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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAGgtattatgccatttctgtacatgtgagaactgcctccaggttatacagcttgtgaaatgtttactgaactctgccgtgttcttgttaagttcaaagtttc...

Basic information

species Zea mays
transcript GRMZM2G026884_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G026884_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g04460.1 (Oryza sativa), 5'ss of exon 4
GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAGgtattatgccatttctgt-acatgtgaga-actgcctccaggttatacagcttgtgaaatgtttactgaactctgccgtgttcttgttaagttcaaagtttc
||||||| ||||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||| || |  |||||||| || ||||||||||||||  |||| | | |||   |  |     |  |  | |||     |   | | |     ||||| || |  | ||  |||| |    ||||  |||  |  
GTGATGGGAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGACATCATCCCTGATGCTGCTGTACGCAGAGCAATGAATGAAATAAATGCAGgtatggtgccctatatgtcgtacttctttcatagtgtacagtccggaggaccttttctcggtttattggatgccgcaatgttttctcgaagtcaaaacct--

upper sequence: GRMZM2G026884_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA09G28170.1 (Glycine max), 5'ss of exon 4
GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAGgtattatgccat-ttctgtacatgtgagaactgcctccaggttatacagcttgtgaaatgtttactgaactctgccgtgttcttgttaagttcaaagtttc---------
||||||| ||| ||||| || || || |||||||| |||||||||||||| || |||||  ||||||| |||||||||||||| || || ||||| |||| |||    |  ||  |   | | ||| ||   |  |  || ||  ||      ||| |  |   | |  |  | |||   | |  |  ||  ||||||         
GTGATGGGAGAGTATGGCTATAGTATAGAGCACATACTCATGGTTGATATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCCGgtaatatatactactccatggtttttagagctttttttat-ttttatggc------aatatcaa---agcattaacatgtctgtatgcatatcgtagtttctcctctgaa

upper sequence: GRMZM2G026884_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA16G32990.1 (Glycine max), 5'ss of exon 4
GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAGgtattatgccatttctgtacatgtgagaactgcctcca-ggttata-cagcttgtgaaatgtttactgaactctgccgtgttcttgttaagttcaaagtttc
||||||| ||| ||||| || || || |||||||| |||||||||||||| || |||||  ||||||| |||||||||||||| || || |||||||||| |||    |    |    |  |||   |   |  | ||  ||| ||    || | ||||      |    |  | |  | |       |  |||   ||
GTGATGGGAGAATATGGATATAGTATAGAGCACATACTCATGGTTGATATTATACCTGATCCTGCTGTGCGTAAGGCAATGAATGAGATCAATGCAGgtaatatatactacacgatttttagagcttttttttaatggcaatatcaagcagtaacatgtccgt--atgcatatcatagtttctccctctgaaaatactc

upper sequence: GRMZM2G026884_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G51570.1 (Arabidopsis thaliana), 5'ss of exon 4
GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAGgtattatgccatttctgtacatgtgagaactgcctccag-gttatacagcttgtgaaatgtttactgaactctgccgtgttcttgttaagttcaaagtttc--
|||||||  | |||||| |||||||||||||||||||| |||||||| || || |||||  |  |||| || |||||||||||||| || ||||||||||   |    || |  |||    |  | | |  ||      | | ||| |    ||  |||  ||  ||     |        |  |  || | |  ||   
GTGATGGGTGCTTATGGATACAGCATTGAGCACATTCTAATGGTTGACATTATTCCTGATCCCTCTGTACGCAAGGCAATGAACGAAATCAATGCAGgtaacctttatttccgatactgagggaatcagtgtctgatacttttcaggtctctaatggttccctacac---atcaaagcacagaaagatttatacatttta

upper sequence: GRMZM2G026884_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv16s0022g01690.t01 (Vitis vinifera), 5'ss of exon 4
GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAGgtattatgccatttctgtacatgtgagaactgcctccaggttatacagcttgtgaaatgtttactgaactctgccgtgttcttgttaagttcaaagtttc----
||||||| || ||| || || | ||| |||||||| || ||||||||||| || ||||| ||| |||| || ||||||||||| || |||||||||||| ||   |   | ||||   | |          |      |  |||  || |   ||    |||    ||    ||        |   ||   | | ||    
GTGATGGGAGCTTACGGATATAACATAGAGCACATACTGATGGTTGATATTATACCTGATGCTTCTGTACGCAAGGCAATGAATGAGATAAATGCAGgttttgaccttctactgtttttttcttgttcttattgcaactggacaaattttctcattcaaact----tccaatgtaggtagaatggattttcaatatccaga

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|211355404|gb|FL266319.1|FL266319
EST:     GTAAGGCAATGAACGACATAAATGCAG                         CCCAAAGGCTTCAACTGGCAAGTGTTTACAAGGGAGAAGCAGAGAAGATCC
genomic: GTAAGGCAATGAACGACATAAATGCAGgtattatgcc ... actcctacagCCCAAAGGCTTCAACTGGCAAGTGTTTACAAGGGAGAAGCAGAGAAGATCC
EST: gi|211355405|gb|FL266320.1|FL266320
EST:     TCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAG                         CCCAAAGGCTTCAACTGGCAAGTGTTTACAAGGGAGAAGCAGWGAAGATCC
genomic: TCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAGgtattatgcc ... actcctacagCCCAAAGGCTTCAACTGGCAAGTGTTTACAAGGGAGAAGCAGAGAAGATCC
EST: gi|18167263|gb|BM337102.1|BM337102
EST:     TATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATATATGCAG                         CCCAAAGGCTTCAACTGGCAAGTG-TTACAAGGGAGAAGCAGAGAAGATCC
genomic: TATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAGgtattatgcc ... actcctacagCCCAAAGGCTTCAACTGGCAAGTGTTTACAAGGGAGAAGCAGAGAAGATCC
EST: gi|111991179|gb|EE332274.1|EE332274
EST:     TATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAG                         CCCAAAGGCTTCAACTGGCAAGTGTTTACAAGGGAGAAGCAGAGAAGATCC
genomic: TATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAGgtattatgcc ... actcctacagCCCAAAGGCTTCAACTGGCAAGTGTTTACAAGGGAGAAGCAGAGAAGATCC

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), 47 (downstream exon)
Score: 97

GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAGgtattatgcc ... actcctacagCCCAAAGGCTTCAACTGGCAAGTGTTTACAAGGGAGAAGCAGAGAAGATCCTTATGGTGAAGAAAGCGGAGGCAGAAGCAGAGGCGAAATATCTTTCTGG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 127

GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAGgtattatgcc ... actcctacagCCCAAAGGCTTCAACTGGCAAGTGTTTACAAGGGAGAAGCAGAGAAGATCCTTATGGTGAAGAAAGCGGAGGCAGAAGCAGAGGCGAAATATCTTTCTGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 188

GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAGgtattatgcc ... actcctacagCCCAAAGGCTTCAACTGGCAAGTGTTTACAAGGGAGAAGCAGAGAAGATCCTTATGGTGAAGAAAGCGGAGGCAGAAGCAGAGGCGAAATATCTTTCTGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 109

GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAGgtattatgcc ... actcctacagCCCAAAGGCTTCAACTGGCAAGTGTTTACAAGGGAGAAGCAGAGAAGATCCTTATGGTGAAGAAAGCGGAGGCAGAAGCAGAGGCGAAATATCTTTCTGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGATGGCAGATTATGGTTACAGCATTGAGCACATTCTCATGGTTGATATCATCCCTGACGCTGCTGTTCGTAAGGCAATGAACGACATAAATGCAGgtattatgccatttctgtacatgtgagaactgcctccaggttatacagcttgtgaaatgtttactgaactctgccgtgttcttgttaagttcaaagtttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT