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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACCAACTTTATGTCAGACATAGCTGATGAGTTTAAGATTGTTGTTGTTGAAGCAATAAGATCCCTGTGCTTGAAGTTCCCTCTGAAATATCGCTCATTgtatgtatatagaagcgtgtttgcactattcttgttaaacatcgtaaactacctttttcatctataagcattaattttcatttatctgttccag

Basic information

species Zea mays
transcript GRMZM2G178618_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os07g10150.1 (Oryza sativa), 5'ss of exon 9
TGACCAACTTTATGTCAGACATAGCTGATGAGTTTAAGATTGTTGTTGTTGAAGCAATAAGATCCCTGTGCTTGAAGTTCCCTCTGAAATATCGCTCATTgtatgtatatagaagcgtgt--ttgcactattcttgttaaacatcgtaaactacctttttcatctataagcattaattttcatttatctgttccag
||||||| |||||||| ||||| || ||||| || ||||||||||| || || || ||||||||| |||||||||||||||| || |||||||| ||| |||| ||| |     |  | |  ||  ||     || ||||| |||   ||||| ||| | ||||    | |||| |  ||  ||  | | || |||
TGACCAATTTTATGTCGGACATTGCCGATGAATTCAAGATTGTTGTCGTAGAGGCCATAAGATCCTTGTGCTTGAAGTTCCCCCTAAAATATCGGTCACTgtacgtagaatagcgtatattcttatacagaaatttttaaagatccagaactagcttgt-catcag--aacattgaactttgtt-gtgt-ttgcag

upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA12G04820.1 (Glycine max), 5'ss of exon 9
TGACCAACTTTATGTCAGACATAGCTGATGAGTTTAAGATTGTTGTTGTTGAAGCAATAAGATCCCTGTGCTTGAAGTTCCCTCTGAAATATCGCTCATTgtatgtatatagaagcgtgtttgcactattcttgttaaacatcgtaaactacctttttcatctataagcattaattttcatttatctgttccag--------------------------------
| || || || ||||| || || ||||||||||| || |||||||||||||||||||||||||| || |||||||| |||||| | |||||| | ||  |||  ||||||   |  ||  ||  |    | |  ||   |  |  ||  ||| | |||||| |  | |  ||   |   |  |   || || |                                 
TTACAAATTTCATGTCTGATATTGCTGATGAGTTCAAAATTGTTGTTGTTGAAGCAATAAGATCACTATGCTTGAAATTCCCTTTAAAATATAGATCTCTgtgagtatatgtcaatgtcattctataggtttctttc--ccccagaagttacatatttcatttgaatgtttt---tcctagatgaatggtctaaattactggtttcttttctgttattattttcag

upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA11G12610.2 (Glycine max), 5'ss of exon 9
TGACCAACTTTATGTCAGACATAGCTGATGAGTTTAAGATTGTTGTTGTTGAAGCAATAAGATCCCTGTGCTTGAAGTTCCCTCTGAAATATCGCTCATTgtatgtatatagaagcgtgtttgcactattcttgttaaacatcgtaaactaccttt------ttcatctataagcat----taattttcatttatctgttccag------------
| || || || ||||| || || ||||||||||| || ||||||||||||||||||||||||||  |||||||||| |||||| | |||||| | ||  |||  ||| |    |   | |  |     |||     | |  |   | | | | |||      ||   ||| | | ||    ||| || |   | ||| |||               
TTACAAATTTCATGTCTGATATTGCTGATGAGTTCAAAATTGTTGTTGTTGAAGCAATAAGATCATTGTGCTTGAAATTCCCTTTAAAATATAGATCTCTgtgagtacaagtcattctataggtttctttccccccagaagttacatatttcatttgaatgtttttcctagatgaatggtctaaattactggtttcttttctgttattattttcag

upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA04G01470.1 (Glycine max), 5'ss of exon 9
TGACCAACTTTATGTCAGACATAGCTGATGAGTTTAAGATTGTTGTTGTTGAAGCAATAAGATCCCTGTGCTTGAAGTTCCCTCTGAAATATCGCTCATTgtatgtatatagaagcgtgtttgcactattcttgttaaacatcgtaaactacctttttcatctataagcattaattttcatttatctgttccag-----------------
| || || || ||||| || || ||||||||||| || ||||||||||||||||||||||||||  ||||| ||||||| ||| | |||||||| ||  ||||||| |     |   |  ||     | ||    ||  | |  |     |  ||| |   ||| ||| | |  |||    | ||   ||  |                  
TCACAAATTTCATGTCTGATATTGCTGATGAGTTCAAAATTGTTGTTGTTGAAGCAATAAGATCATTGTGCCTGAAGTTTCCTTTAAAATATCGATCTCTgtatgtgtccctgaatatagtttt-tgactccccatacgccttatgttgcatatttatttccta-aaggaatgttttatgctgatggtttgtattctgctattattttcag

upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA06G01520.1 (Glycine max), 5'ss of exon 9
TGACCAACTTTATGTCAGACATAGCTGATGAGTTTAAGATTGTTGTTGTTGAAGCAATAAGATCCCTGTGCTTGAAGTTCCCTCTGAAATATCGCTCATTgtatgtatatagaagcgtgttt----gcactattcttgttaaacatcgtaaactacctttttcatctata-agcattaattttcatttatctgttccag-----------------
| || || || ||||| || || ||||||||||| || ||||||||||||||||||||||||||  ||||| ||||||| ||| | |||||||| ||  ||||||| |     |   |  ||     | |    | ||  | |  |   |   | | | |||  |   || || | |  |||    | ||   ||  |                  
TCACAAATTTCATGTCTGATATTGCTGATGAGTTCAAAATTGTTGTTGTTGAAGCAATAAGATCATTGTGCCTGAAGTTTCCTTTAAAATATCGATCTCTgtatgtgtccctgaatatagtttttgactccccacatgccatatgttacatcgtgcatatttatttcctagaggaatgttttatgatgatggtttgtattctgctattattttcag

upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT4G34450.1 (Arabidopsis thaliana), 5'ss of exon 8
TGACCAACTTTATGTCAGACATAGCTGATGAGTTTAAGATTGTTGTTGTTGAAGCAATAAGATCCCTGTGCTTGAAGTTCCCTCTGAAATATCGCTCATTgtatgtatatagaagcgtgtttgcactattcttgttaaacatcgtaaactacctttttcatctataagcattaattttcatttatctgttccag----------------------------------------
| || || ||||||||||| || ||||||||||| || ||||| || || || |||||||||||  ||||  |||| ||||| ||||||||  | || ||||| ||| |       | |||||   | |     ||     |||   | | |  ||||  |  || |  |   || ||    ||||| ||  ||                                        
TAACTAATTTTATGTCAGATATTGCTGATGAGTTCAAAATTGTGGTCGTGGACGCAATAAGATCGTTGTGTGTGAAATTCCCACTGAAATACAGATCCTTgtaagtaaagtttta-gggtttgttatttgtagttttggtctcgagcatttctatttttttgaatgattaaatatgttatggtatct-ttttagcatttggcttatgattgatctatcaccttttcatttgtag

upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 5'ss of exon 9
TGACCAACTTTATGTCAGACATAGCTGATGAGTTTAAGATTGTTGTTGTTGAAGCAATAAGATCCCTGTGCTTGAAGTTCCCTCTGAAATATCGCTCATTgtatgta---------------------tatagaagcgtgtttgcactattcttgt------------taaacatcgtaaactacctttttcatctataa-gcattaattttcatttatctg--ttccag
| || || || |||||||| || |||||||| || || |||||||| || ||||| || |||||  ||||||||||||| ||| |||| ||| |  | ||||| ||                       ||  || | | |  |   |||| || |            | ||||  ||||| |   |   |||| |  ||   | |||   |  ||    ||  || |||
TTACAAATTTCATGTCAGATATTGCTGATGAATTCAAAATTGTTGTAGTGGAAGCCATCAGATCATTGTGCTTGAAGTTTCCTTTGAAGTATAGAGCCTTgtaagtgatatcctgtttttgatgtcatcattaaaacatttgggttttatttttatgtcttttttaaatgaacagtgtaaaatgtttccgtcatgtgaaatagaataaccctttttcccttgcttttcag

upper sequence: GRMZM2G178618_T01 (Zea mays), 5'ss of exon 9
lower sequence: PP1S41_154V6.1 (Physcomitrella patens), 5'ss of exon 9
TGACCAACTTTATGTCAGACATAGCTGATGAGTTTAAGATTGTTGTTGTTGAAGCAATAAGATCCCTGTGCTTGAAGTTCCCTCTGAAATATCGCTCATTgtatgt---atatagaagcgtgtttgcactattcttgt-taaacatcgtaaactacctttttcatctataagcatt--aattttcatttatctgttccag-------------------------------------------------------------------------
| || || || ||||||||||||||||||||||| |||||||| ||||| || || ||  | ||  ||||  | ||||||||||  ||||||||||||||||  |    || | ||  |   |||      ||    | |   |  | |  ||||| | ||  || |    ||  |  || |   | ||   |    |||                                                                         
TCACGAATTTCATGTCAGACATAGCTGATGAGTTCAAGATTGTGGTTGTGGAGGCCATCCGCTCTTTGTGTCTCAAGTTCCCTCAAAAATATCGCTCATTgtgagctccatgttgatacacctttatttctttacaatatcttctgcatggactacatgttatatgtcacggctcttaaaatgctagttgcttaagtcagaataatacttgcttgattgatgatactggtacttacgttctggcatgacgagcgtcctgctcctttttttcag

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|18654639|gb|BM499444.1|BM499444
EST:     GAAATATCGCTCATT                         GATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGAGGATTCGAGTACAA
genomic: GAAATATCGCTCATTgtatgtatat ... tctgttccagGATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGAGGATTCGAGTACAA
EST: gi|18648972|gb|BM497791.1|BM497791
EST:     GAAATATCGCTCATT                         GATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGAGGATTCGAGTACAA
genomic: GAAATATCGCTCATTgtatgtatat ... tctgttccagGATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGAGGATTCGAGTACAA
EST: gi|18654638|gb|BM499443.1|BM499443
EST:     GAAATATCGCTCATT                         GATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGAGGATTCGAGTACAA
genomic: GAAATATCGCTCATTgtatgtatat ... tctgttccagGATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGAGGATTCGAGTACAA
EST: gi|6564183|gb|AW231805.1|AW231805
EST:     CTGTGCTTGAAGTTCCCTCTGAAATATCGCTCATT                         GATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGAGGATTCGAGTACAA
genomic: CTGTGCTTGAAGTTCCCTCTGAAATATCGCTCATTgtatgtatat ... tctgttccagGATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGAGGATTCGAGTACAA
EST: gi|32941909|gb|CF046728.1|CF046728
EST:     GAAGCAATAAGATCCCTGTGCTTGAAGTTCCCTCTGAAATATCGCTCATT                         GATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGAGGATTCGAGT
genomic: GAAGCAATAAGATCCCTGTGCTTGAAGTTCCCTCTGAAATATCGCTCATTgtatgtatat ... tctgttccagGATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGAGGATTCGAGT

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: 49 (upstream exon), 46 (downstream exon)
Score: 396

TGACCAACTTTATGTCAGACATAGCTGATGAGTTTAAGATTGTTGTTGTTGAAGCAATAAGATCCCTGTGCTTGAAGTTCCCTCTGAAATATCGCTCATTgtatgtatat ... tctgttccagGATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGAGGATTCGAGTACAAGAAAGCCATAGTTGATTCAATTATTATACTCATTAGAGATATTCCTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 383

TGACCAACTTTATGTCAGACATAGCTGATGAGTTTAAGATTGTTGTTGTTGAAGCAATAAGATCCCTGTGCTTGAAGTTCCCTCTGAAATATCGCTCATTgtatgtatat ... tctgttccagGATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGAGGATTCGAGTACAAGAAAGCCATAGTTGATTCAATTATTATACTCATTAGAGATATTCCTGAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 296

TGACCAACTTTATGTCAGACATAGCTGATGAGTTTAAGATTGTTGTTGTTGAAGCAATAAGATCCCTGTGCTTGAAGTTCCCTCTGAAATATCGCTCATTgtatgtatat ... tctgttccagGATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGAGGATTCGAGTACAAGAAAGCCATAGTTGATTCAATTATTATACTCATTAGAGATATTCCTGAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 485

TGACCAACTTTATGTCAGACATAGCTGATGAGTTTAAGATTGTTGTTGTTGAAGCAATAAGATCCCTGTGCTTGAAGTTCCCTCTGAAATATCGCTCATTgtatgtatat ... tctgttccagGATGAACTTCTTGAGTAATATTCTACGGGAAGAGGGAGGATTCGAGTACAAGAAAGCCATAGTTGATTCAATTATTATACTCATTAGAGATATTCCTGAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACCAACTTTATGTCAGACATAGCTGATGAGTTTAAGATTGTTGTTGTTGAAGCAATAAGATCCCTGTGCTTGAAGTTCCCTCTGAAATATCGCTCATTgtatgtatatagaagcgtgtttgcactattcttgttaaacatcgtaaactacctttttcatctataagcattaattttcatttatctgttccag

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG