Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcaaatggatttctgttgatgatcatgaccgctgcatcatatatatcctctctgtattgaattcacctgtttccgtctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTTGAGCACGAGTACTTCAAGGACCTTGAGATGGTACAGTGACCTGCTAAAT

Basic information

species Zea mays
transcript GRMZM2G143213_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143213_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g01850.2 (Oryza sativa), 3'ss of exon 7
gtaagtcaaatggatttctgttgatgatcatgaccgctgcatcatatatatcctctctgtattgaatt----cacc--tgtttccgtctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTTGAGCACGAGTACTTCAAGGACCTTGAGATGGTACAGTGACC-TGCTAAAT
||||||| ||      ||   |  || |||| | |    ||| |||||   || |     |    | |    || |  ||| ||  |   ||| |||||||||||| |||| ||||||| |||||| ||||||||||| || || |||||||| ||||||||||||||||||||||||||||| ||||| |||||   
gtaagtcgaacaccactcacctt-tgttcattagcatgtcataatatacccccccaaaaaagaagagtatatcatcgttgtctcgtttcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTTGAGCATGAGTACTTCAAGGACCTTGAGATGGTACAATGACCCTGCTATG-

upper sequence: GRMZM2G143213_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g02680.1 (Oryza sativa), 3'ss of exon 6
gtaagtcaaatggatttctgttgatgatcatgaccgctgcatcatatatatcctctctgtattgaattcacct-gtttccgtctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTTGAGCACGAGTACTTCAAGGACCTTGAGATGGTACAGTGACC-TGCTAAAT
||||||| ||      ||   |  || |||| | |    ||| |||||   |        | |       ||| || ||  |   ||| |||||||||||| |||| ||||||| |||||| ||||||||||| || || |||||||| || |||||||||||||||||||||||||| ||||| |||||   
gtaagtcgaacaccactcacctt-tgttcattagcatgtcataatataccccaaaaaaaaagtatcccatccttgtctcgtttcactgtcagAAAATGCTTCGGTACGAGCCAAACAAAAGGATCACAGCTAGACAGGCTCTTGAGCATGAATACTTCAAGGACCTTGAGATGGTACAATGACCCTGCTATG-
















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|18166338|gb|BM336177.1|BM336177
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|18171982|gb|BM347370.1|BM347370
EST:     GAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: GAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|78093070|gb|DV521444.1|DV521444
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|60397283|gb|DN230099.1|DN230099
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|27575994|gb|CA998688.1|CA998688
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCCCTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|5847313|gb|AW000392.1|AW000392
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTCGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|91051178|gb|EB161596.1|EB161596
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTC
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|32916297|gb|CF021109.1|CF021109
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|31910663|gb|CD651537.1|CD651537
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|60394332|gb|DN227202.1|DN227202
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|110194217|gb|EC876115.1|EC876115
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|60344999|gb|DN211972.1|DN211972
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTCGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|60394730|gb|DN227600.1|DN227600
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|78074515|gb|DV502949.1|DV502949
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|60398759|gb|DN231575.1|DN231575
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|67024512|gb|CO453261.1|CO453261
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTCGGTATGAGCCAAGCAAAAGAATCACAGCTCGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|31909621|gb|CD651010.1|CD651010
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|18166704|gb|BM336543.1|BM336543
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|18650116|gb|BM498935.1|BM498935
EST:     TGGCAACAATAGTCCCAAATCTTGAACCTGCTGGCTTGGACCTTCTCTGT                         AAAATGCTTCGGTATGAGCCAAGCAAAAGAATCACAGCTCGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|4967063|gb|AI692029.1|AI692029
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTCGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|37384260|gb|CF629190.1|CF629190
EST:     TGGCAATAATAGTCCCAAATCTTGAACCTGCTGGCTTGGACCTTCTCTCT                         AAGATGCTTCGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|17929629|gb|BM266589.1|BM266589
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|18162372|gb|BM332211.1|BM332211
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|18167215|gb|BM337054.1|BM337054
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|60398446|gb|DN231262.1|DN231262
EST:     TGGCAATAATAGTCCCAAATCTTGAACCTGCTGGCTTGGACCTTCTCTCT                         AAGATGCTTCGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|12968998|gb|BG265943.1|BG265943
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTCGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|78025082|gb|DV493469.1|DV493469
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTCGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|18163570|gb|BM333409.1|BM333409
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|5525594|gb|AI861487.1|AI861487
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTCGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|5819371|gb|AI987577.1|AI987577
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTCGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
EST: gi|211268426|gb|FL478582.1|FL478582
EST:     TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCT                         AAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT
genomic: TGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTT

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: 111

GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTTGAGCACGAGTACTTCAAGGACCTTGAGATGGTACAGTGACCTGCTAAAT


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 51

GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTTGAGCACGAGTACTTCAAGGACCTTGAGATGGTACAGTGACCTGCTAAAT


Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 36

GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTTGAGCACGAGTACTTCAAGGACCTTGAGATGGTACAGTGACCTGCTAAAT


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 22

GACCTGGCAACAATAGTCCCAAATCTAGAACCTGCTGGCTTGGACCTTCTCTCTgtaagtcaaa ... ctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTTGAGCACGAGTACTTCAAGGACCTTGAGATGGTACAGTGACCTGCTAAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcatcatatatatcctctctgtattgaattcacctgtttccgtctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTTGAGCACGAGTACTTCAAGGACCTTGAGATGGTACAGTGACCTGCTAAAT
                                      tttccgtct  CT-rich tract
     tcatatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcaaatggatttctgttgatgatcatgaccgctgcatcatatatatcctctctgtattgaattcacctgtttccgtctgctgacagAAAATGCTTAGGTATGAGCCAAGCAAAAGAATCACAGCTAGGCAAGCACTTGAGCACGAGTACTTCAAGGACCTTGAGATGGTACAGTGACCTGCTAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG