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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACAGGCACGGCGACTTCTTCTCTGCCCTGCTCAAGGCTCAGCCGCAGTTCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcgagctattctcctgttaatatacatcagttagctccaaaggttgctgcgcccctctcctaacagctgtgttactatatgaccttttgcag

Basic information

species Zea mays
transcript GRMZM2G081462_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081462_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g17170.1 (Oryza sativa), 5'ss of exon 3
GAACAGGCACGGCGACTTCTTCTCTGCCCTGCTCAAGGCTCAGCCGCAGTTCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttc-gagctattctcctgttaatata---catcagttagctccaaag---gttgctgcgcccctctcctaacagctgtgttactatatgaccttttgcag
|||| | ||||| || |||||||| || ||||||||||| ||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| || |||||||||   ||||   ||    || |||||  | |  |||   ||| ||| || ||||| ||||||| |   ||  | | ||| | |||||||
GAACCGTCACGGTGATTTCTTCTCCGCGCTGCTCAAGGCGCAGCCGCAGTTCCTCAACGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatctccgagctattccgttgtttgcatggaccaacagttcacactgaagattgttactgtgctcctcttctaacagtt---tttgtgtgtgatcctttgcag

upper sequence: GRMZM2G081462_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA19G30350.1 (Glycine max), 5'ss of exon 3
GAACAGGCACGGCGACTTCTTCTCTGCCCTGCTCAAGGCTCAGCCGCAGTTCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcgagctattctcctgttaatatacatcagtt--agctccaaaggttgctgcgcccc-tctcctaacagctgt-gttactatatgaccttttgcag
||||||||| || || ||||||||||||||| | ||||| ||||| || || || |||||||||||||| ||| | ||||| || |||||||| || ||||||| ||    || ||  | |   | ||| |||   ||  || | |  || |     | |     ||  |  ||| ||| | ||   || |    |  | | 
GAACAGGCATGGAGATTTCTTCTCTGCCCTGATGAAGGCACAGCCACAATTTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCGgtaacttttccct-tttgcttaccattatgcattcctttaagattcttagatgaaacctcaatacctagtgccagttgttgctagcttaaggttgtgagaa-

upper sequence: GRMZM2G081462_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA03G27380.1 (Glycine max), 5'ss of exon 3
GAACAGGCACGGCGACTTCTTCTCTGCCCTGCTCAAGGCTCAGCCGCAGTTCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcgagctattctcctgttaatatacatcagtt--agctccaaaggttgctgcgcccctctcctaacagctgt-gttactatatgaccttttgcag-
|||||| || || || ||||||||||||||| | ||||| ||||| || || || |||||||||||||| ||| | ||||| || |||||||| || ||||||| |     || ||| |||   | | | |||   ||  || | |  | | ||   | | |    ||||    | || ||| |||  | |  |||   || 
GAACAGACATGGAGATTTCTTCTCTGCCCTGATGAAGGCACAGCCACAATTTCTAAATGACTGGAAGGCAAAGTTGTGGTCTCGATTCTTCTGTCTATCGgtaactattccct-ttcgcctaccattttgcattcctttaagattcttaagatgaaac-ctcaatacctagtgccagttgttgctagcttaagtttgtgaga

upper sequence: GRMZM2G081462_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT3G56940.2 (Arabidopsis thaliana), 5'ss of exon 4
GAACAGGCACGGCGACTTCTTCTCTGCCCTGCTCAAGGCTCAGCCGCAGTTCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcgagctattctcctgttaatatacatcagttagctccaaaggttgctgcgcccctctcctaacagctgtgttactatatgaccttttgcag
|||| | || || || |||||||||||  || | || |||||||| |||||||||||||||||| | |||||||||||||| || |||||||||||||||||||||   | |||  |||   ||| |     ||| |  |      |  |||    |||   |   ||| ||   ||    || |             
GAACCGTCATGGTGATTTCTTCTCTGCTTTGATGAAAGCTCAGCCTCAGTTCCTCAATGACTGGCAAGCCAAGCTCTGGTCTCGCTTCTTCTGCCTCTCGgtaatt--aaactaaactctctttagttc---tcaatgtgtcttgcacattg----gcctaaccagtaagaggattggctttacag------------

upper sequence: GRMZM2G081462_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv08s0040g00390.t01 (Vitis vinifera), 5'ss of exon 3
GAACAGGCACGGCGACTTCTTCTCTGCCCTGCTCAAGGCTCAGCCGCAGTTCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcgagcta-----ttctcctgttaatatacatcagttagctccaaaggttgctgcgcccctctcctaacagctgtgttactatatgaccttttgcag---------------------------------------------------
||||||||| || || |||||||||||  || | ||||| || || |||||||||||||| |||||||| ||| | ||| | || ||||||||||| |||||||||      ||     ||      || |  |  || | |    | ||||  ||          | | |       ||| | | | | || | | | |                                                      
GAACAGGCATGGTGATTTCTTCTCTGCATTGATGAAGGCACAACCCCAGTTCCTCAATGATTGGAAGGCAAAGTTGTGGGCTCGATTCTTCTGCCTATCGgtaattatagtataataagtttctacattcaattgtat-actagattgcaaatattatcttaattttttaccctagtgtgtttaaatctttggcttctcgagaacctctgggattcctctggtcctcttatgacttcccaaatttgtcttgcag

upper sequence: GRMZM2G081462_T02 (Zea mays), 5'ss of exon 3
lower sequence: PP1S97_248V6.1 (Physcomitrella patens), 5'ss of exon 2
GAACAGGCACGGCGACTTCTTCTCTGCCCTGCTCAAGGCTCAGCCGCAGTTCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcgagct--attctcctgttaatatacatcagttagctccaaa-ggttgctgcgcccctctcctaacagctgtgtta---ctatatgaccttttgcag
|||| | ||||| || |||||||| || ||  | ||||| ||||| |||||||| || |||||||||||||| || ||| | || ||||||||||| || |||| ||  | ||  |||       | |   |   | ||  | |  | |  ||  ||      |  || ||    ||| |||    || |||| |  ||     
GAACCGTCACGGTGATTTCTTCTCGGCTCTCATGAAGGCACAGCCTCAGTTCCTAAACGACTGGAAGGCCAAACTTTGGGCTCGTTTCTTCTGCCTTTCTgtaagtttcacctccatttcttgcctgagtgattcctgtatgttgtagatagtaactatctgacgatcttag-gtctgggttttatctgtatggcacttaa---

upper sequence: GRMZM2G081462_T02 (Zea mays), 5'ss of exon 3
lower sequence: PP1S239_18V6.2 (Physcomitrella patens), 5'ss of exon 2
GAACAGGCACGGCGACTTCTTCTCTGCCCTGCTCAAGGCTCAGCCGCAGTTCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaa---tttcgagctattctcctgttaatatacatcagttagctccaaaggttgctgcgcccctctcctaacagctgtgttactatatgaccttttgcag--
|||| | ||||| || ||||||||||| ||  | ||||| ||||| |||||  | |||||||||||||||||||||||| | || |||||||||||||| ||||   |||||  || |||| || ||    |   |   |  |   | | | | |   |    | |      ||    ||| | | | | | |  | ||||  
GAACCGTCACGGTGATTTCTTCTCTGCACTCATGAAGGCACAGCCCCAGTTTTTGAATGACTGGAAGGCCAAGCTCTGGGCTCGTTTCTTCTGCCTCTCTgtaagtatttcgttct-ttctgcttttccagtgt-ttgatgtgtcaccacgatcggaccctgacacaatgggcattcttgtcaatctttaaacact-gcagtg

upper sequence: GRMZM2G081462_T02 (Zea mays), 5'ss of exon 3
lower sequence: EFJ28505 (Selaginella moellendorffii), 5'ss of exon 3
GAACAGGCACGGCGACTTCTTCTCTGCCCTGCTCAAGGCTCAGCCGCAGTTCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcgagctatt-ctcctgttaatatacatcagttagctccaaaggttgctgcgccc-ctctcctaacagctgtgttactatatgaccttttgcag
|||||||||||||||||||||||| ||  |||| || || ||||| |||||| | || |||||||||||||| |||||| | || |||||||| ||||||||||     | || |  ||| | ||   ||       |||| | |  | | | | || |   |||| | |                              
GAACAGGCACGGCGACTTCTTCTCGGCGTTGCTGAAAGCCCAGCCTCAGTTCTTGAACGACTGGAAGGCCAAACTCTGGGCTCGCTTCTTCTGTCTCTCGgtaaagcaaacctttggctcttcttggaattt-----ttagatgctcatgcttccgctcttgctcttccag-----------------------------

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|78112391|gb|DV530785.1|DV530785
EST:     TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCG                         GTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAG
genomic: TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcga ... ccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAG
EST: gi|32849293|gb|CD988974.1|CD988974
EST:     TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCG                         GTGTATGTGACCATGT
genomic: TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcga ... ccttttgcagGTGTATGTGACCATGT
EST: gi|76016942|gb|DT944112.1|DT944112
EST:     TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCG                         GTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAG
genomic: TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcga ... ccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAG
EST: gi|78107168|gb|DV525586.1|DV525586
EST:     TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCG                         GTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAG
genomic: TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcga ... ccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAG
EST: gi|32849718|gb|CD989399.1|CD989399
EST:     TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCG                         GTGTATGTGACCATGTAC
genomic: TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcga ... ccttttgcagGTGTATGTGACCATGTAC
EST: gi|93016118|gb|EB641638.1|EB641638
EST:     TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCG                         GTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAG
genomic: TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcga ... ccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAG
EST: gi|149097284|gb|EE183107.2|EE183107
EST:     CCTNCA-TGACTGGGAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCG                         GTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAG
genomic: CCT-CAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcga ... ccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAG
EST: gi|32845408|gb|CD985089.1|CD985089
EST:     TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCG                         GTGTATGTGACCATGTA
genomic: TCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcga ... ccttttgcagGTGTATGTGACCATGTA

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), 48 (downstream exon)
Score: 100

GAACAGGCACGGCGACTTCTTCTCTGCCCTGCTCAAGGCTCAGCCGCAGTTCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcga ... ccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAGGGAATTGGTCTGGACACCAAAGAATTCGACATGCATGTGATCATCGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 902

GAACAGGCACGGCGACTTCTTCTCTGCCCTGCTCAAGGCTCAGCCGCAGTTCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcga ... ccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAGGGAATTGGTCTGGACACCAAAGAATTCGACATGCATGTGATCATCGAGG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 24

GAACAGGCACGGCGACTTCTTCTCTGCCCTGCTCAAGGCTCAGCCGCAGTTCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcga ... ccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAGGGAATTGGTCTGGACACCAAAGAATTCGACATGCATGTGATCATCGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 382

GAACAGGCACGGCGACTTCTTCTCTGCCCTGCTCAAGGCTCAGCCGCAGTTCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcga ... ccttttgcagGTGTATGTGACCATGTACCTGAATGACTGCCAACGCACTGCATTCTATGAGGGAATTGGTCTGGACACCAAAGAATTCGACATGCATGTGATCATCGAGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACAGGCACGGCGACTTCTTCTCTGCCCTGCTCAAGGCTCAGCCGCAGTTCCTCAATGACTGGAAGGCCAAGCTCTGGTCACGGTTCTTCTGCCTCTCGgtaatttcgagctattctcctgttaatatacatcagttagctccaaaggttgctgcgcccctctcctaacagctgtgttactatatgaccttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT