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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACAGCTTTGAGTATCTTGATGCACCAGTCGAGAGGATTGCTGGAGCTGATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgtccgtactggtcctttcgctttcatttatgtttgcatacggatttgtggttacacaactcttgttgccggactagtagcacttcaagaaaagaaaaaaa...

Basic information

species Zea mays
transcript GRMZM2G043198_T03
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G043198_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os08g42410.3 (Oryza sativa), 5'ss of exon 12
---------------GGACAGCTTTGAGTATCTTGATGCACCAGTCGAGAGGATTGCTGGAGCTGATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgtccgtactggtcctttcgctttcatttatgtttgcatacggatttgtggttacacaactcttgttgccggactagtagcacttcaagaaaagaaaaaaa
               |||||||||||| ||||||||||| ||||| |||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| | ||| | | ||   |||||  |||                                                                        
CATGTCTGTTGTAGAGGACAGCTTTGAATATCTTGATGCGCCAgttgagaggattgctggagctgatgtgcccatgccctacgctgccaaccttgagaggatggctgttccacaggtacttacggctgct---gcttt-gtttgaac--------------------------------------------------------------------

upper sequence: GRMZM2G043198_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 11
GGACAGCTTTGAGTATCTTGATGCACCAGTCGAGAGGATTGCTGGAGCTGATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgtccgtactggtcctttcgctttcatttatgtttgcatacggatttgtggttacacaactcttgttgccggactagtagcacttcaagaaaagaaaaaaa--
|||||||||||| ||||||||||| ||||| |||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| | ||| | | ||      ||     | |    | |  ||| ||     |    |   |  |||     |||  |   | | ||  | ||  |   |   
GGACAGCTTTGAATATCTTGATGCGCCAGTTGAGAGGATTGCTGGAGCTGATGTGCCCATGCCCTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgtacttacggctgctgctttgtttgaacaaga--actttaggaattccatctcgttatgccaagttcagcaactgttgctattccaccataacgacctagcc

upper sequence: GRMZM2G043198_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA02G46380.1 (Glycine max), 5'ss of exon 13
GGACAGCTTTGAGTATCTTGATGCACCAGTCGAGAGGATTGCTGGAGCTGATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgt--ccgtactggtcctttcgctttcatttatg--tttgc--atacggatttgtggttacacaactcttgttgccggactagtagcacttcaagaaaagaaaaaaa
||| || ||||  |||||||||||||| || ||||| ||||| || |||||||| |||||||| || || || || || || || |||||||| ||||||||     | ||      ||   | |  | | ||  ||||     | |  || |  | ||        || ||   |  | || |     |    |     |     
GGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAGAATTGCCGGGGCTGATGTTCCCATGCCATATGCAGCAAATCTGGAAAGAATGGCTGTCCCACAGgtaatgattcttaaatattaattgttttctgtgactttgtcagcatgatttggaagatattttttcattatt-ttgatccagaaatgtatttctattttga-----

upper sequence: GRMZM2G043198_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA14G36540.3 (Glycine max), 5'ss of exon 13
GGACAGCTTTGAGTATCTTGATGCACCAGTCGAGAGGATTGCTGGAGCTGATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgtccgtactggtcctttcgctttcatttatgtttgcatacggatttgtg-gttacacaactcttgttgccggactagtagcacttcaagaaaagaaaaaaa------
 || || ||||  |||||||||||||| || ||||| |||||||| |||||||| |||||||| || || || || || || || |||||||| ||||||||    | || | |||     || |||  | | ||        |  |   | |    ||   |||||| |    |  |     | ||  ||   |     |      
AGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAGAATTGCTGGGGCTGATGTTCCCATGCCTTATGCAGCAAATCTGGAAAGAATGGCTGTCCCACAGgt----aatgattcttaaatattaattgttttctgtgactttgtcagcatgatttggaagatttgttgtca---ttattttgatccagaaatgtatttctatttcga

upper sequence: GRMZM2G043198_T02 (Zea mays), 5'ss of exon 12
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 14
GGACAGCTTTGAGTATCTTGATGCACCAGTCGAGAGGATTGCTGGAGCTGATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgtccgtactggtcctttcgctttcatttatgtttgcatacggatttgtggttacacaactcttgttgccggactagtagcacttcaagaaaagaaaaaaa
 || ||||||  |||  | |||||||| |||||||||||||| ||||||||||| || |||||||| || || ||||| |||||  ||||| |||| |||||  ||  ||  ||||    || |||  |    |   | |   |||||   |    ||    | |     ||  | |    || ||              
AGAGAGCTTTTCGTACTTGGATGCACCGGTCGAGAGGATTGCAGGAGCTGATGTTCCAATGCCGTATGCAGCTAACCTAGAGAGATTGGCTCTTCCTCAGgtttgttttgtcccttct--ttgcatcgaaaacttggttcaattttgtctgttattaatgaatttgagatga--aatgattctgcag-------------

upper sequence: GRMZM2G043198_T02 (Zea mays), 5'ss of exon 12
lower sequence: Vv01s0146g00310.t01 (Vitis vinifera), 5'ss of exon 14
GGACAGCTTTGAGTATCTTGATGCACCAGTCGAGAGGATTGCTGGAGCTGATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgt-----ccgtactggtcctttcgctttcatttatgtttgcatacggatttgtggttacacaactcttgttgccggactagtagcacttcaagaaaagaaaaaaa
||| |||||||  ||||||||||||||||| || |||||||| || |||||||| |||||||| || ||||| || || ||||| |||||||| ||||||||     |  |  || | |||     || |||| | ||  |||| |   ||||  || |||    ||||   ||     | | |    || |       | |  |
GGAGAGCTTTGGTTATCTTGATGCACCAGTGGAAAGGATTGCCGGGGCTGATGTTCCCATGCCTTATGCTGCTAATCTCGAGAGAATGGCTGTCCCACAGgtagattcttttttgattcttctagcttgattt-tattatcataagctcttgttcttccac----cttgcatccaataaatttgggtatccatgtttttagatta

upper sequence: GRMZM2G043198_T02 (Zea mays), 5'ss of exon 12
lower sequence: Vv17s0000g00690.t01 (Vitis vinifera), 5'ss of exon 13
GGACAGCTTTGAGTATCTTGATGCACCAGTCGAGAGGATTGCTGGAGCTGATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgtccgtactggtcctttcgctttcatttatgtttgcatacggatttgtggttacacaactcttgttgccggactagtagcacttcaagaaaagaaaaaaa-
||| |||||||| | |||||||||||| ||||| |||||||| || || ||| | |||||||| || || || || |||||||| |||||| ||||||||||  | |        ||| | ||  ||| |  ||| |     |||     ||     |   ||| ||  |  || | |     |             ||  
GGAGAGCTTTGATTCTCTTGATGCACCTGTCGAAAGGATTGCAGGGGCAGATATTCCCATGCCTTATGCAGCAAATCTTGAGAGAATGGCTCTTCCACAGgtatgcatcctgatattctcctttgttt-ttcttgtaattacattctacattgtttcagatttgctggtgatctggaaatttatggcctgtccttggaatt

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|211534128|gb|FL427385.1|FL427385
EST:     ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAG                         GTCGATGACATCGTCCGGGCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA
genomic: ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgtccgtactg ... acacctgcagGTCGATGACATCGTCCGGGCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA
EST: gi|6056687|gb|AW091092.1|AW091092
EST:     ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAG                         GTCGATGACATCGTCCGGGCAGCCAAGCGAGCTTGCTACAGGGCAGCAGTA
genomic: ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgtccgtactg ... acacctgcagGTCGATGACATCGTCCGGGCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA
EST: gi|60352148|gb|DN219121.1|DN219121
EST:     ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAG                         GTCGATGACATCGTCCGGGCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA
genomic: ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgtccgtactg ... acacctgcagGTCGATGACATCGTCCGGGCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA
EST: gi|148928998|gb|EC874173.2|EC874173
EST:     ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGAGGGGTGTTCCACAG                         GTCGATGACATCGTCCGGGCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA
genomic: ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgtccgtactg ... acacctgcagGTCGATGACATCGTCCGGGCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA
EST: gi|76282095|gb|DV021663.1|DV021663
EST:     ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAG                         GTCGATGACATCGTCCGGGCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA
genomic: ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgtccgtactg ... acacctgcagGTCGATGACATCGTCCGGGCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA
EST: gi|67038743|gb|CO464998.1|CO464998
EST:     ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAG                         GTCGATGACATCGTCCGGGCAGCCAAGCGAGCTTGCTACAGGGCAGCAGTA
genomic: ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgtccgtactg ... acacctgcagGTCGATGACATCGTCCGGGCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA
EST: gi|60396979|gb|DN229798.1|DN229798
EST:     ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAG                         GTCGATGACATCGTCCGGGCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA
genomic: ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgtccgtactg ... acacctgcagGTCGATGACATCGTCCGGGCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA
EST: gi|15082843|gb|BI389527.1|BI389527
EST:     ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAG                         GTCGATGACATCGTCCGGGCAGCCAAGCGAGCTTGCTACAGGGCAGCAGTA
genomic: ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgtccgtactg ... acacctgcagGTCGATGACATCGTCCGGGCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA
EST: gi|4610194|gb|AI601033.1|AI601033
EST:     ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAG                         GTCGATGACATCGTCCGGGCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA
genomic: ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgtccgtactg ... acacctgcagGTCGATGACATCGTCCGGGCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA
EST: gi|6031329|gb|AW076186.1|AW076186
EST:     ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAG                         GTCGATGACATCGTCCGGGCAGCCAAGCGAGCTTGCTACAGGGCAGCAGTA
genomic: ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgtccgtactg ... acacctgcagGTCGATGACATCGTCCGGGCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA
EST: gi|24765246|gb|CA400405.1|CA400405
EST:     ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAG                         GTCGATGACATCGTCCGGCCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA
genomic: ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgtccgtactg ... acacctgcagGTCGATGACATCGTCCGGGCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA
EST: gi|14206753|gb|BG840431.1|BG840431
EST:     ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAG                         GTCGATGACATCGTCCGGGCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA
genomic: ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgtccgtactg ... acacctgcagGTCGATGACATCGTCCGGGCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA
EST: gi|6828052|gb|AW331695.1|AW331695
EST:     ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAG                         GTCGATGACATCGTCCGGGCAGCCAAGCGAGCTTGCTACAGGGCAGCAGTA
genomic: ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgtccgtactg ... acacctgcagGTCGATGACATCGTCCGGGCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA
EST: gi|60340970|gb|DN207943.1|DN207943
EST:     ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAG                         GTCGATGACATCGTCCGGGCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA
genomic: ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgtccgtactg ... acacctgcagGTCGATGACATCGTCCGGGCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA
EST: gi|44900498|gb|CK827043.1|CK827043
EST:     ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAG                         GTCGATGACATCGTCCGGGCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA
genomic: ATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgtccgtactg ... acacctgcagGTCGATGACATCGTCCGGGCAGCCAAGCGTGCTTGCTACAGGGCAGCAGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACAGCTTTGAGTATCTTGATGCACCAGTCGAGAGGATTGCTGGAGCTGATGTGCCCATGCCGTACGCTGCCAACCTTGAGAGGATGGCTGTTCCACAGgtccgtactggtcctttcgctttcatttatgtttgcatacggatttgtggttacacaactcttgttgccggactagtagcacttcaagaaaagaaaaaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaaaaa