Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcattatagatgaagcatgctggcctaatatttttttatacagcatttacctccttttctctggtgcattctttaattcaattgattgctttattg...

Basic information

species Zea mays
transcript GRMZM2G097726_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097726_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g08880.3 (Oryza sativa), 5'ss of exon 3
GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcattatagatgaagcatgctggcctaatatttttttatacagcatttacctccttttctctggtgcattctttaattcaattgattgctttattg
||| |||||||| ||||||||||||||||| |||||||||||||||||||| |||||||| ||||| ||||||| | |  | || |  |||        |   ||||  |  || ||  |    | | ||| | ||||    ||  |  | |                 
GTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATgtgaggaatgctctgattggtgagtaatg-aaataattcatttaaattcatctttttcctgaactgcgctggtgtacattt-tatggttttatccctcttgc-----------------

upper sequence: GRMZM2G097726_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g08880.2 (Oryza sativa), 5'ss of exon 3
GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcattatagatgaagcatgctggcctaatatttttttatacagcatttacctccttttctctggtgcattctttaattcaattgattgctttattg-
||| |||||||| ||||||||||||||||| |||||||||||||||||||| |||||||| ||||| ||||||| | |  | || |  |||        |   ||||  |  || ||  |    | | |||    | |  || | |     || | | |   |       
GTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTGgtgagtaatg-aaataattcatttaaattcatctttttcctgaactgcgctggtgtacattttatggttttatccctcttgccactgggtgaataggacaa

upper sequence: GRMZM2G097726_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT4G39100.1 (Arabidopsis thaliana), 5'ss of exon 3
GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatt-atagatgaagcatgctggcctaatattttt---ttata--cagcatttacctccttttctctggtgcattctttaattcaattgattgctttattg
||| |||||||| |||||||| || || ||||||||| | ||| | ||||||||||| |||||||| |||| ||  || |   ||     |  |||   |||| || ||   | | |  | | | || |     | | | | ||| || | | |  ||   |  ||| | |    
GTTCTGCAAGTGTGAGATGCCGTATAACCCAGATGACTTGATGGTGCAATGCGAGGAGTGTTCTGAGTGgtaagtgttcacttatttgaaactctgttttaatcttcttgagtcacaatctggaattgctcgtatgtttttcgtgtatccatgaggtc--ctagttgatat----

upper sequence: GRMZM2G097726_T02 (Zea mays), 5'ss of exon 3
lower sequence: PP1S298_65V6.1 (Physcomitrella patens), 5'ss of exon 3
GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcat-tatagatgaagcatgctggcctaatatttttttatacagcatttacctccttttctctggtgcattctttaattcaattgattgctt-tattg
 | |||||||||||||||||| |||||||| |||||| | ||| | ||||| ||    ||    |||||||  || | |     |        |||    ||  |   ||| |   | |||| ||    | | |            ||  || | |     ||||  |   
TTATTGCAAGTGCGAGATGCCTTACAATCCTGATGACTTGATGGTTCAATGTGAAATCTGCAAAGACTGgtaggcctatgcttctctgttcaactgcgacaaagtgcatttct-ttgtatttgcccggatatttgcaagaggacggtttcttgagtgaggagcttgcacc-

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|148940632|gb|EC885443.2|EC885443
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|78180631|gb|DV550959.1|DV550959
EST:     TCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: TCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|211072810|gb|FL228287.1|FL228287
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGGATGACA-TCAAAGAAGCAAAGAAACTCG
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGG-ATGACAATCAAAGAAGCAAAGAAACTCG
EST: gi|148942300|gb|EC887317.2|EC887317
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|148941206|gb|EC886093.2|EC886093
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|93282376|gb|EB674640.1|EB674640
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|8551650|gb|BE128821.1|BE128821
EST:     CCATGCAATCCAGATG-CCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|91872374|gb|EB402331.1|EB402331
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|32825292|gb|CD965014.1|CD965014
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|78082597|gb|DV511009.1|DV511009
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|211072814|gb|FL228291.1|FL228291
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCNAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|78074295|gb|DV502729.1|DV502729
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|76927199|gb|DV171172.1|DV171172
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|67022285|gb|CO451034.1|CO451034
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|50336946|gb|CO532072.1|CO532072
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|9743182|gb|BE519330.1|BE519330
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|91872230|gb|EB402187.1|EB402187
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|22818819|gb|BU498909.1|BU498909
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAAGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|148951992|gb|EC897774.2|EC897774
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|148957892|gb|EC904047.2|EC904047
EST:     ATACAATCCAGATGACCCTTATGATCCAATGCGAGGAATGTTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCG
genomic: ATACAATCCAGATGACC-TTATGATCCAATGCGAGGAATGTT-CTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCG
EST: gi|32823010|gb|CD962719.1|CD962719
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGGGGAATGGTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|60354816|gb|DN221789.1|DN221789
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
EST: gi|60357704|gb|DN224677.1|DN224677
EST:     CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG                         GTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA
genomic: CCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGA

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), 49 (downstream exon)
Score: 394

GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGAGCATTTTTTCTGCCAGACCTGTACAGCTGAAAATGGTAAGATGGTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGAGCATTTTTTCTGCCAGACCTGTACAGCTGAAAATGGTAAGATGGTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGAGCATTTTTTCTGCCAGACCTGTACAGCTGAAAATGGTAAGATGGTTGAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 129

GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcatta ... cctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGAGCATTTTTTCTGCCAGACCTGTACAGCTGAAAATGGTAAGATGGTTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTGgtgagcattatagatgaagcatgctggcctaatatttttttatacagcatttacctccttttctctggtgcattctttaattcaattgattgctttattg

- - - - - - - - - - - - - -  CAGATG