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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTGgtatgttactcatctctgtcctcaaattggtttcttttaaaataataagtaaataacagattatagaaacaaaaattttaaaaaataaaatagtctctgg...

Basic information

species Zea mays
transcript GRMZM2G421857_T04
intron # 13
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 12
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 12
AATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTGgtatgttactcatctctgtcctcaaattggtttcttttaaaataataagtaaataacagattatagaaacaaaaattttaaaaaataaaatagt-ctctgg---
 || |||||||||| |||||| ||||| ||||| ||||| ||||||||||| |||||||| || |||||||||||||||||||| || || |||||||||||| |||  |  |||    ||  |  |||   || |||       |  |||  |  ||   ||  | |    || ||  | |||      |  |  |||     
GATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGATGGCTGATTCCACCTCACGATGGGCTGAGGCATTGCGTGAAATTTCTGGGCGTTTGgtacgttgtttttcttctgccatac-ttgccctcatttc---ctttttgtatttctcatcctagtgtactttaacttgcacaaagctctgtcctattctcattg

upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 13
AATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTGgtatgttactcatctctgtcctcaa-attggtt--tcttttaaaataataagtaaataacagattatagaaacaaaaattttaaaaaataaaatagtc-tctgg
| | |||||||||||| | |||||||| || || |||||||||||||| || || || ||  | ||||| || ||||||||||| ||||| || ||  ||||  |    | || || ||  |     ||  |   ||||||| ||  ||   |   |    | |||   ||| | | ||||||     |||  |     | || 
ATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGGACGACTGgtgagaattttatttcagtaatagttgttcatcagtcttttagaaagatttcttttttgt-gctta---aaatacagattttattttgtaactttacaatatga

upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 12
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 13
AATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTGgta-tgttactcatctctgtcct--caaattggt-------ttcttttaaaataataagtaaataacagattatagaaacaaaaattttaaaaaataaaatagtctctgg
||| ||||| |||||  | |||||||||||||| || ||||||||||| ||||| || ||||| ||||| || |||||  | || || ||||| ||  ||||| | |||  | | ||  |  |   | || | |       || |  | |  | |    |   |  |  | | ||   |||   |||||      |   ||||       
AATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGATGGCAGACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGGACGGCTGgtaatcttatgcgtttcacttttgctatatggatgttcgtgttgtcctcatctcacttttctttttctcagtttattgacacctattttgctttgttttatag-------

upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 12
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 13
AATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTGgtatgtta-ctcatctctgtcctca------aattggtttcttttaaaataataagtaaat-aacagattata--gaaacaaaaattttaaaaaataaaatagtctctgg
|||||| || || ||  | || ||||| ||||| |||||||||||||| || || || || || ||||||||||| ||||||||||| || ||  |  ||||  | |  |  || ||| |  |||      | ||  ||| ||||      |||||||||| ||  | | |||  |||   | || | | | | ||  ||          
AATTGCCGAATACTTTAGAGACATGGGTTACAATGTCAGTATGATGGCAGATTCAACATCTCGTTGGGCTGAGGCTTTGCGTGAGATATCTGGAAGACTGgtgagatggcctatttcttttgtcattatttattttattttttttctttctataagtaaatcaattgttaatattgaattgagaagtgtgatatatgcaa----------

upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 12
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 13
AATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTGgtatgt--tactcatctctgtcct-caaattggtttcttttaaaataataagtaaataacagattatagaaacaaaaattttaaaaaataaaatagtctctgg
 || ||||| || ||| | |||||||||||||| || ||||||||||| || || || || || ||||| ||||||||||| || || ||||| ||  ||||| ||  | ||||  | |  | |        |||||| || |  | | || | |       ||  |  | |    | |     |||      ||   | |  
TATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGGACGGCTGgtaagtccttctcagttttagcttatgtggaagtttctgttgattttagaaattaccttttaatgcttcatatgtga-tgggggaaagccttttaaagttt--

upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 12
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 5'ss of exon 13
AATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTGgtatgttactcatctctgtcctcaaattggtttcttttaaaataataa----gtaaataacagattatagaaacaaaaattttaaaaaataaaatagtctctgg-----------------------------------------------
  | || || || ||| | |||||||| ||||| |||||||||||||| ||||| || || || |||||||||||  | |||||||| || |||||  | ||||||| ||||   || ||||    |  |||| |||||   |   ||    || | || ||  | ||  |   |   |   || |        | |||  ||                                                
TTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGATGGCAGACTCTACATCTCGCTGGGCTGAGGCGCTTCGTGAGATTTCTGGGCGACTTgtatgtt-ctcaggactttcctttggt--gttttttttagggtttcaaacttgttagtatcatgt-atttatttatggacagtataggcaggttttgtccatgcaatgtcattcagactctaagacatgcagttactctgtggttttgcag

upper sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 12
lower sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 13
AATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTGgtatgttactcatctctgtcctcaaattggtttcttttaaaataataagtaaataacagattatagaaacaaaaattttaaaaaataaaatagtctctgg
  | ||||||||||||||||| |||||||| || |||||||||||||||||||| || ||  | ||||| || || |||||||| || || || ||  | ||| ||  || || |   | ||     |  |||      |||      | |                                                 
TCTGGCTGAGTATTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGACTCGACGTCGAGATGGGCCGAAGCCTTGCGTGAAATATCCGGTCGACTCgtaagtctctgattttctttctattcctaatttac----aaacgccgcgcag------------------------------------------------

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:     ACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTG                         GCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTG
genomic: ACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTGgtatgttact ... tctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTG
EST: gi|6637071|gb|AW261343.1|AW261343
EST:     ACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTG                         GCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTG
genomic: ACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTGgtatgttact ... tctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTG
EST: gi|31360193|gb|CD444550.1|CD444550
EST:     ACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTG                         GCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGGTGCACGTTTG
genomic: ACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTGgtatgttact ... tctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTG
EST: gi|51592889|gb|CV072035.1|CV072035
EST:     ACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTG                         GCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTG
genomic: ACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTGgtatgttact ... tctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTG
EST: gi|61118945|gb|DN559906.1|DN559906
EST:     ACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTG                         GCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTG
genomic: ACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTGgtatgttact ... tctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTG
EST: gi|19437277|gb|BM953687.1|BM953687
EST:     ACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTG                         GCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTG
genomic: ACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTGgtatgttact ... tctggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCACGTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGGGCGTTTGgtatgttactcatctctgtcctcaaattggtttcttttaaaataataagtaaataacagattatagaaacaaaaattttaaaaaataaaatagtctctgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC