtgtttgttgatgcatggatcttactatactttgccaatttacattca-cttatgtattg---gttgtt-tgctaagtgt-----gtgcacttttatgtagACTGTGGACAATGATCTTGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACAC
                                                     |  |||  | | | |  |    |    |  |  |||   | |  |||  |||  | | | | |||||     |||| |  ||| | |     |    ||    |||||||||||||||||||||||||  | |||||||| || || || || || || || |||||||||||||| |||||||| ||||||||||||||||| |  |
gttgggttgcattaaaatttgaaaaattcaatattattctgttatttataactttgtactctatctttctaattgtctgccaaaa-atagggtactgattctcatctaacctgtttattgtgaaatgttgtattaacttttacaagcatgctcccttgtagACTGTGGACAATGATCTTGCTTTAAAAATATATATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCGTTTGCTGAGAGGAGGGAGTTTGACAAAATTC

upper sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 12
----------------------------------------------------------------------tgtcataccgtgttt-gttgatgcatggat-cttactat-actttgccaatttacattcacttat-gtattg-gttgtttgctaagtgtgtgcacttttatgtagACTGTGGACAATGATCTTGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACAC
                                                                      | ||  |  || |       ||  | || | || | | | |  | |||  ||||   | |  | | |||||   ||  ||  ||   |  ||| |  ||  ||||||||||||||||||||||||  | |||||||| || || || || || || || |||||||||||||| |||||||| ||||||||||||||||| |  |
gttgggttgcattaaaattttgaaaaattcaatattattttgttatttataactttgcttgtactctatctttctaattgtctcccaaaaatataggggtactgattctcatctagcctgtttattgtgaaatgttgtattctattaatttttacaagcatgctccctt--gtagACTGTGGACAATGATCTTGCTTTAAAAATATATATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCATTTGCTGAGAGGAGGGAGTTTGACAAAATTC

upper sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 12
----tgtcataccgtgtttgttgatgcatggatcttactatactttgccaatttacattcacttatgtattggt--tgtttgctaagtgtgtgcacttttatgtagACTGTGGACAATGATCTTGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACAC
    || |||    | |||  |  |  | |||  | |  ||   ||  || ||| | || | || | | ||| |  | |||   |      |||| | | | | |||| ||||| ||||| || ||| |||||||||  || || || || || || || ||||||||||| || |||||||| |||||||| ||||||||||  |
ttactgccattttttatttcct--tcaagggaattca--atgtcttttcagtttgc-tttatttttattttgctgatctttatgagagacatgca-tataacgcagACAGTGGATAATGACCTCGCATTGAAAATATTTATCAAAGCCAGAGCCACACCGAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAATTTGACAAGATTC

upper sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 12
----tgtcataccgtgtttgttgatgcatggatcttactatactttgccaatttacattcacttatgtattggttgtttgctaagtgtgtgcacttttatgtagACTGTGGACAATGATCTTGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACAC
    |  | |     |    |   |   ||   | |  | |   || |  | ||  || |  |||| |      | ||| | | |  ||   |   | ||| |||| ||||| ||||| |||||| ||||||| || || || ||||| || || || ||||||||||| |||||||| || |||||||| ||||| ||||  |
tcaattccttttaaaggaactcattctctgttccctgatttgtgtttcacacttctatcc-tttattttcctaatttttacgaggcttgcata---taatgcagACAGTGGATAATGACCTTGCATTGAAAATTTATATTAAAGCTAGAGCCACACCAAAAGTTGTTGCAGCTTTTGCGGAGAGGAGGGAATTTGATAAGATCC

upper sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 12
----------------------------------------------------------------------------------------tgtcataccgtgtttgttgatgcatggatcttactatactttgcc-aatttacattc-acttatgtattggttgtttgctaagtgtgtgca---ctt-----ttatgtagACTGTGGACAATGATCTTGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACAC
                                                                                         |  |  ||   ||  ||  |  ||||| || | | |   || ||  ||||   ||   |   | |||   || ||| |  | | | |      |||     | |||||||| ||||| ||||| |||||| ||||||| || || || ||||| || || || ||||||||||| |||||||| || |||||||| ||||| ||||  |
gtcctgacagaaatttaaattgttttatctttttcatatgaacttatttattagttttatttcatggacagtttgggtgtttggggaaggaaaatccaaattcctt--ttaatggaactcattctctgttccctgatttgtgttttgcacttctatcctttattttcccaatttttatgaggcttgcaaataatgtagACAGTGGATAATGACCTTGCATTGAAAATTTATATCAAAGCTAGAGCCACACCGAAAGTTGTTGCAGCTTTTGCAGAGAGGAGGGAATTTGATAAGATCC

upper sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 12
tgtcataccgtgtttgttgatgcatggatcttactatactttgccaatttacattcacttatgtattggttgtttgctaagtgtgtgcacttttatgtagACTGTGGACAATGATCTTGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACAC
         ||  |  || |       || ||  | ||   || |   |   ||   ||| |   || ||    ||  | |    |    | | ||  |||||||||| ||||| ||||| || ||||||||||| || ||||| || || || ||||| ||||| |||||||| ||  | |||||||||||||| | | 
---------gtaatc-ttaaaatgaccattttcatttaaagtgtc---tcctatgggcttct---ttagtatgctgtaacggtaatattttctgattcagACTGTGGATAATGACCTTGCTCTAAAAATATACATCAAAGCTAGAGCTACTCCAAAAGTCGTTGCAGCTTTTGCAGAGCGAAGGGAGTTTGACAAAATAT

upper sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 12
tgtcataccgtgtttgttgatgcatggatcttactatactttgccaatttacattcacttatgtattggttgtttgctaagtgtgtgcacttttatgtagACTGTGGACAATGATCTTGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACAC
         ||  |  |  |      ||| ||| |  |  |     || |   | |  |  ||| |||  ||   | |||       |  | |  |  |||||||||| |||||||| || |||||||||||||| || ||| |||| || || |||||||| || |||||||| ||||| |||||||||||||| | ||
---------gtaatcttgaaatggacgattttattcaaaatgtgtgatatgtctcctatggtgtgttg--tgac-gataaac-----ctttctgttccagACTGTGGATAATGATCTCGCTCTGAAAATATACATCAAAGCTCGGGCGACTCCAAAAGTTGTAGCAGCTTTTGCAGAAAGAAGGGAGTTTGACAAAATAC

upper sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 12
tgtcataccgtgtttgttgatgcatggatcttactatactttgcc-aatttacattcacttatgtattggttgtttgctaagtgtgtgcacttttat-gtagACTGTGGACAATGATCTTGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACAC
   | |     |     || |  |    | ||   || || ||    ||||   ||  | |   | |||||  ||       |||     ||   || |||||| ||||| ||||| ||||||||||||||||| || || |||||||| || || ||||||||||| || |||||||| ||||||||||| || || |  |
--acttggaaaggagtatggtctaatagttttttcatgctctgtttgatttgtgtttcccttccttttggtctttctgatgttgtaattgctaacattgtagACGGTGGATAATGACCTTGCACTGAAAATATATATCAAAGCTAGGGCCACTCCAAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAGTTCGATAAAATTC

upper sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 12
-----------------------------------------tgtcataccgtgtt----tgttgat--gcatggatcttactatactt----tgccaatttacat-------tcacttatgtattggttgtttgctaagtgtgtgcacttttatgtagACTGTGGACAATGATCTTGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACAC
                                          | ||   | ||||    || | ||  |  |  || ||| |||  ||    ||| |||||| ||       |   |||  |||   ||      | |          |||| ||||||||||||| | ||| |||||||| |||||||| || || || || ||||| || ||||||||||| || ||||||||  |  ||||||||||||| |  |
gtttgaaatgcaattggagatgattattttttgtccacttaagacaattcttgttgggatgctaatttgagtttattttattatttttatcctgctaatttaaatgatttttttttttaaatataattttgacattgaaaaccatgttttttttgtagACTGTGGATACTGACCTTGCACTCAAAATATATATTAAAGCGAGAGCAACTCCGAAAGTTGTTGCAGCCTTTGCTGAGCGTCGGGAGTTTGACAAAATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttacattcacttatgtattggttgtttgctaagtgtgtgcacttttatgtagACTGTGGACAATGATCTTGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACAC
                                          cactttt  CT-rich tract
             ttatgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtcataccgtgtttgttgatgcatggatcttactatactttgccaatttacattcacttatgtattggttgtttgctaagtgtgtgcacttttatgtagACTGTGGACAATGATCTTGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- -cataccg
- - - - - tgtttgt
- - - - - - - - - - tgcatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttgc