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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAGTTAAGGGAGCAGATGTTGTGTATACAGATGTTTGGGCCAGCATGGGCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgttttcacactttctagaatttccgtgtcttgctggacaccaactacatatactttgattaagcccgtgaggcgactgagttaaaactagag...

Basic information

species Zea mays
transcript GRMZM2G046748_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046748_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os02g47590.1 (Oryza sativa), 5'ss of exon 4
AGCAGTTAAGGGAGCAGATGTTGTGTATACAGATGTTTGGGCCAGCATGGGCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgttttcacactttctagaatttccgtgtcttgctggacaccaactacatatactttgattaagcccgtgaggcgactgagttaaaactagag------------------------------------------------------
|||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||| |||||||| ||||||||| |   |||||| |||||||||||| |  |   | |     | ||    || |  |||  ||   | ||| ||||   | |||    | ||   | || || |  ||    ||  |   |                                                        
AGCAGTTAAGGGAGCAGATGTTGTGTATACAGATGTCTGGGCCAGCATGGGCCAAAAGGAGGAAGCTGAATATAGAAAAAAAGTGTTCCAAGGATTCACGgttagaatacctccttttatgctcttgttccgatgttctgtctg-cacaaactcattttacacataatatctcagt-agtcctctccactattatctgcatatgggatctggctaatactttattctcaatactttgtttctttgttcctgcag

upper sequence: GRMZM2G046748_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA04G03280.1 (Glycine max), 5'ss of exon 4
AGCAGTTAAGGGAGCAGATGTTGTGTATACAGATGTTTGGGCCAGCATGGGCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgttttcacactttctagaatttccgtgt--cttgctggacaccaactacatatactttgattaagcccgtgaggcgactgagttaaaactagag-
 || ||||| ||||| |||||||||||| ||||||| |||||||||||||||||||||||||||||||| ||  |    ||    ||  | |||||   |||   |    |   |    |   |  |||| | |    |   ||   ||     |||| ||    || ||| |  |   |  |   || ||| |   ||  | 
GGCTGTTAAAGGAGCTGATGTTGTGTATTCAGATGTCTGGGCCAGCATGGGCCAAAAGGAAGAAGCTGAATACCGGCGCCAAGCTTTTAAAGGATTTCAGgtactttacataatatttctgacattattttcttacagccacctaatcaaatggtacacatggggtggtta-gtgcagaaatca--tgtgttgagtttaacga

upper sequence: GRMZM2G046748_T02 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA06G03360.1 (Glycine max), 5'ss of exon 4
AGCAGTTAAGGGAGCAGATGTTGTGTATACAGATGTTTGGGCCAGCATGGGCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgttttcacactttctagaatttccgtgt--cttgctggacaccaactacatatactttgattaagcccgtgaggcgactgagttaaaactagag-
||| ||||| ||||| |||||||||||| ||||||| |||||||||||||| ||||||||||||||||| ||  |    ||    ||  | |||||   |||   |    |   |    |   |  |||| | |    |   ||   ||     |||| ||    || |||     |    |    |  ||| ||  || |  
AGCTGTTAAAGGAGCTGATGTTGTGTATTCAGATGTCTGGGCCAGCATGGGGCAAAAGGAAGAAGCTGAATACCGTCGCCAAGTTTTTAAAGGATTTCAGgtactttacataatatttctgtcattattttcttacagccatctaatcaaatggtacagatggggtggttag---tgcagagatcataggttgaatttaaaaa

upper sequence: GRMZM2G046748_T02 (Zea mays), 5'ss of exon 5
lower sequence: AT1G75330.1 (Arabidopsis thaliana), 5'ss of exon 4
AGCAGTTAAGGGAGCAGATGTTGTGTATACAGATGTTTGGGCCAGCATGGGCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgttttcacactttctagaatttccgtgtcttgctggacacca--actacatatactttgattaagcccgtgaggcgactgagttaaaactagag
||| ||||  |||||||||||||||||  |||| || |||||||| ||||| |||||||| ||||| ||   | |     |    ||||| ||||||  |||     |   || |  ||  ||  | |||  |||   |||| |  ||    |||| || |||  || ||   | ||       | |  ||| ||  |  ||
AGCTGTTATTGGAGCAGATGTTGTGTACTCAGACGTATGGGCCAGTATGGGTCAAAAGGATGAAGCCGAAGCTCGCCGGAAAGCATTCCAAGGATTCCAGgtaaacataagtttaatctggctt-agttttggtgcaatgctcggtactcttactaaat-tacactgctt---cacgcttacatattatgttcaa-ttgcag

upper sequence: GRMZM2G046748_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv18s0001g12780.t01 (Vitis vinifera), 5'ss of exon 4
AGCAGTTAAGGGAGCAGATGTTGTGTATACAGATGTTTGGGCCAGCATGGGCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgt-ctgttttcacactttctagaatttccgtgtcttgctggacaccaactacatatactttgattaagcccgtgaggcgactgagttaaa-actagag--
||| ||||  |||||||||||||| ||  ||||||||||||| |||||||| ||||||||||| ||    ||| |    ||   ||| || |||||   |||   |  |||||| | |  ||  |   | |   | |  | ||  |||   | | | | |   |      |  |  | |    ||  | || || |  ||    
AGCTGTTAGAGGAGCAGATGTTGTATACTCAGATGTTTGGGCTAGCATGGGGCAAAAGGAAGAGGCCTCATATCGCCGGCAAGTGTTTCAAGGATTTCAGgtacctgttgttttaaaagcttgcaatttattaatttgattctt-acattga-tgcttgttgctcag--gaaactatcacatcacaaactttaacatcagtatc

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|30032213|gb|CB834064.1|CB834064
EST:     GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgt ... tatattgcagGTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
EST: gi|211455121|gb|FL324015.1|FL324015
EST:     ATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: ATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgt ... tatattgcagGTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
EST: gi|32836208|gb|CD975886.1|CD975886
EST:     GCCAGAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgt ... tatattgcagGTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
EST: gi|71438747|gb|DR819797.1|DR819797
EST:     GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgt ... tatattgcagGTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
EST: gi|32837712|gb|CD977390.1|CD977390
EST:     GCCAGAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgt ... tatattgcagGTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
EST: gi|31910469|gb|CD651439.1|CD651439
EST:     GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgt ... tatattgcagGTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
EST: gi|78093456|gb|DV521830.1|DV521830
EST:     GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgt ... tatattgcagGTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
EST: gi|71764923|gb|DR962860.1|DR962860
EST:     GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgt ... tatattgcagGTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
EST: gi|78111650|gb|DV530047.1|DV530047
EST:     GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgt ... tatattgcagGTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
EST: gi|211257433|gb|FL317240.1|FL317240
EST:     GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgt ... tatattgcagGTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
EST: gi|211455117|gb|FL324011.1|FL324011
EST:     TAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: TAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgt ... tatattgcagGTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
EST: gi|60348417|gb|DN215390.1|DN215390
EST:     GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgt ... tatattgcagGTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
EST: gi|32943713|gb|CF048532.1|CF048532
EST:     GCCAGAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgt ... tatattgcagGTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
EST: gi|211235251|gb|FL454390.1|FL454390
EST:     GCCAAAAGGAAGAAGCTGATTATAGAAWACAGAAGTTCCAGGGATTCACG                         GTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgt ... tatattgcagGTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
EST: gi|50324509|gb|CO519635.1|CO519635
EST:     GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgt ... tatattgcagGTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
EST: gi|88757625|gb|DY541766.1|DY541766
EST:     GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgt ... tatattgcagGTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
EST: gi|32834620|gb|CD974298.1|CD974298
EST:     GCCAGAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgt ... tatattgcagGTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
EST: gi|113814581|gb|DW932358.1|DW932358
EST:     AAAAGGAAGAAGCTGATTATAG-AAACAGAAG-TCCAGGGATTCACG                         GTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: AAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgt ... tatattgcagGTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
EST: gi|71759632|gb|DR957569.1|DR957569
EST:     GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgt ... tatattgcagGTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
EST: gi|67023762|gb|CO452511.1|CO452511
EST:     GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACG                         GTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC
genomic: GCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgt ... tatattgcagGTGGATGAAGCCCTGATGGAGATTGCTGGCCCACAGGCCTACCTTATGCAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCAGTTAAGGGAGCAGATGTTGTGTATACAGATGTTTGGGCCAGCATGGGCCAAAAGGAAGAAGCTGATTATAGAAAACAGAAGTTCCAGGGATTCACGgtttgtctgttttcacactttctagaatttccgtgtcttgctggacaccaactacatatactttgattaagcccgtgaggcgactgagttaaaactagag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT