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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgattttggtccagatgcttgtcaaaagcatcacatagtgaaaaatcttcttaacattattataagtttatagcttctttataccacatcattgtttagGTGGACCCACAGATGAAGCACGAGGGGTTCTGGATCTTAGTGTGCAGTACTGGACAAGCCGAGGATGGGCATTTGTTGATGTTAACTATGGGGGAAGCTC

Basic information

species Zea mays
transcript GRMZM2G000231_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000231_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os06g11190.1 (Oryza sativa), 3'ss of exon 11
ttgattttggtccagatgcttgtcaaaagcatcacatagtgaaaaat-cttcttaacattattataagtttatagcttctttataccacatc---attgtttagGTGGACCCACAGATGAAGCACGAGGGGTTCTGGATCTTAGTGTGCAGTACTGGACAAGCCGAGGATGGGCATTTGTTGATGTTAACTATGGGGGAAGCTC
    ||    | |  | |     || ||   | | |||  ||||  | ||| ||   |     |  |  |   | ||  | |  ||    |    ||| |||||||||||| |||||||||||||| || |||||||||||| |||| |||||||||||||||||||||||||||||||||||||||||||||||||||||| |
----ttgaattgctaagggaaagcagaacattaaaataaggaaatgtacttttttttaaagaaaggaaatggaaactcgtattgacattgttgcaattctttagGTGGACCTACAGATGAAGCACGTGGAGTTCTGGATCTTGGTGTTCAGTACTGGACAAGCCGAGGATGGGCATTTGTTGATGTTAACTATGGGGGAAGCAC

upper sequence: GRMZM2G000231_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA08G42730.1 (Glycine max), 3'ss of exon 11
--ttgattttggtccagatgcttgtcaaaagcatcacatagtgaaaaatcttcttaacattattataagtttatagcttctttataccacatcattgttt-agGTGGACCCACAGATGAAGCACGAGGGGTTCTGGATCTTAGTGTGCAGTACTGGACAAGCCGAGGATGGGCATTTGTTGATGTTAACTATGGGGGAAGCTC
   |  |||||| | |  |  || |  |  |  || | || |||  |||   ||| | |  |    |  ||||||  ||| ||||      | | | ||| ||||||||| || | |||| |||| ||  || |  |  | ||  | ||||||||||| || || || |||||||| ||||||||||| ||||| |||||| |
taattgttttgg-caaactttttatgcatgggttctcttaatgagtaatga-cttcatac-aacgcacttttatattttcattattttgtttgaatatttcagGTGGACCAACTGCTGAAACACGTGGAATTTTAAACTTGAGCATTCAGTACTGGACTAGTCGGGGTTGGGCATTCGTTGATGTTAATTATGGTGGAAGCAC

upper sequence: GRMZM2G000231_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT5G36210.1 (Arabidopsis thaliana), 3'ss of exon 11
----------------------------------------------------------------------------------ttgattttggtccagatgcttgtcaaaagcatcacatagtgaaaaatcttcttaacatt--attataagtttatagcttctttataccacatcattgtttagGTGGACCCACAGATGAAGCACGAGGGGTTCTGGATCTTAGTGTGCAGTACTGGACAAGCCGAGGATGGGCATTTGTTGATGTTAACTATGGGGGAAGCTC
                                                                                   || ||| | | ||  |   |     |    | |||||   || | |    | | |  |  ||   |  |  ||   || | |  || |  | | | |  ||| ||||| || | |||| |||| ||     |  |||| | | | || ||||||||||| ||||| ||||||||||||||||| || ||||| |||||| |
gtatgttaaacttacgacatcccgatttttcaaaacttaatcaaaataattcctcagtttcagtcttgttcatcttaagatcatgttttcgtttcaagtatgtactttagctgtaacata---aatattgcaatcagctatgcatggcacatcgatcatttttgttgacaatctgaatctacagGAGGACCTACTGCTGAATCACGTGGATCCTTAAATCTGAATATCCAATACTGGACAAGTCGAGGTTGGGCATTTGTTGATGTCAATTATGGTGGAAGCAC

upper sequence: GRMZM2G000231_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv18s0001g11150.t01 (Vitis vinifera), 3'ss of exon 11
ttgattttggtccagatgcttgtcaaaagcatcacatag-tgaaaaatcttcttaacattattataagtttatagcttctttatac-cacatcattgtttagGTGGACCCACAGATGAAGCACGAGGGGTTCTGGATCTTAGTGTGCAGTACTGGACAAGCCGAGGATGGGCATTTGTTGATGTTAACTATGGGGGAAGCTC
 | ||  || |  |     || || | | | || | ||  |||| | |    |   |  ||   | |  || ||  |  | || |        ||  |  ||| || || || |||||||| |         |  || | ||| | |||||||||||||| ||||| ||||||||||| ||||| || ||||| |||||| |
-taatcatgatagatgattttctctataccttctcttaaatgaacagtaaattattctatacattgaacttgtaa-tggtatacatgtgtgatatactgcagGAGGGCCGACCGATGAAGCGCACCAAAGCTTAAATTTGAGTATCCAGTACTGGACAAGTCGAGGTTGGGCATTTGTGGATGTGAATTATGGTGGAAGCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttcttaacattattataagtttatagcttctttataccacatcattgtttagGTGGACCCACAGATGAAGCACGAGGGGTTCTGGATCTTAGTGTGCAGTACTGGACAAGCCGAGGATGGGCATTTGTTGATGTTAACTATGGGGGAAGCTC
    tcttaac  putative branch site (score: 2)
           attattataagtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgattttggtccagatgcttgtcaaaagcatcacatagtgaaaaatcttcttaacattattataagtttatagcttctttataccacatcattgtttagGTGGACCCACAGATGAAGCACGAGGGGTTCTGGATCTTAGTGTGCAGTACTGGACAAGCCGAGGATGGGCATTTGTTGATGTTAACTATGGGGGAAGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - ttttggt
- - - - - - - - tgcttgt
- - - - - - - - - - - - - - gcatcac
- - - - - - - - - - - - - - - - - - - - gaaaaatc