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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGAAGCTGTTCACTGCTTTGCTTTGTCGAAGAATGATTCATATGTCATGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaatctttacagtttcatacaatagttttttttttctagaaacaatctttgatctttatttttactgcag

Basic information

species Zea mays
transcript GRMZM2G030422_T02
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030422_T03 (Zea mays), 5'ss of exon 22
lower sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 21
TGAAGAAGCTGTTCACTGCTTTGCTTTGTCGAAGAATGATTCATATGTCATGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaatctttacagtttcatacaatagtt--ttttttttctagaaac-aatctttgatctttatttttactgcag
|||||||||||| || |||||||||||||| |||||||||||||||||||||||||| |||||||| ||||| ||||||||||||||||||||||| |||||| || |        |||||  | | || |||  | | || | ||||||   | |||| ||| | ||  | |||||||
TGAAGAAGCTGTCCATTGCTTTGCTTTGTCAAAGAATGATTCATATGTCATGTCTGCATCTGGAGGGAAAATATCTCTGTTCAACATGATGACTTTTAAGgttagttaca------agtttatttctattgtttgtctcttatgtagaaattgaactttaatcat-atggtgactgcag

upper sequence: GRMZM2G030422_T03 (Zea mays), 5'ss of exon 22
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 20
TGAAGAAGCTGTTCACTGCTTTGCTTTGTCGAAGAATGATTCATATGTCATGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttgg-----taaatctttaca---gtttcatacaatagttttttttttctagaaacaatctttgatctttatttttactgcag----------------
|||||| ||||| |  ||| | ||  | |||||||||||||| ||||| ||||| || || ||||||||| ||||| ||||||| |||||||| |||||||| |        ||| |  |||   | ||  |    |  |    || ||   ||||||    |  || | |   ||    | ||                
TGAAGATGCTGTGCCTTGCATAGCGCTATCGAAGAATGATTCTTATGTGATGTCCGCCTCGGGAGGAAAAGTCTCTTTGTTCAATATGATGACATTCAAGgtagagcttacgaatttagacattggctttctcagctgatgaacttgtttatgaaacagcgatgcatttctggcttctaggaagttcgctttgtttcttt

upper sequence: GRMZM2G030422_T03 (Zea mays), 5'ss of exon 22
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 5'ss of exon 20
TGAAGAAGCTGTTCACTGCTTTGCTTTGTCGAAGAATGATTCATATGTCATGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttg-----gtaaatctttacagtttcatacaatagttttttttt----tctagaaacaatc--tttgatctttatttttactgcag--------------------------------------------
|||||| || || |  ||| | ||  | || || || || || ||||| |||||||| || ||||| ||| | ||| |||||||||||||||| ||||||||       |  |||| | |    |  ||   ||  ||| || |     | | |  | || |  |||| | ||  |  ||    |||                                            
TGAAGATGCCGTGCCTTGCATAGCGCTCTCTAAAAACGACTCTTATGTGATGTCTGCGTCCGGAGGGAAAGTTTCTTTGTTCAACATGATGACATTCAAGgtaaagtccgcgaatcatgaggagtctattttattctttgttctaataatatggtgagaagcgttttgtttttggtaattttgacagttgtcaatttttattctgacgcttttcttcggattttgactcag

upper sequence: GRMZM2G030422_T03 (Zea mays), 5'ss of exon 22
lower sequence: EFJ32018 (Selaginella moellendorffii), 5'ss of exon 20
TGAAGAAGCTGTTCACTGCTTTGCTTTGTCGAAGAATGATTCATATGTCATGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaatctttacagtttca----tacaatagttttttttttctagaaacaatctttgatctttatttttactgcag
 ||||||||||| |  ||| |||| ||||| |||||||| || || || ||||| ||||| ||||| ||| | ||||| || || |||||||||||||||||  | | || ||| |   || |    |  || |  ||    | || ||                               
GGAAGAAGCTGTGCCTTGCATTGCCTTGTCAAAGAATGACTCTTACGTGATGTCCGCTTCGGGAGGCAAAGTTTCTCTATTTAATATGATGACTTTCAAGgtatgcacatttttccttcttgaccggtgtaagaacttgccatgtccag-------------------------------

upper sequence: GRMZM2G030422_T03 (Zea mays), 5'ss of exon 22
lower sequence: EFJ30926 (Selaginella moellendorffii), 5'ss of exon 20
TGAAGAAGCTGTTCACTGCTTTGCTTTGTCGAAGAATGATTCATATGTCATGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaatctttacagtttcatacaatagttttttttttctagaaacaatctttgatctttatttttactgcag
 |||||||||||||  ||| | || ||||| || |||||||||||||| |||||||| || || |||||| |    || |||||||||||||| || |||||  |   || | |     ||  | || |  |       || | ||||||                          
AGAAGAAGCTGTTCCGTGCATCGCCTTGTCTAAAAATGATTCATATGTGATGTCTGCCTCGGGTGGAAAAGTTCTGCTTTTCAACATGATGACGTTTAAGgtatgccgatttgttgctctttctccagtgatgaaaccattgtcgaaacag-------------------------

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|87156341|gb|DY401130.1|DY401130
EST:     TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
EST: gi|211016182|gb|FL013386.1|FL013386
EST:     TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
EST: gi|211016174|gb|FL013378.1|FL013378
EST:     TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
EST: gi|211016178|gb|FL013382.1|FL013382
EST:     TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
EST: gi|211018955|gb|FL013387.1|FL013387
EST:     TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
EST: gi|211016172|gb|FL013376.1|FL013376
EST:     TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
EST: gi|37422204|gb|CF648808.1|CF648808
EST:     TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
EST: gi|211016173|gb|FL013377.1|FL013377
EST:     TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
EST: gi|211016170|gb|FL013374.1|FL013374
EST:     TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
EST: gi|211018956|gb|FL013388.1|FL013388
EST:     TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
EST: gi|211016176|gb|FL013380.1|FL013380
EST:     TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
EST: gi|31360482|gb|CD444839.1|CD444839
EST:     TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
EST: gi|211016181|gb|FL013385.1|FL013385
EST:     TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
EST: gi|211016177|gb|FL013381.1|FL013381
EST:     TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
EST: gi|211016179|gb|FL013383.1|FL013383
EST:     TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
EST: gi|22473365|gb|BU037845.1|BU037845
EST:     TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
EST: gi|6095542|gb|AW120209.1|AW120209
EST:     TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
EST: gi|76010934|gb|DT938104.1|DT938104
EST:     TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAG                         ACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT
genomic: TGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTT

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: 323

TGAAGAAGCTGTTCACTGCTTTGCTTTGTCGAAGAATGATTCATATGTCATGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTTCATCCCCAAGATAACAACATAATTGCAATTGGAATGGATGACTCAACCA


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 202

TGAAGAAGCTGTTCACTGCTTTGCTTTGTCGAAGAATGATTCATATGTCATGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTTCATCCCCAAGATAACAACATAATTGCAATTGGAATGGATGACTCAACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 155

TGAAGAAGCTGTTCACTGCTTTGCTTTGTCGAAGAATGATTCATATGTCATGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTTCATCCCCAAGATAACAACATAATTGCAATTGGAATGGATGACTCAACCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 292

TGAAGAAGCTGTTCACTGCTTTGCTTTGTCGAAGAATGATTCATATGTCATGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaat ... tttactgcagACAATGACAACGTTTATGCCTGCACCGCCGGCAGCAACTTTTCTTGCATTTCATCCCCAAGATAACAACATAATTGCAATTGGAATGGATGACTCAACCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGAAGCTGTTCACTGCTTTGCTTTGTCGAAGAATGATTCATATGTCATGTCTGCTTCTGGAGGAAAAATCTCTCTGTTCAACATGATGACTTTCAAGgttggtaaatctttacagtttcatacaatagttttttttttctagaaacaatctttgatctttatttttactgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA