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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCCgtaagacaatttatgatccccgcataaatatggtagcttgatttccctcccaccctgaaaattctaatgtttgcag

Basic information

species Zea mays
transcript GRMZM2G079196_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079196_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 8
ATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCCgtaagacaatttatgatccccgcataaatatggtagcttgatttccctcccaccctgaaaattct-aatgtttgcag
||||||||| ||||| ||||||||||||||||||||||||||||| |||||||| |||||||| ||||||||||||| || ||||| ||| ||||||| | ||| ||| |||||  | |||||||| || | ||  ||| || |||
ATATCTTGTTCTTGCAAATATGTTGATGGAATCTGAAGTGAATCCCTTTGATGGGCAAGAGGCTAAGCCgtaagacatttgatgattccctcataaatcttgtatcttaatttca-tgccaccctgtaactccttgatgctttcag

upper sequence: GRMZM2G079196_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA19G17660.1 (Glycine max), 5'ss of exon 8
ATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCCgtaagacaatttatgatccccgcataa-atatggtagcttgatttccctcccaccctgaaaattctaatgtttgcag--------------------------------------------------------------
||| ||||| |||||||| ||||||||||| |||||||| ||||| ||||||||||| || || |||||||||| |  | | |  |       ||| ||||  || ||  |||| | |  | |        ||||  | |   | |                                                              
ATACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCATTTGATGGACAGGAAGCTAAGCCgtaagtcc-tctgtattttgtttttaatatatttta-ctcaattttcatttctctgattctgttctt-tatccactgaggtgaggatgatataccttcacttctttctgttctcaccttgcatatattctatactgcag

upper sequence: GRMZM2G079196_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA19G30100.1 (Glycine max), 5'ss of exon 8
ATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCCgtaaga---caatttatgatcc--ccgcataaat--------------atggtagcttgatttccctcccac--cctgaaaattctaatgtttgcag---
 || ||||| |||||||| ||||||||||| |||||||| ||||| |||||||| || ||||| ||||||||||    |  ||| | ||      |  |||||              |  |  |||||| || | | |  |  ||   | ||| |||  | | ||    
GTACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCGTTTGATGGGCAGGAGGCTAAGCCgtaagttctctgtttttaatttatttgagtaaattatgctctcccttaagagatgcttgaattgcattctccttcccacatattttaaaatatacacctc

upper sequence: GRMZM2G079196_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA05G14170.1 (Glycine max), 5'ss of exon 8
ATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCCgtaagacaatttatgatccccgcataaatatggtagcttgatttccctcccaccctgaaaattctaatgtttgcag----------------------------------------------------
 || ||||| |||||||| ||||||||||| |||||||| ||||| |||||||| || || || |||||||||| |  | | |  |        | ||||  || ||  ||||  |      ||       |    | |   | |                                                    
GTACCTTGTTCTTGCCAACATGTTGATGGAGTCTGAAGTAAATCCATTTGATGGGCAGGAAGCTAAGCCgtaagtcc-tctgtattttgttttaatatatttta-ctcaatttttcatttctccgattctgttctttatccactgaggtgaggatcacttctttctgttctcaccttgcatatattctatactgcag

upper sequence: GRMZM2G079196_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA03G00670.1 (Glycine max), 5'ss of exon 8
ATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCCgtaagac----------aatttatgatccccgcataaatatggtagcttgatttccctcccac--cctgaaaattctaatgtttgcag------------
 || ||||| || ||||| ||||||||||| |||||||| |||||||||||||| || ||||| |||||||||| |          |||||||           |  ||  |  |||| | || | | || |  ||   | ||| |||  | ||||             
GTACCTTGTTCTGGCCAACATGTTGATGGAGTCTGAAGTAAATCCTTTTGATGGGCAGGAGGCTAAGCCgtaagtcctctgtttttaatttatttgtgttctccatttagagatgcttaaattgcattccccttcccacatattttaaaatatgcacttccctccctat

upper sequence: GRMZM2G079196_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT2G26990.1 (Arabidopsis thaliana), 5'ss of exon 8
ATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCCgtaagacaatttatgatccccgcataaatatggtagcttgatttccctcccaccctgaaaattctaatgtttgcag
 |||||||| || || |||||| ||||||| || ||||||||||| |||||||| |||||||| |||||||||| || ||    ||       |   | | | |   |  |||   | |    ||  | | |    | | |||||
GTATCTTGTTCTGGCGAATATGCTGATGGAGTCAGAAGTGAATCCGTTTGATGGCCAAGAGGCAAAGCCgtaagtcatttccgtatatattttt---tgttgaacactcgttttggttcgttgcttcatagttggctctctgcag

upper sequence: GRMZM2G079196_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 8
ATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCCgtaagacaat-ttatgatccccgcataaatatggta-gcttgatttccctcccaccctgaaaattctaatgtttgcag-------------------------------------
|||  | || || || || ||| | ||||| || ||||| ||||||||||||||||| ||||| ||||||||||    | |||||||       || || || |  |  || |||   |      |||    |   ||||||    |                                     
ATACTTGGTTCTGGCTAACATGCTCATGGAGTCAGAAGTTAATCCTTTTGATGGACAGGAGGCAAAGCCgtaagttgctcttatgattt----gtatatttgatctgtgtgtttttgttattggtctgttggtggcaatgttctttgttattccttgtggccacttacaattgctcttttccag

upper sequence: GRMZM2G079196_T01 (Zea mays), 5'ss of exon 8
lower sequence: PP1S124_47V6.1 (Physcomitrella patens), 5'ss of exon 8
ATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCCgtaagac----aattta--tgatccccgca-taaatatggtagcttgattt-ccctcccaccctgaaa-attctaat--gtttgcag-------------
 || || || ||||| || ||||||||||| ||||||||||| || |||||||  || ||||| || |||||||||    || |||  |||    |||| |  |  | | || |||||   | ||   |   ||  | ||  |||    ||| |               
GTACCTGGTACTTGCTAACATGTTGATGGAGTCTGAAGTGAACCCATTTGATGCTCAGGAGGCTAAACCgtaagactctgaagttaactgaaaaacgcacttgaattagcagattgatacactctaaaagtttgtgatatgataactgatttactcaaatgtaatgctt

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|67012630|gb|CO441379.1|CO441379
EST:     TGGACAAGAGGCCAAGCC                         GTACAAG-ATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTA
genomic: TGGACAAGAGGCCAAGCCgtaagacaat ... atgtttgcagGTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTA
EST: gi|211507840|gb|FL110003.1|FL110003
EST:     ATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC                         GTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTA
genomic: ATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCCgtaagacaat ... atgtttgcagGTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTA
EST: gi|67023333|gb|CO452082.1|CO452082
EST:     ATGTTGATGGAATCTGAATTGAATCCTTTTGATGGACAAGAGGCCAAGCC                         GTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTA
genomic: ATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCCgtaagacaat ... atgtttgcagGTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTA
EST: gi|211507839|gb|FL110002.1|FL110002
EST:     ATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC                         GTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTA
genomic: ATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCCgtaagacaat ... atgtttgcagGTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTA
EST: gi|211507837|gb|FL110000.1|FL110000
EST:     ATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC                         GTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTA
genomic: ATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCCgtaagacaat ... atgtttgcagGTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTA
EST: gi|74246199|gb|DT654113.1|DT654113
EST:     AAGAGGCCAAGCC                         GTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTA
genomic: AAGAGGCCAAGCCgtaagacaat ... atgtttgcagGTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTA
EST: gi|18659527|gb|BM500385.1|BM500385
EST:     ATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC                         GTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTA
genomic: ATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCCgtaagacaat ... atgtttgcagGTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTA
EST: gi|83279086|gb|DV943094.1|DV943094
EST:     ATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC                         GTACAAGAATGACCCTGAAATTCTTGCAATGACAAACCTGATTGCAGCGTA
genomic: ATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCCgtaagacaat ... atgtttgcagGTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTA
EST: gi|211507835|gb|FL109998.1|FL109998
EST:     ATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC                         GTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTA
genomic: ATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCCgtaagacaat ... atgtttgcagGTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTA
EST: gi|211450033|gb|FL052875.1|FL052875
EST:     GAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC                         GTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTA
genomic: GAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCCgtaagacaat ... atgtttgcagGTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTA
EST: gi|45847141|gb|CN071084.1|CN071084
EST:     ATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC                         GTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTA
genomic: ATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCCgtaagacaat ... atgtttgcagGTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTA
EST: gi|211507838|gb|FL110001.1|FL110001
EST:     ATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCC                         GTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTA
genomic: ATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCCgtaagacaat ... atgtttgcagGTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTA

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: 48 (upstream exon), 49 (downstream exon)
Score: 185

ATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCCgtaagacaat ... atgtttgcagGTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 135

ATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCCgtaagacaat ... atgtttgcagGTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 151

ATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCCgtaagacaat ... atgtttgcagGTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 165

ATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCCgtaagacaat ... atgtttgcagGTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATCTTGTCCTTGCCAATATGTTGATGGAATCTGAAGTGAATCCTTTTGATGGACAAGAGGCCAAGCCgtaagacaatttatgatccccgcataaatatggtagcttgatttccctcccaccctgaaaattctaatgtttgcag

- - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG