Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAAGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaactagatagtacgtacgcacgtacgtacctcctagctagctaggattacttagctgtgattgacatatatgatctacgacctagctcgatcttcccttgatctcttctgtgtgcatgcatggcgcttttgcttgttgttcttgcag

Basic information

species Zea mays
transcript GRMZM2G025954_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G025954_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g68480.1 (Oryza sativa), 5'ss of exon 2
GTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAAGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaactagatagtacgtacgcacgtacgtacctcctagctagctaggattacttagctgtgattgacatatatgatctacgacctagctcgatcttcccttgatctcttctgtgtgcatgcatggcgcttttgcttgttgttcttgcag
|||||| |||||||| |||||||| || || ||||||||||||||||||||| ||| |||||| ||||||||||| || |||||||| || ||||||||||||||  |   |  |  |       | | |   |||   | | | | |    |||| |       |||||  || |||   ||     |  |    |      ||    ||| |  ||| |   |  | ||                       
GTGCGGCCCTTGCAAGGTGATGGCACCGAAATTCCAGGAGATGTCCGAGAAGGACCAGGACGTTGTGTTCCTCAAACTCGACTGCAATCAAGACAACAAGgtcagttag--aactgattttctttctcttgtctacgctccacccacc----attattc------gattggaatgtatctgctgttttcctgaataaatcgtgctaagcctccttggtgcgtgcgattcgcag---------------------

upper sequence: GRMZM2G025954_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv04s0023g00740.t01 (Vitis vinifera), 5'ss of exon 2
GTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAAGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaact---agatagtacgtacgcac--gtacgtacctcctagctagctaggatt-acttagctgtgattgacatatatgatctacgacctagctcgatcttcccttgatctcttctgtgtgcatgcatggcgcttttgcttgttgttcttgcag
||| || || ||||||||||||||||| || ||||| ||  |||| | |||| | || ||||| || || || ||||||||||||||||| |||||||||||| | || ||   |  |  | |  |  | |   |||  |    | ||||  |   |||| |  |        ||| ||                                                                                 
GTGTGGTCCCTGCAAAGTGATGGCTCCAAAATTCCAAGAATTGTCTGGGAAGTATCTTGACGTTGTCTTTCTAAAGCTGGACTGCAACCAAGACAACAAGgtctgtaatcttttacctgatcccaattccctgatacaaatgcacgagctcacactgattcatctgagaactgttggcag--------------------------------------------------------------------------------
















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|32841806|gb|CD981487.1|CD981487
EST:     AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG                         CCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
genomic: AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaac ... gttcttgcagCCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
EST: gi|91873796|gb|EB403753.1|EB403753
EST:     AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG                         CCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
genomic: AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaac ... gttcttgcagCCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
EST: gi|211388824|gb|FL111188.1|FL111188
EST:     AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG                         CCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
genomic: AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaac ... gttcttgcagCCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
EST: gi|6952325|gb|AW424393.1|AW424393
EST:     AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG                         CCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
genomic: AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaac ... gttcttgcagCCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
EST: gi|211391451|gb|FL111189.1|FL111189
EST:     AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG                         CCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
genomic: AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaac ... gttcttgcagCCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
EST: gi|6195037|gb|AW147141.1|AW147141
EST:     AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG                         CCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
genomic: AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaac ... gttcttgcagCCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
EST: gi|149096373|gb|EE182103.2|EE182103
EST:     AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG                         CCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
genomic: AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaac ... gttcttgcagCCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
EST: gi|211391453|gb|FL111191.1|FL111191
EST:     AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG                         CCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
genomic: AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaac ... gttcttgcagCCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
EST: gi|16379905|gb|BI993210.1|BI993210
EST:     AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG                         CCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
genomic: AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaac ... gttcttgcagCCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
EST: gi|148947826|gb|EC893315.2|EC893315
EST:     AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG                         CCTCTCGCGAACGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
genomic: AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaac ... gttcttgcagCCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
EST: gi|148947825|gb|EC893314.2|EC893314
EST:     AGAACCTGGACGTCGTGTTCCTCAAGCTGGACGGCAACCAGGACAACAAG                         CCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGTTCCTC
genomic: AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaac ... gttcttgcagCCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
EST: gi|13515893|gb|BG518169.1|BG518169
EST:     AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG                         CCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
genomic: AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaac ... gttcttgcagCCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
EST: gi|13490722|gb|BG517486.1|BG517486
EST:     AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG                         CCTCTCGCGAAGGAGCTGGGCATAAAG
genomic: AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaac ... gttcttgcagCCTCTCGCGAAGGAGCTGGGCATAAAG
EST: gi|211391452|gb|FL111190.1|FL111190
EST:     GAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGAACA-CAAG                         CCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCT
genomic: GAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGA-CAACAAGgtcagcaaac ... gttcttgcagCCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCT
EST: gi|13491074|gb|BG517838.1|BG517838
EST:     AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG                         CCTCTCGCGAAGGAGCTGGGCATAAA
genomic: AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaac ... gttcttgcagCCTCTCGCGAAGGAGCTGGGCATAAA
EST: gi|148991280|gb|EE032751.2|EE032751
EST:     AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG                         CCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
genomic: AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaac ... gttcttgcagCCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
EST: gi|16379812|gb|BI993161.1|BI993161
EST:     AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG                         CCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
genomic: AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaac ... gttcttgcagCCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
EST: gi|6166616|gb|AW144880.1|AW144880
EST:     AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG                         CCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
genomic: AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaac ... gttcttgcagCCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
EST: gi|148930342|gb|EE284761.2|EE284761
EST:     AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG                         CCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
genomic: AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaac ... gttcttgcagCCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
EST: gi|211256127|gb|FL475672.1|FL475672
EST:     AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAG                         CCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC
genomic: AGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaac ... gttcttgcagCCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTC

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 23

GTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAAGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaac ... gttcttgcagCCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTCAAGGGCGGGAAGGTCGTGAAGGAGGTCACCGGCGCCAAGATCGACGAGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 148

GTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAAGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaac ... gttcttgcagCCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTCAAGGGCGGGAAGGTCGTGAAGGAGGTCACCGGCGCCAAGATCGACGAGC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 58

GTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAAGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaac ... gttcttgcagCCTCTCGCGAAGGAGCTGGGCATAAAGGTTGTGCCGACGTTCAAGATCCTCAAGGGCGGGAAGGTCGTGAAGGAGGTCACCGGCGCCAAGATCGACGAGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCGGGCCTTGCAAAGTGATGGCTCCCAAGTTCCAGGAGATGTCCGAGAAGAACCTGGACGTCGTGTTCCTCAAGCTGGACTGCAACCAGGACAACAAGgtcagcaaactagatagtacgtacgcacgtacgtacctcctagctagctaggattacttagctgtgattgacatatatgatctacgacctagctcgatcttcccttgatctcttctgtgtgcatgcatggcgcttttgcttgttgttcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA