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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTAGCTGCATCTGGCTCCATGCTGGCCTAATCCATTTGGTTGTGAACATGCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTGgtaagcttttaaaatcattttcatcgtacgcgaatatcgatccaaccattcatttcagttaagtgttccaaccattcgcccttcatggtcatttcactgacactgtttttcctgcttgcaag

Basic information

species Zea mays
transcript GRMZM2G116514_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116514_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os09g35730.1 (Oryza sativa), 5'ss of exon 2
ATTAGCTGCATCTGGCTCCATGCTGGCCTAATCCATTTGGTTGTGAACATGCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTGgtaagcttttaaaatcattttcatcgtacgcgaatatcgatc-caaccattcatttcagttaagtgttccaaccattcgcccttcatggtcatttca-ctgacactgtttttcctgcttgcaag
|||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||||||||||||||||| ||||||||||| || |||||| || | |    ||  | ||     |  | | |  |     |  || | ||     | ||||||   | |||    | || |    |||  || || | |   |||              
ATTAGCTGTATCTGGCTCCATGCTGGCCTAATCCATTTGGTTGTGAACATGCTGAGTTTACTGTTTATTGGAATCCGCCTTGAACAGCAATTTGGGTTCGgtaagtttctta--ctatgctgattcagtgtcatttttaactatgagaatacgttc----ttagtgtt---aacatatatctttgaata-catgccatctcatagaattt--------------

upper sequence: GRMZM2G116514_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT1G63120.1 (Arabidopsis thaliana), 5'ss of exon 2
ATTAGCTGCATCTGGCTCCATGCTGGCCTAATCCATTTGGTTGTGAACATGCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTGgtaagcttttaaaatcattttcatcgtacgcgaatatcgatccaaccattcatttcagttaagtgttccaaccattcgcccttcatggtcatttcactgacactgtttttcctgcttgcaag
 |    || || ||||| || |||||  | || ||| |  ||   |||||| | |||||| | || ||||| ||||||||||||||||||||||| ||  |||||  ||      | ||| | | ||||  ||||     | ||  ||    ||  | |    |  |  || |               | || |   |  |     | || |||  ||||  
CTCTCTTGTATGTGGCTTCACGCTGGTATCATTCATCTTCTTACAAACATGTTGAGTTTGATCTTCATTGGTATCCGCCTTGAGCAGCAATTTGGCTTCAgtaagtctta-----cctttacgt-gtacaagaattattgttcagtcaagttttagactctctttgtttaatcgccaagtgaaacatttgatctttatcgcgggaatgttactg--tgcag-
















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|101386352|gb|EB815195.1|EB815195
EST:     GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTG                         TTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
genomic: GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTGgtaagctttt ... tgcttgcaagTTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
EST: gi|76286369|gb|DV025937.1|DV025937
EST:     GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTG                         TTCGCATTGGTGCCATATACCTACTGTC
genomic: GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTGgtaagctttt ... tgcttgcaagTTCGCATTGGTGCCATATACCTACTGTC
EST: gi|67024823|gb|CO453572.1|CO453572
EST:     GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTG                         TTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
genomic: GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTGgtaagctttt ... tgcttgcaagTTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
EST: gi|15100365|gb|BI396156.1|BI396156
EST:     GCTAAGTTTGCTGTTTATTGGAATCCGTCTTGAGCAGCAATTTGGATTTG                         TTCGCATTGGTGCCATATACCTACTGTCTG
genomic: GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTGgtaagctttt ... tgcttgcaagTTCGCATTGGTGCCATATACCTACTGTCTG
EST: gi|71319572|gb|DR796532.1|DR796532
EST:     GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTG                         TTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
genomic: GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTGgtaagctttt ... tgcttgcaagTTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
EST: gi|26457322|gb|CA828905.1|CA828905
EST:     GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTG                         TTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
genomic: GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTGgtaagctttt ... tgcttgcaagTTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
EST: gi|149072555|gb|EE040236.2|EE040236
EST:     GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTG                         TTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
genomic: GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTGgtaagctttt ... tgcttgcaagTTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
EST: gi|148967078|gb|EE018245.2|EE018245
EST:     GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTG                         TTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
genomic: GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTGgtaagctttt ... tgcttgcaagTTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
EST: gi|32915209|gb|CF020021.1|CF020021
EST:     GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTG                         TTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
genomic: GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTGgtaagctttt ... tgcttgcaagTTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
EST: gi|87155865|gb|DY400654.1|DY400654
EST:     GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTG                         TTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
genomic: GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTGgtaagctttt ... tgcttgcaagTTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
EST: gi|78075433|gb|DV503867.1|DV503867
EST:     GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTG                         TTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
genomic: GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTGgtaagctttt ... tgcttgcaagTTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
EST: gi|21390183|gb|BQ528232.1|BQ528232
EST:     GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTG                         TTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
genomic: GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTGgtaagctttt ... tgcttgcaagTTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
EST: gi|148982101|gb|EE028150.2|EE028150
EST:     GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTG                         TTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
genomic: GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTGgtaagctttt ... tgcttgcaagTTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
EST: gi|26558680|gb|CA830915.1|CA830915
EST:     GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTG                         TTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
genomic: GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTGgtaagctttt ... tgcttgcaagTTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
EST: gi|76020120|gb|DT947290.1|DT947290
EST:     GTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGA-TTG                         T
genomic: GTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTGgtaagctttt ... tgcttgcaag-
EST: gi|76020120|gb|DT947290.1|DT947290
EST:     GTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGA-TTG                         T
genomic: GTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTGgtaagctttt ... tgcttgcaag-
EST: gi|71764176|gb|DR962113.1|DR962113
EST:     GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTG                         TTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
genomic: GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTGgtaagctttt ... tgcttgcaagTTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
EST: gi|22473298|gb|BU037778.1|BU037778
EST:     GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTG                         TTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
genomic: GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTGgtaagctttt ... tgcttgcaagTTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
EST: gi|76020121|gb|DT947291.1|DT947291
EST:     GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTG                         TTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT
genomic: GCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTGgtaagctttt ... tgcttgcaagTTCGCATTGGTGCCATATACCTACTGTCTGGTTTTGGTGGCAGCGTGTTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTAGCTGCATCTGGCTCCATGCTGGCCTAATCCATTTGGTTGTGAACATGCTAAGTTTGCTGTTTATTGGAATCCGCCTTGAGCAGCAATTTGGATTTGgtaagcttttaaaatcattttcatcgtacgcgaatatcgatccaaccattcatttcagttaagtgttccaaccattcgcccttcatggtcatttcactgacactgtttttcctgcttgcaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG