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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGAACAACCATGGACCCAACTCTAACACGTGCTGACAGACTGGTTGGCCAGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaatctttgctcgctcatgattttagattggcagaaatagttgttaaacttaagtatgtcattgaacatttgctttgcag

Basic information

species Zea mays
transcript GRMZM2G107654_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107654_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os12g41400.1 (Oryza sativa), 5'ss of exon 8
GGGAACAACCATGGACCCAACTCTAACACGTGCTGACAGACTGGTTGGCCAGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaatctttgctcgctcatgattttagattggcagaaatagttgttaaacttaagtatgtcattgaacatttgctttgcag
||||||||||||||| |||||  | ||||||||||| ||||||||||| |||||||| |||||||| || ||||| |||||||| || || ||||||||||||||| || |||| | |   ||| ||||| ||   |    ||| | |  ||   ||||| | ||   ||  |    |||       
GGGAACAACCATGGATCCAACCTTGACACGTGCTGATAGACTGGTTGGTCAGGTTCTAGGTGAAGTTGGATCACTTCCTGATGTCTATGTGGAGCTTGAGgtttgtcaactcttcgttgcatcaagattt-agtgagaataaaacattcattg--cttaaatctggactttcatgcatgcag-----

upper sequence: GRMZM2G107654_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os12g07740.1 (Oryza sativa), 5'ss of exon 8
GGGAACAACCATGGACCCAACTCTAACACGTGCTGACAGACTGGTTGGCCAGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttg---taaaatctttgctcgctcatgattttagattggcagaaatagttg-ttaaacttaagtatgtcattgaacatttgctttgcag
 |||||||||||||| |||||| | |||||||| || ||||||||||| |||||||| |||||||| || || || |||||||| || || ||||||||||||||   |||    |||| |   ||| | |||||| |   |  |  |  ||  ||| |  | |   | |||   |               
TGGAACAACCATGGATCCAACTTTGACACGTGCCGATAGACTGGTTGGGCAGGTTCTGGGTGAAGTTGGATCCCTTCCTGATGTCTATGTGGAGCTTGAGgtttgccataactcatttgtttcttcagggttttag-tgaacgaatgtcattacttacatctgaacctttcacacag--------------

upper sequence: GRMZM2G107654_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT1G04170.1 (Arabidopsis thaliana), 5'ss of exon 8
GGGAACAACCATGGACCCAACTCTAACACGTGCTGACAGACTGGTTGGCCAGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaatctttg-----ctcgctcatgattttagattggcagaaatagttgttaaacttaagtatgtcattgaacatttgctt-tgcag---------
 |||||||| |||||||||||||| || ||||| ||  || | ||||| || || ||||||||| | |||||||| |||||||| |  || || || ||||| |  | ||    |      |   ||| | | | |  || | |  ||   ||   | |   ||  |    | || ||  | || || || |          
TGGAACAACAATGGACCCAACTCTCACTCGTGCAGATCGATTAGTTGGTCAAGTCCTTGGTGAAATCGGTTCACTTCCTGATGTATTTGTTGAACTCGAGgtataaacaactcctcacaaccatactcttcagtctttatggtcctaatgggtctcttagtgtattttctccttttaatttgtggttatgtaaaatctgtag

upper sequence: GRMZM2G107654_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv13s0074g00310.t01 (Vitis vinifera), 5'ss of exon 8
GGGAACAACCATGGACCCAACTCTAACACGTGCTGACAGACTGGTTGGCCAGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgt------------ttgtaaaatc--tttgctcgctcatgattttagattggcagaaatagttgttaaacttaagtatgtcattgaacatttgctttgcag--
 || |||||||||||||| ||| |||||||||||||  ||||||| || || |||||||| || || || ||||| ||||||||||  || || || |||||             || || |    ||      |  ||   ||   ||  ||  | ||| | ||   || |||  | |  |||     | | || |  ||  
TGGTACAACCATGGACCCCACTTTAACACGTGCTGATCGACTGGTGGGGCAAGTTCTTGGGGAGGTTGGGTCACTCCCTGATGTTTTTGTTGAACTAGAGgtaaccaactaaacctgaaagactgattaaactccgtatctattcctatacgcgcagataat-gtcgtacataa--aagcaattttgtttcttctatatagtt

upper sequence: GRMZM2G107654_T01 (Zea mays), 5'ss of exon 8
lower sequence: PP1S207_94V6.1 (Physcomitrella patens), 5'ss of exon 7
GGGAACAACCATGGACCCAACTCTAACACGTGCTGACAGACTGGTTGGCCAGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgt---ttgtaaaatcttt-----gctcgctcatgattttagattggcagaaatag--ttgttaaacttaagtatgtca----ttgaacatttgctttgcag
|||||||||||| || || ||||| || |||||||||||||||||||| || || |||||||| || ||    || |||||||| |  || ||| | |||||   || |   | || |     ||||| | |  |||    |||  || |    |  ||||     ||    ||| ||    || || |  || |||  | 
GGGAACAACCATTGATCCTACTCTTACTCGTGCTGACAGACTGGTTGGGCAAGTGCTTGGTGAGGTTGGGGAGCTTCCTGATGTCTTTGTGGAGTTGGAGgtaatttatttcacctgttacgtgctcgtttaatattgctcatttccaaatgcggaattgtctgtgtttgtgatggcagacgttcaagaagtggttttta-

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|211112537|gb|FL352687.1|FL352687
EST:     AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAG                         ATCAATTTCTTCCTACTCCGGAGGC
genomic: AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGC
EST: gi|211534491|gb|FL328418.1|FL328418
EST:     AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAG                         ATCAATTTCTTCCTACTCCGGAG-CTGTTGGGTGTGAGGACGAAAGGTACA
genomic: AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
EST: gi|28930895|gb|CB334256.1|CB334256
EST:     AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAG                         ATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
genomic: AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
EST: gi|28873829|gb|CB329766.1|CB329766
EST:     AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAG                         ATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
genomic: AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
EST: gi|18162027|gb|BM331866.1|BM331866
EST:     AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAG                         ATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
genomic: AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
EST: gi|21331218|gb|BQ486599.1|BQ486599
EST:     AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAG                         ATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
genomic: AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
EST: gi|78103987|gb|DV522405.1|DV522405
EST:     AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAG                         ATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
genomic: AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
EST: gi|60342089|gb|DN209062.1|DN209062
EST:     AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAG                         ATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
genomic: AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
EST: gi|211475135|gb|FL331172.1|FL331172
EST:     GAAGTAGGTTCACTACCTGATGTTTACCTTGAGCTTGAG                         ATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
genomic: GAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
EST: gi|29129944|gb|CB380648.1|CB380648
EST:     AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAG                         ATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
genomic: AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
EST: gi|60346436|gb|DN213409.1|DN213409
EST:     AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAG                         ATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
genomic: AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
EST: gi|13382167|gb|BG458842.1|BG458842
EST:     AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAG                         ATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
genomic: AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
EST: gi|14700954|gb|BI233372.1|BI233372
EST:     AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAG                         ATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
genomic: AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
EST: gi|32831035|gb|CD970713.1|CD970713
EST:     AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAG                         ATCAATTTCTTCCTACTCCGG
genomic: AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGG
EST: gi|211394215|gb|FL229509.1|FL229509
EST:     AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAG                         ATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
genomic: AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
EST: gi|91870409|gb|EB400862.1|EB400862
EST:     TGATGTTTACGTAGAGCTTGAG                         ATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
genomic: TGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
EST: gi|16927572|gb|BM080641.1|BM080641
EST:     AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAG                         ATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
genomic: AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
EST: gi|32909291|gb|CF014103.1|CF014103
EST:     AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAG                         ATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
genomic: AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
EST: gi|31357361|gb|CD441718.1|CD441718
EST:     AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAG                         ATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
genomic: AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
EST: gi|7216833|gb|AW562955.1|AW562955
EST:     AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAG                         ATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
genomic: AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
EST: gi|71595718|gb|DR906469.1|DR906469
EST:     AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAG                         ATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
genomic: AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
EST: gi|13515657|gb|BG517933.1|BG517933
EST:     GTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAG                         ATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
genomic: GTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
EST: gi|33094840|gb|CF054834.1|CF054834
EST:     AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAG                         ATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTAC
genomic: AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTAC
EST: gi|4630598|gb|AI621472.1|AI621472
EST:     AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAG                         ATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
genomic: AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
EST: gi|78025059|gb|DV493446.1|DV493446
EST:     AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAG                         ATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA
genomic: AGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 570

GGGAACAACCATGGACCCAACTCTAACACGTGCTGACAGACTGGTTGGCCAGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACAGAGAAGGCAGGGAAGGTGTCGAAGCTCACCAAGGGTGAGATCCTCATGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 444

GGGAACAACCATGGACCCAACTCTAACACGTGCTGACAGACTGGTTGGCCAGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACAGAGAAGGCAGGGAAGGTGTCGAAGCTCACCAAGGGTGAGATCCTCATGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 451

GGGAACAACCATGGACCCAACTCTAACACGTGCTGACAGACTGGTTGGCCAGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACAGAGAAGGCAGGGAAGGTGTCGAAGCTCACCAAGGGTGAGATCCTCATGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 306

GGGAACAACCATGGACCCAACTCTAACACGTGCTGACAGACTGGTTGGCCAGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaa ... tgctttgcagATCAATTTCTTCCTACTCCGGAGGCTGTTGGGTGTGAGGACGAAAGGTACAGAGAAGGCAGGGAAGGTGTCGAAGCTCACCAAGGGTGAGATCCTCATGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGAACAACCATGGACCCAACTCTAACACGTGCTGACAGACTGGTTGGCCAGGTTCTTGGTGAAGTAGGTTCACTACCTGATGTTTACGTAGAGCTTGAGgtttgtaaaatctttgctcgctcatgattttagattggcagaaatagttgttaaacttaagtatgtcattgaacatttgctttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT