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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAGgtaacttcttggcatttacgttattattacttagcccttttaattttatcttcagctgtattataattcttgtgatttaccatggtgctagtgaacttct...

Basic information

species Zea mays
transcript GRMZM2G085474_T04
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085474_T04 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os09g07830.1 (Oryza sativa), 5'ss of exon 9
TTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAGgtaact-tcttggcatttacgtta--ttattacttagcccttttaattttatcttcagctgtattataattcttgtgatttaccatggtgctagtgaacttct--
||||||||||  ||||||||||| || || || ||||||||||||||||||||||| ||||| ||||| |||||||||||||||||||   |   ||| || |||  |||  |||||  | ||   | | |  | | |||  || |  ||  |     ||  || |  | ||| |   ||   | || |  
TTTGACCCAGTGAAACTGAAGAAGCTCCGTCCTAGTTTCAAGGAGAATGGTGGTACTGTTACTGCTGGGAATGCTTCTAGTATAAGgtgcttgctttgacacttattttaatttatttttaagatttgtgaggtatttctgtag-tacatggt----tttaggactacctatgttagcagaacagttgtat

upper sequence: GRMZM2G085474_T04 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA14G00760.1 (Glycine max), 5'ss of exon 8
TTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAGgtaact----tcttggcatttacgttattattacttagcccttttaattttatcttcagctgtattataattcttgtgatttaccatggtgctagtgaacttct
|||||  | || ||  |    |||||||| |||||||||||||||| ||| ||| | ||||||||||| |||||||| || ||||||| | |    | | |  ||||     | | || | || |      | || ||| |  |      |    ||| || || | ||  ||  |     |  |     
TTTGATGCTGCCAAGTTACGCAAACTTCGGCCAAGTTTCAAGGAGACTGGAGGTTCTGTTACAGCTGGCAATGCTTCCAGCATAAGgttaatatattttcgaaatttgttaaactttttccta-cataacgatttgtatttggatgcccttgtcgattattttgttataaaatactatatatatata---

upper sequence: GRMZM2G085474_T04 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA02G47860.1 (Glycine max), 5'ss of exon 8
TTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAGgtaacttcttggcatttacgttattattacttagcccttttaattt-tatcttcagctgtattataattcttgtgatttaccatggtgctagtgaacttct
|||||  | || ||  |    |||||||| |||||||||||||||| ||| ||| | ||||| ||||| |||||||| || ||||||| | |   |   ||| |  ||    | ||||     |  || | | | | |     || || | ||| ||  ||   || ||                  
TTTGATGCTGCCAAGTTACGCAAACTTCGGCCAAGTTTCAAGGAGACTGGAGGTTCTGTTACTGCTGGCAATGCTTCCAGCATAAGgttaata--tattattgaaatttgcttaactt--ttttcctagtgtgtgtgtgtgtgtgaatgaaaatgctcttg--ctaacag-----------------

upper sequence: GRMZM2G085474_T04 (Zea mays), 5'ss of exon 9
lower sequence: AT5G48230.1 (Arabidopsis thaliana), 5'ss of exon 8
TTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAGgtaactt-cttggc-------atttacgttattattacttagcccttttaattttatcttcagctgtattataatt---cttgtgatttaccatggtgct-agtgaacttct--------------
|||||  | |||||| ||| |||||| || || |||||||| |||||||| || || ||||||||||||||||| ||||| |||||||   || | | ||       || || ||| |||    ||||     | |  |      | |  || ||  |  ||    |||  | ||    |  |  | ||| || ||                
TTTGATGCTGCAAAATTGAGGAAACTCCGTCCTAGTTTCAAAGAGAATGGAGGGACTGTTACAGCTGGAAATGCGTCTAGCATAAGgtccttttcctagctgaccatatatatgttcttagcttttagagaactcatgtaacgtatgaagtggatcttggttagatttgcaacttttttttctctttagtaaattttgtctctctttgacag

upper sequence: GRMZM2G085474_T04 (Zea mays), 5'ss of exon 9
lower sequence: Vv00s0531g00050.t01 (Vitis vinifera), 5'ss of exon 8
TTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAGgtaacttcttggcatttacgttattattacttagcccttttaattttatcttcagctgtattataattcttgtgatttaccatg-gtgctagtgaacttct----
|||||  | |||||||| | ||||||||| |||||||||||||   |||| ||| | ||||| || || ||||||||||| ||||||||   | |  |  | |  | | |    |    ||| |||   |   |   |||      ||||  || ||||    |   |   |  | | |||| |||     
TTTGATGCTGCAAAACTAAGGAAACTTCGACCAAGTTTCAAGG---ATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAGgta---tgtgtgtgtgtgtgctctcgc-atgctgccttttccttaagagtctcaaacaccttatc-ttgttgtagcatgtgagatgaacaattgaatttcccaag

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|226431382|gb|GO477718.1|GO477718
EST:     TTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAG                         TGATGGGGCGGCTGCATTAGTTTTGGTGAGTGGGCAGAAGGCTCAAGAGCT
genomic: TTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAGgtaacttctt ... tatggatcagTGATGGGGCGGCTGCATTAGTTTTGGTGAGTGGGCAGAAGGCTCAAGAGCT
EST: gi|19822712|gb|BQ048736.1|BQ048736
EST:     TTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAG                         TGATGGGGCGGCTGCATTAGTTTTGGTGAGTGGGCAGAAGGCTCAAGAGCA
genomic: TTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAGgtaacttctt ... tatggatcagTGATGGGGCGGCTGCATTAGTTTTGGTGAGTGGGCAGAAGGCTCAAGAGCT
EST: gi|89106387|gb|DY576604.1|DY576604
EST:     TTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAG                         TGATGGGGCGGCTGCATTAGTTTTGGTGAGTGGGCAGAAGGCTCAAGAGCT
genomic: TTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAGgtaacttctt ... tatggatcagTGATGGGGCGGCTGCATTAGTTTTGGTGAGTGGGCAGAAGGCTCAAGAGCT
EST: gi|211292809|gb|FL187023.1|FL187023
EST:     TTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAG                         TGATGGGGCGGCTGCATTAGTTTTGGTGAGTGGGCAGAAGGCTCAAGAGCT
genomic: TTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAGgtaacttctt ... tatggatcagTGATGGGGCGGCTGCATTAGTTTTGGTGAGTGGGCAGAAGGCTCAAGAGCT
EST: gi|6526946|gb|AW216191.1|AW216191
EST:     TTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAG                         TGATGGGGCGGCTGCATTAGTTTTGGTGAGTGGGCAGAAGGCTCAAGAGCT
genomic: TTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAGgtaacttctt ... tatggatcagTGATGGGGCGGCTGCATTAGTTTTGGTGAGTGGGCAGAAGGCTCAAGAGCT
EST: gi|211535814|gb|FL146743.1|FL146743
EST:     TACAGCTGGAAATGCTTCTAGTATAAG                         TGATGGGGCGGCTGCATTAGTTTTGGTGAGTGGGCAGAAGGC
genomic: TACAGCTGGAAATGCTTCTAGTATAAGgtaacttctt ... tatggatcagTGATGGGGCGGCTGCATTAGTTTTGGTGAGTGGGCAGAAGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGACCCAGCAAAACTGAAGAAACTTCGCCCAAGTTTCAAGGAGAATGGTGGTACCGTTACAGCTGGAAATGCTTCTAGTATAAGgtaacttcttggcatttacgttattattacttagcccttttaattttatcttcagctgtattataattcttgtgatttaccatggtgctagtgaacttct

- - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA