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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGGCACCTTCCAGAAGGTTCCTGCCTTGAACGAAAGGATACTGTCATCCATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtacacgctctagcttgacaaatggtcagccgttgatctctgctatttgcaaccagagcttaagttcatcttggattcatgcag

Basic information

species Zea mays
transcript GRMZM2G137930_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137930_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g02310.1 (Oryza sativa), 5'ss of exon 2
---ACAGGCACCTTCCAGAAGGTTCCTGCCTTGAACGAAAGGATACTGTCATCCATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtacacgctctagcttgacaaatggtcagccgttgatctctgctatttgcaaccagagcttaagttcatcttggattcatgcag
    ||| | || ||   ||||  |||||  |||| ||||||||||||||||| |||||| |||| ||| |||| ||||| || ||||||||||| ||||| ||||    |||   |  | |||||||||   |||    |  || | |     |   |||       || |||| |      ||| |||||
GGCTCAGCCCCCGTC---AAGGCCCCTGCTCTGAATGAAAGGATACTGTCATCTATGTCCCGGAGATCTATTGCAGCACATCCATGGCATGATCTTGAGATTGgtacatgacat--ttcatcttgacaaaccatcaattttctatatttctc--tcataacttacttataggttcctgacttcttcctgcag

upper sequence: GRMZM2G137930_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g74350.1 (Oryza sativa), 5'ss of exon 3
ACAGGCACCTTCCAGAAGGTTCCTGCCTTGAACGAAAGGATACTGTCATCCATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtacacg---ctcta-----------gcttgacaaa----tggtcagccgttgatctctgctatttgcaaccagagcttaagttcatcttggattcatgcag----------------------------------------------------------------------
 |   |  |     |||||  || ||  | || || |||||||| ||||||||||||| ||| |||||||| |||||||| |||||||| || ||||| ||||   ||| ||   |||||            ||  || ||    || ||| ||      || ||   | |      |    |   | |   ||||| | || |                                                                         
TCCACCCGCGAGGGGAAGGCACCAGCTCTCAATGAGAGGATACTCTCATCCATGTCCAAGAGATCTGTTGCAGCACACCCATGGCATGACCTTGAGATTGgtaaaatactcgtaactctattctctactctactctactaactgctgctcaaccacctcactttggagtatttcgttactagtagtgatttccttgggtacacgttacccttcagatttctattatatttcttaggttcaaaaattcatcattttccctcctttgctttgcttgcag

upper sequence: GRMZM2G137930_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA03G33000.6 (Glycine max), 5'ss of exon 4
ACAGGCACCTTCCAGAAGGTTCCTGCCTTGAACGAAAGGATACTGTCATCCATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtacacgctctagcttgacaaatggtcagccgttgatctctgctatttgcaaccagagcttaagttcatcttggattcatgcag
       |||  ||       ||| |  | || || |||||  | ||||||||| |||| || ||||||||||||||||| ||||| || || ||||||||||  | |  |         | | ||| ||| |   |||  |  || | ||| |    |  || |  |    ||  ||  || ||||||
TATCATTCCTCACACTCACACCCTCCTCTTAATGAGAGGATTATTTCATCCATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAGgtaa-gcattcagaaataggtaaaaaacggtgacttgttagtg-cttcaattggtttgccaaggt--aaccaattctgttttaatgcag

upper sequence: GRMZM2G137930_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA13G19500.2 (Glycine max), 5'ss of exon 2
-ACAGGCACCTTCCAGAAGGTTCCTGCCTTGAACGAAAGGATACTGTCATCCATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgta--ttgtacacgctctagcttgacaaatggtcagccgttgatctctgctatttgcaaccagagcttaagttcatcttggattcatgcag-------------------
  |   || |   |   |    |  | ||| ||||| ||||| || |||||||| ||||||||    |||||||||||||| ||||| ||||| ||||||||||   | |  |      |  |||  | ||  | |    ||||||   |  || |    |       | | || || ||| ||     | |                   
AGCTATCAACAGTCCCCAAACCCTCGTCTT-AACGAGAGGATTCTTTCATCCATTTCCAGGAGACACGTTGCTGCACACCCGTGGCACGATCTTGAGATAGgtaagctatgtaattgtaaaattgtgacatcttaatgttttgatc---gtgatgtatttcttttttcttactttattttgtatgttaactgtattttctccacaatgcag

upper sequence: GRMZM2G137930_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA19G35710.1 (Glycine max), 5'ss of exon 4
-ACAGGCACCTTCCAGAAGGTTCCTGCCTTGAACGAAAGGATACTGTCATCCATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtacacgctctagcttgacaaatggtcagccgttgat-ctctgctatttgcaaccagagcttaagttcatcttggattcatgcag------------------------------------
      || | | |   |    ||| || | || || |||||  | ||||||||| ||||||| ||||||||||||||||| |||||||| || ||||||||||  | |  |         ||| ||||||| |   |||  | ||    |     | |   | | ||       ||||    | |    |                                    
ATTTCTCATCATTCCTCACAC-CCTCCCCTTAATGAGAGGATTATTTCATCCATGACCAGGAGATCTGTTGCTGCACACCCATGGCATGACCTTGAGATAGgtaa-gcattcagaaataggtgaaaaatggtgacttgttagtgcttcaattacatcgaattgtgtttcttcgtttcttttccttaattggtttgccaaggtaactatgttttcttccgcaatgcag

upper sequence: GRMZM2G137930_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA10G05130.1 (Glycine max), 5'ss of exon 2
----ACAGGCACCTTCCAGAAGGTTCCTGCCTTGAACGAAAGGATACTGTCATCCATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtacac-gctctagcttgacaaatggtcagccgttgatctctgctatttgcaaccagagcttaagttcatcttggattcatgcag--------------------
    |   ||||   ||| |     |  | ||| ||||| ||||| || |||||||| |||||||    ||||||||| ||||| ||||||||||| ||||||||||    | ||   | ||   |    |    | ||  |||  |      ||| |    |       | | || || ||| ||     | |                    
AGCTATCAGCACTCCCCAAA---CCCTCGTCTT-AACGAGAGGATTCTTTCATCCATTTCCAGGAAACATGTTGCTGCTCACCCGTGGCATGATCTTGAGATAGgtaagcaataccattgtaaaattgtgacatcttaggtgttt-tgatcattatgtatttcttttttcttactttattttgtatattaactgaatttccccctgcaatgcag

upper sequence: GRMZM2G137930_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT3G53620.1 (Arabidopsis thaliana), 5'ss of exon 2
----ACAGGCACCTTCCAGAAGGTTCCTGCCTTGAACGAAAGGATACTGTCATCCATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtacacg---------------ctctagcttgacaa-atggtcagc-cgttgatctctgctatttgcaaccagagcttaagttcatcttggattcatgcag------
    | |  ||  || ||     ||||| |  | || || |||||||| || ||||||      || || || ||||||||||| ||||||||||| ||||||||||   || |||               || |   ||| |   | | |||   | ||| | | |  || |  |    | | |||   ||    | | |||| |          
GTTGAGAAACATGTTTCAC----TTCCTACTCTTAATGAGAGGATACTTTCGTCCATGAGTCACAGATCAGTAGCTGCACACCCATGGCATGATCTCGAGATAGgtaagctatacgtaaaggtttctttttcttttttttggctctaagatcatttcattgttttttagtaataactcttatacctt--ttttgcttcgcattcctttgtttacag

upper sequence: GRMZM2G137930_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 5'ss of exon 2
-ACAGGCACCTTCCAGAAGGTTCCTGCCTTGAACGAAAGGATACTGTCATCCATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtat-tgtacacgctctagcttgacaaatggtcagccgttgatctctgctatttgcaaccagagcttaagtt---catcttggattc--atgcag
 ||   || |  |    |    |    ||| || |||||||| || ||||||||| || ||||| |||||||||||||||| ||||||||||| ||||||||||  |      | | || |   |      || |    || || ||| || ||| | |   |   || | |    ||| ||  |||   ||||||
AACTCTCATCAACACTCACACCCACCTCTT-AATGAAAGGATTCTTTCATCCATGACCCGGAGGGCTGTTGCTGCACACCCCTGGCATGATCTTGAGATAGgtacctacttttgttgtaacgc-atgttgagttaattcttaatgtctcctttttactagtggccttttattatgacattttttatttcaatgcag

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|9742923|gb|BE519071.1|BE519071
EST:     CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAG                         GTCCTGGTGCTCCAACCATATTCAACTGC
genomic: CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtaca ... attcatgcagGTCCTGGTGCTCCAACCATATTCAACTGC
EST: gi|91878963|gb|EB408920.1|EB408920
EST:     CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAG                         GTCCTGGTGCTCCAACCATATTCAACTGC
genomic: CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtaca ... attcatgcagGTCCTGGTGCTCCAACCATATTCAACTGC
EST: gi|91870587|gb|EB400969.1|EB400969
EST:     CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAG                         GTCCTGGTGCTCCAACCATATTCAACTGC
genomic: CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtaca ... attcatgcagGTCCTGGTGCTCCAACCATATTCAACTGC
EST: gi|9794549|gb|BE552857.1|BE552857
EST:     CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAG                         GTCCTGGTGCTCCAACCATATTCAACTGC
genomic: CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtaca ... attcatgcagGTCCTGGTGCTCCAACCATATTCAACTGC
EST: gi|89252994|gb|DY624780.1|DY624780
EST:     CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAG                         GTCCTGGTGCTCCAACCATATTCAACTGC
genomic: CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtaca ... attcatgcagGTCCTGGTGCTCCAACCATATTCAACTGC
EST: gi|23357487|gb|BU645136.1|BU645136
EST:     CATGATCTGGAGATAG                         GTCCTGGTGCTCCAACCATATTCAACTGC
genomic: CATGATCTGGAGATAGgtattgtaca ... attcatgcagGTCCTGGTGCTCCAACCATATTCAACTGC
EST: gi|211153963|gb|FL101500.1|FL101500
EST:     CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAG                         GTCCTGGTGCTCCAACCATATTCAACTGC
genomic: CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtaca ... attcatgcagGTCCTGGTGCTCCAACCATATTCAACTGC
EST: gi|78109928|gb|DV528343.1|DV528343
EST:     CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAG                         GTCCTGGTGCTCCAACCATATTCAACTGC
genomic: CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtaca ... attcatgcagGTCCTGGTGCTCCAACCATATTCAACTGC
EST: gi|60400269|gb|DN233076.1|DN233076
EST:     ATGATCTGGAGATAG                         GTCCTGGTGCTCCAACCATATTCAACTGC
genomic: ATGATCTGGAGATAGgtattgtaca ... attcatgcagGTCCTGGTGCTCCAACCATATTCAACTGC
EST: gi|22521401|gb|BU080212.1|BU080212
EST:     CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAG                         GTCCTGGTGCTCCAACCATATTCAACTGC
genomic: CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtaca ... attcatgcagGTCCTGGTGCTCCAACCATATTCAACTGC
EST: gi|21432147|gb|BQ547637.1|BQ547637
EST:     CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAG                         GTCCTGGTGCTCCAACCATATTCAACTGC
genomic: CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtaca ... attcatgcagGTCCTGGTGCTCCAACCATATTCAACTGC
EST: gi|71441944|gb|DR822994.1|DR822994
EST:     CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAG                         GTCCTGGTGCTCCAACCATATTCAACTGC
genomic: CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtaca ... attcatgcagGTCCTGGTGCTCCAACCATATTCAACTGC
EST: gi|22546627|gb|BU098938.1|BU098938
EST:     CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAG                         GTCCTGGTGCTCCAACCATATTCAACTGC
genomic: CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtaca ... attcatgcagGTCCTGGTGCTCCAACCATATTCAACTGC
EST: gi|86471929|gb|DY238299.1|DY238299
EST:     CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAG                         GCCCTGGTGCTCCAACCATATTCAACTGC
genomic: CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtaca ... attcatgcagGTCCTGGTGCTCCAACCATATTCAACTGC
EST: gi|60397937|gb|DN230753.1|DN230753
EST:     CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAG                         GTCCTGGTGCTCCAACCATATTCAACTGC
genomic: CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtaca ... attcatgcagGTCCTGGTGCTCCAACCATATTCAACTGC
EST: gi|23357695|gb|BU645344.1|BU645344
EST:     CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAG                         GTCCTGGTGCTCCAACCATATTCAACTGC
genomic: CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtaca ... attcatgcagGTCCTGGTGCTCCAACCATATTCAACTGC
EST: gi|71445656|gb|DR826706.1|DR826706
EST:     CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAG                         GTCCTGGTGCTCCAACCATATTCAACTGC
genomic: CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtaca ... attcatgcagGTCCTGGTGCTCCAACCATATTCAACTGC
EST: gi|91870563|gb|EB400947.1|EB400947
EST:     CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAG                         GTCCTGGTGCTCCAACCATATTCAACTGC
genomic: CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtaca ... attcatgcagGTCCTGGTGCTCCAACCATATTCAACTGC
EST: gi|74035433|gb|DT535921.1|DT535921
EST:     CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAG                         GTCCTGGTGCTCCAACCATATTCAACTGC
genomic: CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtaca ... attcatgcagGTCCTGGTGCTCCAACCATATTCAACTGC
EST: gi|76287732|gb|DV027300.1|DV027300
EST:     CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAG                         GTCCTGGTGCTCCAACCATATTCAACTGC
genomic: CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtaca ... attcatgcagGTCCTGGTGCTCCAACCATATTCAACTGC
EST: gi|22472706|gb|BU037186.1|BU037186
EST:     CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAG                         GTCCTGGTGCTCCAACCATATTCAACTGC
genomic: CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtaca ... attcatgcagGTCCTGGTGCTCCAACCATATTCAACTGC
EST: gi|31557952|gb|CD527164.1|CD527164
EST:     CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAG                         GTCCTGGTGCTCCAACCATATTCAACTGC
genomic: CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtaca ... attcatgcagGTCCTGGTGCTCCAACCATATTCAACTGC
EST: gi|22133615|gb|BQ833806.1|BQ833806
EST:     CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAG                         GTCCTGGTGCTCCAACCATATTCAACTGC
genomic: CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtaca ... attcatgcagGTCCTGGTGCTCCAACCATATTCAACTGC
EST: gi|71444627|gb|DR825677.1|DR825677
EST:     CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAG                         GTCCTGGTGCTCCAACCATATTCAACTGC
genomic: CATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtaca ... attcatgcagGTCCTGGTGCTCCAACCATATTCAACTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAGGCACCTTCCAGAAGGTTCCTGCCTTGAACGAAAGGATACTGTCATCCATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtacacgctctagcttgacaaatggtcagccgttgatctctgctatttgcaaccagagcttaagttcatcttggattcatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT