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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgccataccatcgtggggaaaaacaaaataaaacctacctgtccatggtgcccgtgtgtacaatgctgttactttttcttgtccatgcagCTGCCCTGATGTCTGCCATCTACGAGGAGAACAAGGACGAGGACGGGTTCCTCTACATGACCTACAGCGGCGAGAACACCTTTGGGCTGCTATGAGTGGC

Basic information

species Zea mays
transcript GRMZM2G014975_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014975_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g09240.1 (Oryza sativa), 3'ss of exon 5
gt-ttgccataccatcgtggggaaaaacaaaataaa-----acctacctgtccatggtgcccgtgtg--tacaatgctgttactttttcttgtccatgcagCTGCCCTGATGTCTGCCATCTACGAGGAGAACAAGGACGAGGACGGGTTCCTCTACATGACCTACAGCGGCGAGAACACCTTTGGGCTGCTATGAGTGGC-
|| | || |||  | |   ||||  |   |  | ||     || ||       ||  |    | |||    | |   ||     ||   |||  | | |||||||||||||||| || ||||| |||||||||||||| |||||||| ||||||||||||||||||||||| ||||||||||| || ||| | ||  ||   
gtatggcaatatgagctctgggagcactcagttcaacatcaacataaaaaaaaatcataattgcgtgatccctaaaatgccttgttgcattgctcctacagCTGCCCTGATGTCCGCTATCTATGAGGAGAACAAGGATGAGGACGGCTTCCTCTACATGACCTACAGCGGGGAGAACACCTTCGGCCTGTT-TGTCTGAGT

upper sequence: GRMZM2G014975_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv19s0090g00580.t01 (Vitis vinifera), 3'ss of exon 5
--------gtttgccataccatcgtggggaaaaacaaaataa-aaccta---cctgtccatggtgcccgtgtgtacaatgctgttactttttcttgtccatgcagCTGCCCTGATGTCTGCCATCTACGAGGAGAACAAGGACGAGGACGGGTTCCTCTACATGACCTACAGCGGCGAGAACACCTTTGGGCTGCTATGAGTGGC
        |  | || |   |   |    | | ||| |   |  |  ||    ||||   |  |     | | ||      | ||  | |||  |||     |||||||| |||||||||||||||| ||||| ||||| || ||||| || ||||| || ||||| ||||| || || ||||| |||||     | | |  |  
gtgagaaagaattcctttttaatattcaaatacacatatcgatgatgtagtttctgtaactatttattatttatattcatttatttgtattttgtgttatcacagCTGCCATGATGTCTGCCATCTATGAGGAAAACAAAGATGAGGATGGTTTCCTGTATATGACTTACAGTGGGGAAAACACATTTGGATCATTCTAACGGAA

upper sequence: GRMZM2G014975_T02 (Zea mays), 3'ss of exon 3
lower sequence: EDO98830 (Chlamydomonas reinhardtii), 3'ss of exon 4
------gtttgccataccatcgtggggaaaaacaaaataaaacctacctgtccatggtgcccgtgtgtacaatgctgttactttt--tcttgtccatgcagCTGCCCTGATGTCTGCCATCTACGAGGAGAACAAGGACGAGGACGGGTTCCTCTACATGACCTACAGCGGCGAGAACACCTTTGGGCTGCTATGAGTGGC-
      |               || || |   |    |  | | |  |||||  || |  ||  ||       ||   | |||     |   |||   |||| || || |||||  ||||||| |||||  ||||||| |||||||| || || ||||| |||||||||||||||||||| || ||    |   |||  || 
cagcagggccagagccgggcgctgtggcaccgccgtgtgcaccgtcgctgtctttgctcaccacgt-ccttgcgcccctccttgcaacccactcctcacagCCGCGCTCATGTCATCCATCTATGAGGACCACAAGGATGAGGACGGCTTTCTGTACATCACCTACAGCGGCGAGAACACGTTCGG-TGCCGGGGAGCAGCT

upper sequence: GRMZM2G014975_T02 (Zea mays), 3'ss of exon 3
lower sequence: PP1S26_103V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------------------------------gtttgccataccat-cgtggggaaaaacaaaataaaacctacctgtccatggtgcccgtgtgta--caatgctgttactttttct-------tgtccatgcagCTGCCCTGATGTCTGCCATCTACGAGGAGAACAAGGACGAGGACGGGTTCCTCTACATGACCTACAGCGGCGAGAACACCTTTGGGCTGCTATGAGTGGC
                                                                                       |||   |   || | |||        | |        |  |||| ||  |      || | |   | ||  || | |   |         |||  ||||||| ||  |||||||  | ||||| || ||| |||||||||| ||||||||||| ||  | ||||||||||| |||||||| || |||||     |  |   
gtacgttagttgaatatgcgtgcaagtgaatggagtagtggtggcttgtgtgttagattttggatggaagtaattgtgattgaaaccttgtggtcgtatgcatggcactgcgtagatgtggttgtgtctgtgcactgcagatctgagaagttagtgtagtgaatggattggatgggatgtgaatgcagCGGCTATGATGTCATCTATCTATGACGAGCACAAGGACGAAGACGGGTTCCTTTATTTTACCTACAGCGGTGAGAACACGTTCGGGCTATCGAGGATCTG

upper sequence: GRMZM2G014975_T02 (Zea mays), 3'ss of exon 3
lower sequence: EFJ09352 (Selaginella moellendorffii), 3'ss of exon 4
gtttgccataccatcgtggggaaaaacaaaataaaacctacctgtccatggtgcccgtgtgtacaatgctgttactttttcttgtccatgcagCTGCCCTGATGTCTGCCATCTACGAGGAGAACAAGGACGAGGACGGGTTCCTCTACATGACCTACAGCGGCGAGAACACCTTTGGGCTGCTATGAGTGGC-
                               ||  | |   |    | |  | |||  || ||      |      ||   ||     || ||| ||  |||| ||  |||||||||||||| ||||||||||||| || ||||||||| | || |||||||| ||||| ||||| || |    | ||      
------------------------------gtatgagccgtcgagacgtaat-cccacgtatattgatttacactgttcctttccttttgtagCGGCATTGATATCGACCATCTACGAGGAGCACAAGGACGAGGATGGATTCCTCTACTTCACGTACAGCGGGGAGAATACCTTCGG-CCAAGAAGAACACTA

upper sequence: GRMZM2G014975_T02 (Zea mays), 3'ss of exon 3
lower sequence: EFJ35003 (Selaginella moellendorffii), 3'ss of exon 4
gtttgccataccatcgtggggaaaaacaaaataaaacctacctgtccatggtgcccgtgtgtacaatgctgttactttttcttgtccatgcagCTGCCCTGATGTCTGCCATCTACGAGGAGAACAAGGACGAGGACGGGTTCCTCTACATGACCTACAGCGGCGAGAACACCTTTGGGCTGCTATGAGTGGC-
                               ||  | |   |    | |  | |||  || ||      |      ||   ||     || ||| ||  |||| ||  |||||||||||||| ||||||||||||| || ||||||||| | || |||||||| ||||| ||||| || |    | ||      
------------------------------gtatgagccgtcgagacgtaat-cccacgtatattgatttacactattcctttccttttgtagCGGCATTGATATCGACCATCTACGAGGAGCACAAGGACGAGGATGGATTCCTCTACTTCACGTACAGCGGGGAGAATACCTTCGG-CCAAGAAGAACACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacctgtccatggtgcccgtgtgtacaatgctgttactttttcttgtccatgcagCTGCCCTGATGTCTGCCATCTACGAGGAGAACAAGGACGAGGACGGGTTCCTCTACATGACCTACAGCGGCGAGAACACCTTTGGGCTGCTATGAGTGGC
                                 ttactttttcttgtcc  CT-rich tract
                                 ttacttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgccataccatcgtggggaaaaacaaaataaaacctacctgtccatggtgcccgtgtgtacaatgctgttactttttcttgtccatgcagCTGCCCTGATGTCTGCCATCTACGAGGAGAACAAGGACGAGGACGGGTTCCTCTACATGACCTACAGCGGCGAGAACACCTTTGGGCTGCTATGAGTGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT