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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCCTGATGGCCGTGAGGAGTCTGTCATGAAGAGAACAACACTGGTGGCTAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccctgttaccttgatattcacttggccatgtagccacagatgtaagccctgaaactagtgctgtggtagggaacatatcaatattagaaatatt...

Basic information

species Zea mays
transcript GRMZM2G421857_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 11
TTGCCTGATGGCCGTGAGGAGTCTGTCATGAAGAGAACAACACTGGTGGCTAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccctgttaccttgatattcacttggccatgtagccacagatgtaagccctgaaactagtgctgtggtagggaacatatca-atattagaaatatt---
      ||||| ||||| |||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| || |||||     | || |      ||| | |    |||  ||||| |   ||     |||| |    |   |||      |   | ||| ||| |||   | ||   
ACAGAGGATGGACGTGAAGAGTCTGTGATGAAGAGAACAACACTGGTGGCTAACACATCCAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTATACAGgtaatggtgtattgctcctg-attgattgctacattaagccataatagtg---tctgatatccatatagtgtgccccactttgtcatatagtagttgttttgtt

upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 12
TTGCCTGATGGCCGTGAGGAGTCTGTCATGAAGAGAACAACACTGGTGGCTAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccctgttaccttgatattc--acttggccatgtagccac-agatgtaagccctgaaactagtgctgtggtagggaacatatcaatattagaaatatt
|| |||||||| ||||| || |||||||||||| | |||||||| ||||||||||| ||||||||||| || ||||||||||||||||| ||||| || ||| |     | |  | |  ||  |   |  |  | || ||      |||  |||    |   ||||   || |  ||  |   ||   ||| | |      | 
TTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGTACAACACTAGTGGCTAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtgactttgtatctcttgaattctaggatatctctatttattgttgagaaataatattt---actaactctttcctattgccaattgtaatttaattggcttg

upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 12
TTGCCTGATGGCCGTGAGGAGTCTGTCATGAAGAGAACAACACTGGTGGCTAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccctgttac-cttgatattcacttggccatg--tagccacagatgtaagccctgaaactagtgctgtggtagggaacatatcaatattagaaatatt
|| |||||||| ||||| || |||||||||||| | |||||||| ||||||||||| ||||||||||| || ||||||||||||||||| ||||| || ||| |  |  |||  | |||||  |  | ||    ||   ||   |   || |   |        | ||  |||     | ||  |||     ||   ||  | 
TTACCTGATGGTCGTGAAGAATCTGTCATGAAGCGCACAACACTAGTGGCTAACACTTCAAACATGCCAGTGGCTGCTCGTGAAGCTTCAATTTATACAGgtga--ctttgtagctcttgaattctatttatttattgttaagaattaatatttactaattctttcgtattgtcaactgtaatttatttggcttgtgaaagt-

upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 11
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 12
TTGCCTGATGGCCGTGAGGAGTCTGTCATGAAGAGAACAACACTGGTGGCTAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccctgttaccttgatatt-cacttggccatgtagccacagatgtaagccc-tgaaactagtgctgtggtagggaacatatcaatattagaaatatt
|||||||||||||||||||| |||||||||||  | || ||||| || |||||||| || ||||||||||| |||||||||||||| || |||||||| |||||    | |  ||   ||| |   | ||    ||| | ||       || || | |     |  |  | |  ||  |   ||  ||              
TTGCCTGATGGCCGTGAGGAATCTGTCATGAAACGTACCACACTTGTTGCTAACACCTCTAACATGCCTGTGGCTGCTCGTGAAGCCTCAATTTACACAGgtaatgttcaggcacacagatttaatagttattgatgaatcccattgcctatgctcattttttttttttttttttaatgtgaattccag-------------

upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 11
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 12
TTGCCTGATGGCCGTGAGGAGTCTGTCATGAAGAGAACAACACTGGTGGCTAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccctg-------ttaccttgatattcacttggccatgtagccacagatgtaagccctgaaactagtgctgtggtagggaacatatcaatattagaaatatt
 ||||||||||  | || || ||||||||||||||||| || || || |||||||| || ||||||||||| |||||  | || ||||| ||||| || |||||  |  ||       ||   ||| |||  | | ||  ||        |  ||||    ||     |  |  | |   |  |  |  | |  | || ||      
CTGCCTGATGGGAGAGAAGAATCTGTCATGAAGAGAACTACGCTCGTAGCTAACACTTCTAACATGCCTGTGGCTGCAAGGGAGGCTTCAATTTATACAGgtaatgctttgatcttcattgttttgttatgaattggg--attcttttgtatgtgtagtttctacccttcattttttt-catagggctaaactttgtttgagc----

upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 11
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 12
TTGCCTGATGGCCGTGAGGAGTCTGTCATGAAGAGAACAACACTGGTGGCTAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccctgttaccttgatattcacttggccatg---tagccacagatgtaagccctgaaactagtgctgtggtagggaacatatcaatattagaaatatt
 |||||||||||||||| || |||||||||||| |||| ||||| ||||| ||||| ||||| |||||||| ||||||||||| ||||| ||||| || ||||||    | |     |  |  | ||| |  ||||   | ||         ||    ||||   | |  |   |         |  ||||  | |   | ||
CTGCCTGATGGCCGTGAAGAATCTGTCATGAAGCGAACTACACTTGTGGCCAACACTTCAAATATGCCTGTGGCTGCTCGTGAGGCTTCAATTTATACAGgtaaatatatttacttctattcattactagcacatgaaatggctgggtgaaaaaattttgaagtcaatatta--gcttcatcttttgcaattcttgtg-tgtt

upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 11
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 12
TTGCCTGATGGCCGTGAGGAGTCTGTCATGAAGAGAACAACACTGGTGGCTAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccctgtta-----ccttgatattcacttggccat----gtagccacagatgtaagccctgaaactagtgctgtggtagggaacatatcaatattagaaatatt----------------------------------------------
|| || || || || |||||||| ||||||||| | || || || ||||| |||||||||||||||||||| |||||||||||||| || ||||| || |||     ||| ||      |  | |  || |  ||  |||    |  ||  |  || ||     |    | |  | | |  | |    | |   | | |   | ||| |                                              
TTACCCGACGGTCGGGAGGAGTCCGTCATGAAGCGTACTACGCTTGTGGCCAACACATCAAACATGCCTGTGGCTGCTCGTGAAGCATCTATTTATACAGgtttcctcctttttattctctctaaagtttaagtgttcattgctgcggcacctcatctagataatttctcaaacgttttcatcgcttccttggaattttcgcatataattgcgtcctttctacatttgctctgaagattctgttttctgttgcag

upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 11
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 5'ss of exon 12
TTGCCTGATGGCCGTGAGGAGTCTGTCATGAAGAGAACAACACTGGTGGCTAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccct---gttaccttgatattcacttggccatgtagccacagatgtaagccctgaaact----agtgctgtg-gtagggaacatatcaatattagaaatatt
|||||||| || || ||||||||||| |||||| | || || || ||||| || |||||||| |||||||| |||||||||||||||||||| || || |||      ||   ||||   |||   | |  |    ||             |||    |||||      ||   | |  ||     |||| |   |||  |    |  
TTGCCTGACGGACGAGAGGAGTCTGTTATGAAGCGGACCACTCTCGTGGCCAATACATCAAATATGCCTGTGGCTGCTCGTGAAGCTTCCATCTATACAGgttcccatcttgagttattctgaagcttaacttttgatcgcaatgtgaccttaaagtttgaaatcttgaaggattttacgttcatcacattttgttatctgttgcag-

upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 11
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 5'ss of exon 12
TTGCCTGATGGCCGTGAGGAGTCTGTCATGAAGAGAACAACACTGGTGGCTAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccctgttaccttgatattc-actt----------------ggccatgtagccacagatgtaagccctgaaactagtgctgtggtagggaacatatcaatattag-----aaatatt--------------
|| |||||||| ||||| |||||||| |||||| | || || || ||||| ||||| |||||||||||||| |||||||||||||| || || ||||| ||| |    || ||    ||| | || ||||                  |||| |   |     || | |     ||     | ||||   |  | | |  ||   || |      ||||  |              
TTACCTGATGGTCGTGAAGAGTCTGTTATGAAGCGTACCACTCTCGTGGCCAACACCTCAAACATGCCTGTGGCTGCTCGTGAAGCATCTATCTACACAGgttattttcttttcttctgagactctactttctaggtgctgtatgaaaccatttcatcctctttggatgtttgaaatgctatcctgtatgatcgcatacttccgcatcattatgcaaatgctgtttcctgttgcag

upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 11
lower sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 12
TTGCCTGATGGCCGTGAGGAGTCTGTCATGAAGAGAACAACACTGGTGGCTAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccctgttaccttgatattcacttggccatgtagccacagatgtaagccctgaaactagtgctgtggtagggaacatatcaatattagaaatatt
 | |||||||| || || ||||||||||||||| | ||||| || || ||||| || ||||| |||||||| || || || |||||||| |||||||| ||||   || |   |  || |   |||   |   || |   |   | | | ||                                                
CTCCCTGATGGACGCGAAGAGTCTGTCATGAAGCGTACAACTCTCGTCGCTAATACTTCAAATATGCCTGTGGCGGCACGAGAAGCTTCAATTTACACGGgtatgtccttccaa--ttcaggctcaac-gctgattttatcgatggtttcag------------------------------------------------

upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 11
lower sequence: EFJ33015 (Selaginella moellendorffii), 5'ss of exon 11
TTGCCTGATGGCCGTGAGGAGTCTGTCATGAAGAGAACAACACTGGTGGCTAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccctgttaccttgatattcacttggccatgtagccacagatgtaagccctgaaactagtgctgtggtagggaacatatcaatattagaaatatt
 | |||||||| || || ||||||||||||||| | ||||| || || ||||| || ||||| |||||||| || || || |||||||| |||||||| ||||   || |   |  || |   |||   |   || |   |   | | | ||                                                
CTTCCTGATGGACGCGAAGAGTCTGTCATGAAGCGTACAACTCTCGTCGCTAATACTTCAAATATGCCTGTGGCGGCACGAGAAGCTTCAATTTACACGGgtatgtccttccaa--ttcaggctcagc-gctgattttatcgatggtttcag------------------------------------------------

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|67026160|gb|CO454909.1|CO454909
EST:     TAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACAG                         GAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGA
genomic: TAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccct ... tttaactcagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGA
EST: gi|31360193|gb|CD444550.1|CD444550
EST:     TAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACAG                         GAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGA
genomic: TAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccct ... tttaactcagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGA
EST: gi|51592889|gb|CV072035.1|CV072035
EST:     TAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACAG                         GAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGA
genomic: TAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccct ... tttaactcagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGA
EST: gi|61118945|gb|DN559906.1|DN559906
EST:     TAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACAG                         GAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGA
genomic: TAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccct ... tttaactcagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGA
EST: gi|6012344|gb|AW061700.1|AW061700
EST:     TAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTG                         GAATTACAATTGCT
genomic: TAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccct ... tttaactcagGAATTACAATTGCT
EST: gi|19437277|gb|BM953687.1|BM953687
EST:     TAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACAG                         GAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGA
genomic: TAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccct ... tttaactcagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCCTGATGGCCGTGAGGAGTCTGTCATGAAGAGAACAACACTGGTGGCTAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccctgttaccttgatattcacttggccatgtagccacagatgtaagccctgaaactagtgctgtggtagggaacatatcaatattagaaatatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC