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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCAGGGAGGTGGTTGCTGTGACAGGCGATGGTACCAATGACGCTCCAGCATTGCATGAAGCAGATATTGGGCTTGCAATGGGCATAGCAGGAACAGAGgtactaactatacctcgcaatttctactgttcttactgtgaatgtaaaaacctcttgcaaggccatcagaagctaagaactcctcacttgcaattgcaaggccatcatgcccttcggcaattctgtgcgtcccttgaaaagataaataacagtataagcttacatacttgcag

Basic information

species Zea mays
transcript GRMZM2G104730_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104730_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os12g04220.1 (Oryza sativa), 5'ss of exon 4
GTTCAGGGAGGTGGTTGCTGTGACAGGCGATGGTACCAATGACGCTCCAGCATTGCATGAAGCAGATATTGGGCTTGCAATGGGCATAGCAGGAACAGAGgtactaactatacctcgcaatttctactgttcttactgtgaatgtaaaaacctcttgcaag---gccatcagaagctaagaactcctcacttgcaattgcaaggccatcatgcccttcggcaattc--tgtgcgtcccttgaaaagataaataacagtataagcttacatacttgcag
|||    ||||||||| |||||||||| |||||||| ||||| ||||| ||||| || |||||||||||||||||||| |||||||| |||||||||||||||||   | | |   ||| ||   |   |    ||   | ||  | | || |     |||   |  ||      | || |  ||   | |  |  || |      |   ||  | | |  ||| |  | | | ||   ||||| |      |  | | |   |||  ||   |||||
GTTTGATGAGGTGGTTTCTGTGACAGGTGATGGTACAAATGATGCTCCTGCATTACACGAAGCAGATATTGGGCTTGCTATGGGCATTGCAGGAACAGAGgtactg--tttcctatgcagttcaaaacttatgaacgtagcatcaatagacattaaaaaagtcagatatttaggacgaatatgtcagtattcactcttactgaattaagttgatcct-gataatccatttttcatcttctgaaatgg-----agtaattttgtcttgtatttgtgcag

upper sequence: GRMZM2G104730_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os11g04460.1 (Oryza sativa), 5'ss of exon 4
GTTCAGGGAGGTGGTTGCTGTGACAGGCGATGGTACCAATGACGCTCCAGCATTGCATGAAGCAGATATTGGGCTTGCAATGGGCATAGCAGGAACAGAGgtactaa---ctatac--ctcgcaatttctac-tgttcttactgtgaatgt-aaaaacctcttgcaaggccatcaga-agctaagaactcctcact--tgcaattgcaaggccatcatgccc---ttcggcaattctgtgcgtcccttgaaaa-----gataaataacagtataagcttacatacttgcag
|||    ||||||||| |||||||||| |||||||| ||||| ||||| ||||| || ||||||||||| |||||||| |||||||| |||||||||||||||||     |||| |   ||  || || |   |||     |  |  |  | |||||  ||    |       || | |  | || | || |   |  || |||     | || | ||  ||   || ||  | | |||   | | ||   |      || |   |  | | |   |||  ||   |||||
GTTTGATGAGGTGGTTTCTGTGACAGGTGATGGTACAAATGATGCTCCTGCATTACACGAAGCAGATATCGGGCTTGCTATGGGCATTGCAGGAACAGAGgtactgtttcctatgcagttcaaaacttatggatgtagcatcaatagacattaaaaaagtcagatatttaggacaaatatgtcagtattcattcttactgaaataagttgaccctgataacccattttggatactttgtattttctttttcatcttctgaaatggagtaattttgtcttttatttgtgcag

upper sequence: GRMZM2G104730_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA02G32780.1 (Glycine max), 5'ss of exon 4
GTTCAGGGAGGTGGTTGCTGTGACAGGCGATGGTACCAATGACGCTCCAGCATTGCATGAAGCAGATATTGGGCTTGCAATGGGCATAGCAGGAACAGAGgtactaactatacctcgcaatttctactgttcttactgtgaatgtaaaaacctcttgcaaggccatcagaagctaagaactcctcacttgcaattgcaaggccatcatgcccttcggcaattctgtgcgtcccttgaaaagataaataacagtataagcttacatacttgcag
|||  | ||||| || ||||| || || ||||| |||||||| ||||| ||| |||||||  |||| ||||||||||| ||||||||| | ||||| |||||      | | || |   |||| |    ||  ||  |||  | | |     |   |    ||  |      ||  | |||  |         ||||  ||| ||| ||   ||                                                           
GTTTGGTGAGGTTGTAGCTGTTACTGGTGATGGAACCAATGATGCTCCTGCACTGCATGAGTCAGACATTGGGCTTGCTATGGGCATATCTGGAACTGAGgt-----ttgtgcc-catgatttgt----ttactatggtgtgtctgatggtattaagtgtagcagtt-----ctttgtactgtttttgctttgttgcttggc-atcttgttttttc---------------------------------------------------------

upper sequence: GRMZM2G104730_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA10G15800.1 (Glycine max), 5'ss of exon 4
GTTCAGGGAGGTGGTTGCTGTGACAGGCGATGGTACCAATGACGCTCCAGCATTGCATGAAGCAGATATTGGGCTTGCAATGGGCATAGCAGGAACAGAGgtactaactatacctcgcaatttctactgttcttactgtgaatgtaaaaacctcttgcaaggccatcagaagctaagaactcctcacttgcaattgcaaggccatcatgcccttcggcaattctgtgcgtcccttgaaaagataaataacagtataagcttacatacttgcag
|||  | ||||| || ||||| || || ||||| |||||||| ||||| ||| |||||||  |||| ||||||||||| ||||||||||| |||||||||||      | | || |   |||  |    ||  ||  ||| || | |     |   |    ||  |     |      |||  |       | ||||  ||| ||| ||                                                                
GTTTGGTGAGGTTGTAGCTGTTACTGGTGATGGAACCAATGATGCTCCTGCACTGCATGAGTCAGACATTGGGCTTGCTATGGGCATAGCTGGAACAGAGgt-----ttgtgcc-catgattgat----ttactatggtgtatctgacggtattacgtgtagcagttcattgt-----actgtttttgcttagttgcttggc-atcttgtttaaga---------------------------------------------------------

upper sequence: GRMZM2G104730_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA03G29010.1 (Glycine max), 5'ss of exon 5
GTTCAGGGAGGTGGTTGCTGTGACAGGCGATGGTACCAATGACGCTCCAGCATTGCATGAAGCAGATATTGGGCTTGCAATGGGCATAGCAGGAACAGAGgtactaactatacctcgcaatttctactgttcttactgtgaatgtaaaaacctcttgcaaggccatcagaagctaagaactcctcacttgcaattgcaaggccatcatgcccttcggcaattctgtgcgtcccttgaaaagataaataacagtataagcttacatacttgcag
|||| | ||||| |||||||| || |||||||| || ||||| || || ||| ||| ||| ||||| ||||| ||||||||||||||||||||||| |||||      | || |||     | ||| | |  | | | |||  || |  |  | ||  |      | |        | | |      ||  |  |  ||||   | ||                                                                 
GTTCGGTGAGGTTGTTGCTGTTACTGGCGATGGAACTAATGATGCCCCTGCACTGCGTGAGGCAGACATTGGACTTGCAATGGGCATAGCAGGAACTGAGgt-----ttgtatctcttgtgtactattatgataattctgacagttacgagttgttttagttttgttaattctcctgcatta--tgttttaagatataaggt-gttat-----------------------------------------------------------------

upper sequence: GRMZM2G104730_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA19G31770.1 (Glycine max), 5'ss of exon 2
GTTCAGGGAGGTGGTTGCTGTGACAGGCGATGGTACCAATGACGCTCCAGCATTGCATGAAGCAGATATTGGGCTTGCAATGGGCATAGCAGGAACAGAGgtactaactatacctcgcaatttctactgttcttactgtgaatgtaaaaacctcttgcaaggccatcagaagctaagaactcctcacttgcaattgcaaggccatcatgcccttcggcaattctgtgcgtcccttgaaaagataaataacagtataagcttacatacttgcag
|||  | ||||| |||||||| || || ||||| || ||||| ||||| ||| ||   || ||||| ||||| ||||||||||||||||||||||| |||||      | || |||    || ||||  |  || |||  | |  |     | |||        || | |  |  | |     |   ||  |  |  |||||  |   |                                                                
GTTTGGTGAGGTTGTTGCTGTTACTGGTGATGGAACTAATGATGCTCCTGCACTGTGCGAGGCAGACATTGGACTTGCAATGGGCATAGCAGGAACTGAGgt-----ttgtatctcttgtttactacgataatt-ctggcagttaagtgtacgcttagttttgtataatagtcctaca----ttatgttaaagatataaggcgttagcgt---------------------------------------------------------------

upper sequence: GRMZM2G104730_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT2G41560.1 (Arabidopsis thaliana), 5'ss of exon 4
GTTCAGGGAGGTGGTTGCTGTGACAGGCGATGGTACCAATGACGCTCCAGCATTGCATGAAGCAGATATTGGGCTTGCAATGGGCATAGCAGGAACAGAGgtactaactatacctcgcaatttctactgttcttactgtgaatgtaaaaacctcttg--caaggccatcagaagctaagaactcctcacttgcaattgcaaggccatcatgcccttcggcaattctgtgcgtcccttgaaaagataaataacagtataagcttacatacttgcag
  |  | ||||| ||||| |||||||| ||||| || || || || || || |||||||| ||||| ||||| || |||||||| ||||| ||||||||||||  | |||||  |   | | |||  | ||  |   || |||  ||||| |||  |   ||     ||    | |   || |||  |  ||||                                                                                 
AATTGGAGAGGTAGTTGCAGTGACAGGGGATGGGACAAACGATGCCCCTGCGTTGCATGAGGCAGACATTGGACTAGCAATGGGAATAGCTGGAACAGAGgta--agctatagtt---attctctgttattggtttggttaataaaaaaatctcgagattaacattttcgtttggtgctaattcccgatatgcag--------------------------------------------------------------------------------

upper sequence: GRMZM2G104730_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT3G57330.1 (Arabidopsis thaliana), 5'ss of exon 4
GTTCAGGGAGGTGGTTGCTGTGACAGGCGATGGTACCAATGACGCTCCAGCATTGCATGAAGCAGATATTGGGCTTGCAATGGGCATAGCAGGAACAGAGgtactaactatacctcgcaatttctactgttcttactgtgaatgtaaaaacctcttgcaaggccatcagaagctaagaactcct-cacttgcaattgcaaggccatcatgcccttcggcaattctgtgcgtcccttgaaaagataaataacagtataagcttacatacttgcag
  |  | ||||| ||||| ||||| || ||||| || ||||| ||||| ||||||||||| || || ||||| ||||| ||||| ||||| ||||||||||||     |    |||     ||     ||| |||   | | ||||||| |        | |   ||  | | ||| ||||||  |   | |||   ||  |                                                                        
AATGGGAGAGGTAGTTGCAGTGACTGGGGATGGAACAAATGATGCTCCTGCATTGCATGAGGCTGACATTGGACTTGCCATGGGAATAGCTGGAACAGAGgtagcctttggttctcctctgttactgagttattaa-atcattgtaaaatc-------gatgttctct-atgttaaaaactcccgcgtatacaac-acacag------------------------------------------------------------------------

upper sequence: GRMZM2G104730_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv08s0007g08960.t01 (Vitis vinifera), 5'ss of exon 4
GTTCAGGGAGGTGGTTGCTGTGACAGGCGATGGTACCAATGACGCTCCAGCATTGCATGAAGCAGATATTGGGCTTGCAATGGGCATAGCAGGAACAGAGgtactaactatacctcgcaatttctactgttcttactgtgaatgtaaaaacctcttgcaaggccatcagaagctaagaactcctcacttgcaattgcaaggccatcatgcccttcggcaattctgtgcgtcccttgaaaagataaataacagtataagcttacatacttgcag
||   | ||||| ||||| |||||||| ||||| || ||||| || ||||| |||||||| || || ||||||||||| ||||||||||| |||||||||||  |  || || |   | ||  ||  ||| ||     |           |   ||  |  ||| | |   | |      || |   |     |||||  |  ||  |    ||     ||                                                    
GTATGGTGAGGTTGTTGCAGTGACAGGTGATGGGACAAATGATGCACCAGCTTTGCATGAGGCTGACATTGGGCTTGCCATGGGCATAGCTGGAACAGAGgt--ttgct-tatccgaccat--cttatgtactagtcat-----------ctgtttttactgcccttatctgttg-----tctttcttcttggttgcacagttattttttagttttttgat----------------------------------------------------

upper sequence: GRMZM2G104730_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv13s0158g00360.t01 (Vitis vinifera), 5'ss of exon 4
GTTCAGGGAGGTGGTTGCTGTGACAGGCGATGGTACCAATGACGCTCCAGCATTGCATGAAGCAGATATTGGGCTTGCAATGGGCATAGCAGGAACAGAGgtactaactatacctcgcaattt--ctactgttcttactgtgaatgtaaaaacctcttgcaaggccatcagaagctaagaactcctcacttgcaattgcaaggccatcatgcccttcggcaattctgtgcgtcccttgaaaagataaataacagtataagcttacatacttgcag
 || |  || || || || ||||| |||||||| ||||| || ||||| || |||||||| || || ||||| ||||| ||||||||||||||||| |||||       |||||| || || |   | | |   || || || |   |  | | | || |     |||||    |   |      ||| ||   ||| ||||         |                                                               
ATTTAAAGAAGTTGTGGCAGTGACTGGCGATGGGACCAACGATGCTCCTGCTTTGCATGAGGCGGACATTGGACTTGCCATGGGCATAGCAGGAACTGAGgtttgtttaataccttgccatataattgcagcagtt-ctttggaatcatgatcatttttc----tcatcacttacccgg----tttcattt---attacaagatagattcac---------------------------------------------------------------

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|22490354|gb|BU050277.1|BU050277
EST:     CATTGCATGAAGCAGATATTGGGCTTGCAATGGGCATAGCAGGAACAGAG                         GTAGCCAAGGAGAGTGCCGATGTGATAGTGCTGGACGACAACTTCACAACC
genomic: CATTGCATGAAGCAGATATTGGGCTTGCAATGGGCATAGCAGGAACAGAGgtactaacta ... atacttgcagGTAGCCAAGGAGAGTGCCGATGTGATAGTGCTGGACGACAACTTCACAACC
EST: gi|19057956|gb|BM736623.1|BM736623
EST:     CATTGCATGAAGCAGATATTGGGCTTGCAATGGGCATAGCAGGAACAGAG                         GTAGCCAAGGAGAGTGCC-ATGTGATAGTGCTGGACGACA-CTTC-CAACC
genomic: CATTGCATGAAGCAGATATTGGGCTTGCAATGGGCATAGCAGGAACAGAGgtactaacta ... atacttgcagGTAGCCAAGGAGAGTGCCGATGTGATAGTGCTGGACGACAACTTCACAACC
EST: gi|87152785|gb|DY397574.1|DY397574
EST:     CATTGCATGAAGCAGATATTGGGCTTGCAATGGGCATAGCAGGAACAGAG                         GTAGCCAAGGAGAGTGCCGATGTGATAGTGCTGGACGACAACTTCACAACC
genomic: CATTGCATGAAGCAGATATTGGGCTTGCAATGGGCATAGCAGGAACAGAGgtactaacta ... atacttgcagGTAGCCAAGGAGAGTGCCGATGTGATAGTGCTGGACGACAACTTCACAACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCAGGGAGGTGGTTGCTGTGACAGGCGATGGTACCAATGACGCTCCAGCATTGCATGAAGCAGATATTGGGCTTGCAATGGGCATAGCAGGAACAGAGgtactaactatacctcgcaatttctactgttcttactgtgaatgtaaaaacctcttgcaaggccatcagaagctaagaactcctcacttgcaattgcaaggccatcatgcccttcggcaattctgtgcgtcccttgaaaagataaataacagtataagcttacatacttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT