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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagcacaagtttatggtctgtcatattgaatatgatcaagacttccatacttcatgaacatatctgctatttatacagGCAGAGAGTGCAGTAGATCAGATGGACTGGATTGAAAAGATAACTGGTGTTATTGCCTCTTTACTGAGCTCACAATCGCCAGAACAG

Basic information

species Zea mays
transcript GRMZM5G872204_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G872204_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 13
--------------gtatagcacaagtttatggtctgtcatattgaatatgatcaagacttccatacttcatgaacatatc-tgctattta-tacagGCAGAGAGTGCAGTAGATCAGATGGACTGGATTGAAAAGATAACTGGTGTTATTGCCTCTTTACTGAGCTCACAATCGCCAGAACAG
               | | | |    ||| |  |   | | |  ||   |||| ||  |||      |||||      ||  ||||  | | | ||||||||||||||  | || || ||||| ||||||||||| || |||||||||||||| || |||||||| || ||    || ||   |
gttatttaatgtgttttttggatttttttttaattcat-acaaggatggtgattaaagctttatagtttcattccttaattatgcttgtcagtgcagGCAGAGAGTGCGCTGGACCAAATGGATTGGATTGAAAAAATCACTGGTGTTATTGCTTCATTACTGAGTTCTCAGATTCCTGATAGG

upper sequence: GRMZM5G872204_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA04G37780.1 (Glycine max), 3'ss of exon 13
------gtatagcacaagtttatggtctgtcatattgaatatgatcaagacttccatacttcatgaacatatctgctatttatacagGCAGAGAGTGCAGTAGATCAGATGGACTGGATTGAAAAGATAACTGGTGTTATTGCCTCTTTACTGAGCTCACAATCGCCAGAACAG
       |  |  | ||  |  ||    ||  | | | || | ||||  ||| |  |   || | |  |   |    ||  || |||||||| | |||  | || |||||||| ||||| ||||||||||||||||| |||||| | ||| ||||  ||||| | |        
gtactcattcaaaaaaatctagtgacacgtactttggcattttatcattactcctctgtctcctcactaaggccaaaata-atgcagGCAGAAAATGCCCTGGACCAGATGGATTGGATGGAAAAGATAACTGGTGTAATTGCCACCTTATTGAGTGCACAAACACTG------

upper sequence: GRMZM5G872204_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA05G38550.1 (Glycine max), 3'ss of exon 13
----gtatagcacaagtttatggtctgtcatattgaatatg-atcaagacttccatacttcatgaacatatctgctatttatacagGCAGAGAGTGCAGTAGATCAGATGGACTGGATTGAAAAGATAACTGGTGTTATTGCCTCTTTACTGAGCTCACAATCGCCAGAACAG-------------
    ||||  || || |||||    |   |  |||   ||  ||||  ||||  |||||  | |||              || |||||||| | |||||| ||||||||||| ||||| |||||||||| ||| || |||||||| ||| ||||    ||  | |  | |  |             
gtacgtattccaaaactttatcagtttaaagtttgggcatttatcattactt--atactaaaggaag-----------caatgcagGCAGAAAATGCAGTGGATCAGATGGATTGGATGGAAAAGATAAATGGAGTAATTGCCTCCTTATTGAGTGTCCAGACACTGGGAATGGTACGTAGTAGAT

upper sequence: GRMZM5G872204_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA06G17300.1 (Glycine max), 3'ss of exon 15
---gtatagcacaagtttatggtctgtcatattgaatatgatcaagacttccat----acttcatgaacatatctgctatttatacagGCAGAGAGTGCAGTAGATCAGATGGACTGGATTGAAAAGATAACTGGTGTTATTGCCTCTTTACTGAGCTCACAATCGCCAGAACAG
    |  |  | || ||  ||   |||    ||| || | ||||  |||||  |       || | |  |   |    ||  || |||||||| | |||  | ||||||||||| ||||| ||||||||||||||||| |||||||| ||| ||||  ||||| | |        
gtcattcaaaaaaatttagtgacatgtac--ttgcattttatcattacttctctctctgtctcctcactaaggccaaaata-atgcagGCAGAAAATGCCCTGGATCAGATGGATTGGATGGAAAAGATAACTGGTGTAATTGCCTCCTTATTGAGTGCACAAACACTG------

upper sequence: GRMZM5G872204_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 13
------------gtatagcacaagtttatggtctgtcatattgaatatgatcaagacttccatacttcatgaacatatc-tgctattta-tacagGCAGAGAGTGCAGTAGATCAGATGGACTGGATTGAAAAGATAACTGGTGTTATTGCCTCTTTACTGAGCTCACAATCGCCAGAACAG
            ||     | |  ||| |  |   | | || ||   |||| ||  |||      |||||      ||  ||||  | | | ||||||||||||||| | || || ||||||||||||||||| || |||||||||||||| || |||||||| || |||   || |||  |
gttatttaatgtgttctttagatttttttaattcat-acatggatggtgattaaagctttatagtttcattccttaattatgcttgtcagtgcagGCAGAGAGTGCACTGGACCAAATGGACTGGATTGAAAAAATCACTGGTGTTATTGCTTCATTACTGAGTTCTCAAATTCCTGAAAGG

upper sequence: GRMZM5G872204_T02 (Zea mays), 3'ss of exon 13
lower sequence: AT5G61980.1 (Arabidopsis thaliana), 3'ss of exon 13
-----------------------------------------gtatagcacaagtttatggtctgtcata-ttgaatatgatc----aagacttccatacttcatgaacatatc---tgctatttatacagGCAGAGAGTGCAGTAGATCAGATGGACTGGATTGAAAAGATAACTGGTGTTATTGCCTCTTTACTGAGCTCACAATCGCCAGAACAG---------
                                          |  |       |||| | |   | ||| ||   | |  ||    |  |   ||  |   |  |||  | |    |  |||| ||  ||||||||| ||||   ||||||||||||||||| ||||| |||||||| || ||||| |||||  |||| |  ||| | || |||            
gtatgtttccaagtgaaaagatcttcattttcttcaacatattgaatttttcttttaggattcatgatactttggtgttctcttccatcatccccgaatgaccagaattttttaaatcttattgatgtagGCAGAGAATGCACAGGATCAGATGGACTGGATCGAAAAAATAACTGGAGTAATTGCTTCTTTGTTGAGTTTCCAAACACCTGAAAGAGCAATCATG

upper sequence: GRMZM5G872204_T02 (Zea mays), 3'ss of exon 13
lower sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 13
--------------------------------------------------------------------------------------------------------gtatagcacaagtttatggtctgtcatattgaatatgatcaagacttccatac-ttcatga-acatatctgctattta-tacagGCAGAGAGTGCAGTAGATCAGATGGACTGGATTGAAAAGATAACTGGTGTTATTGCCTCTTTACTGAGCTCACAATCGCCAGAACAG
                                                                                                         |  |        || |    ||| ||  |  || |  |    |||      | || |||    | || ||||  | |  |||||||||||||||| | || || ||||| ||||||||||||||||| || |||||||| || |||||||| || ||  | || ||   |
gtaaatcttacagcttaggttgcactcatgaagttcagtttacttctttgaaattatttgatacctgaaactgtatttttgcttgatggttctgtgaaatactgatggaatggtgaattgttaagtgttattattgatttttttctcactagtgctcattaatgttgtacatttgcttgtcagcacagGCAGAGAGTGCACTGGACCAAATGGATTGGATTGAAAAGATAACAGGGGTTATTGCTTCATTACTGAGTTCTCAGGCTCCTGAGAGG

upper sequence: GRMZM5G872204_T02 (Zea mays), 3'ss of exon 13
lower sequence: Vv17s0000g00310.t01 (Vitis vinifera), 3'ss of exon 13
----------------------------------------------------------------------------------gtat-agcacaagtttatggtctgtc---atattgaatatgat--caagacttc---catacttcatgaac---atatctgctattta-tacagGCAGAGAGTGCAGTAGATCAGATGGACTGGATTGAAAAGATAACTGGTGTTATTGCCTCTTTACTGAGCTCACAATCGCCAGAACAG
                                                                                   ||| ||| ||| |   ||  | ||    ||  ||   || ||  ||  || |    || | |   | |||   ||||   |  || | | |||||||||| |||| | ||||| ||||||||| |||||||||||||||| || || || |||||  |||| ||  |  | |  |||  |
gtacaaaatcaaaggttagatcaaaaatataaatttgggttttcattcatgtttttagactatacttatatgaagctcagcattatcagcccaaatacttgtccagtactaatgctggggattatgtcagtacctagagcagattctctcaactttatattaacacttgaatgcagGCAGAGAATGCACTGGATCAAATGGACTGGGTTGAAAAGATAACTGGAGTAATAGCTTCTTTGTTGAGTTCCGACGCACTTGAAAGG

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|71439574|gb|DR820624.1|DR820624
EST:     TGAGGTTCTGTTTCAGAATTATTTCACCCACAAAGATCTACACATTGCAG                         GCAGAGAGTGCAGTATATCAGATGGACTGGATTGAAAAGATAACTGGTGTT
genomic: TGAGGTTCTGTTTCAGAATTATTTCACCCACAAAGATCTACACATTGCAGgtatagcaca ... atttatacagGCAGAGAGTGCAGTAGATCAGATGGACTGGATTGAAAAGATAACTGGTGTT
EST: gi|71439575|gb|DR820625.1|DR820625
EST:     TGAGGTTCTGTTTCAGAATTATTTCACCCACAAAGATCTACACATTGCAG                         GCAGAGAGTGCAGTAGATCAGATGGACTGGATTGAAAAGATAACTGGTGTT
genomic: TGAGGTTCTGTTTCAGAATTATTTCACCCACAAAGATCTACACATTGCAGgtatagcaca ... atttatacagGCAGAGAGTGCAGTAGATCAGATGGACTGGATTGAAAAGATAACTGGTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgaatatgatcaagacttccatacttcatgaacatatctgctatttatacagGCAGAGAGTGCAGTAGATCAGATGGACTGGATTGAAAAGATAACTGGTGTTATTGCCTCTTTACTGAGCTCACAATCGCCAGAACAG
                                            tatttataca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagcacaagtttatggtctgtcatattgaatatgatcaagacttccatacttcatgaacatatctgctatttatacagGCAGAGAGTGCAGTAGATCAGATGGACTGGATTGAAAAGATAACTGGTGTTATTGCCTCTTTACTGAGCTCACAATCGCCAGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA