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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGCAACTCAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttgttgatctgcatgaacaacaaccaaaaagttatatggattttactatcgagatggtattgttaaaattgttttcaagtcggacgacttgct...

Basic information

species Zea mays
transcript GRMZM2G061745_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G061745_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA11G34980.1 (Glycine max), 5'ss of exon 5
AATGCAACTCAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttgttgatctgcatgaacaacaacca----------aaaagttatatggattttacta---tcgagatggtattgttaaaattgtt--ttcaagtcggacgacttgct------------------------------------------------------
||||| ||||| |||||||| || || ||||| ||||| || ||||| ||||| |||||||||||||||||||| ||||   | ||    ||    | || |     |           |    || | |  |||||  |    || | ||     | | |||||| ||  ||  |  |  || | |   |                                                      
AATGCCACTCAAAAAAGTCAAAAAGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAGgtatttcatgccattcaatgtaaaaactggtcttttttttcttatgttttgtttttattttgtttgattcaaaatttctatatgaaaattcttaattttatccataccattgtgtaacctgtttctcctgttttttgtttttttttaaattcttcttacctttgtgcag

upper sequence: GRMZM2G061745_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA20G03160.1 (Glycine max), 5'ss of exon 5
----------------AATGCAACTCAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttgttgatctgcatgaa---------caacaaccaaaaagttatatggattttacta---tcgagatggtattgttaaaattgtt--ttcaagtcggacgacttgct--------------------------------------------
                ||||| ||||| |||||||| ||||||||| | ||||| || ||||| |||||  || ||||||||||||||||  ||| | | ||    ||    | ||            |  |  |    || | |  |||||  |    || | ||     | | |||||| |   ||  |  |  || | |   |                                            
TTTATTCTGTGTACATAATGCCACTCAAAAAAGTCAAAAGGTATTTATACATGTGCCATCAGAGATTGCTACTAATGAAGTTGAGGAAATATgtatgtcatgccattcaatgtaaaattgatgtatttcttcttatgttttgtttatattttgtttgattcaaaatttctatatgaaaattatgaattttatccatacaattgtgtaaccagtttctcttgtttttttaattcttcttacctttgtgcag

upper sequence: GRMZM2G061745_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA18G03360.1 (Glycine max), 5'ss of exon 5
-AATGCAACTCAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttgttgatctgcatgaa---------caacaaccaaaaagttatatggattttacta---tcgagatggtattgttaaaattgtt--ttcaagtcggacgacttgct--------------------------------------------
 ||||| ||||| |||||||| ||||| ||||| ||||| || ||||| ||||| |||||||||||||||||||| ||||   | ||    ||    | ||            |  |  |    || | |  |||||  |    || | ||     | | |||||| |   ||  |  |  || | |   |                                            
GAATGCCACTCAAAAAAGTCAAAAGGTGTTTGTGCATGTGCCATCAGAGATTGCTGCTCATGAAGTTGAGGAAATAggtatttcatgccattcaatgtaaaactgatgtttttcttcttatgttttgtttatattttgtttgattcaaaatttctatatgaaaattctgaattttatccatacaattgtgtaaccagtttctcctgttttttttaattcttcttacctttgtgca

upper sequence: GRMZM2G061745_T03 (Zea mays), 5'ss of exon 5
lower sequence: AT5G05780.1 (Arabidopsis thaliana), 5'ss of exon 5
AATGCAACTCAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttgttgatctg-catgaacaacaaccaaaaagttatatggattttactatcgagatggtattgttaaaattgttttcaagtcggacgacttgct------------------------------
||||| ||||||||||| ||||| || || || |||||  || |||||||||| |||||||||||||||||||| |||| | |     |      ||         |  |     | || | | ||    | |  |||      | ||   |||||| | | |  |     ||  |                               
AATGCTACTCAGAAAAGCCAGAAAGTTTTCGTTCATGTGTCTACAGAAATTGCTGCTCATGAAGTTGAGGAAATCGgtatgtccaaaagggaaaacagttcttttgatgatttcatcatctcggttgagttttaaagaaatgtgttttgtgattgttctgaggaagattttctgacacttacctgcgtcattcttgttcttgtacag

upper sequence: GRMZM2G061745_T03 (Zea mays), 5'ss of exon 5
lower sequence: AT3G11270.2 (Arabidopsis thaliana), 5'ss of exon 5
AATGCAACTCAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttgttgatctgcatgaacaacaaccaaaaagttatatggattttactatcgag-atggtattgttaaaattgttttcaagtcggacgacttgct------------------------------------------------------------
||||| || |||||||| ||  |||| ||||| || || ||| ||||||||||||||||||||||||||||||||||||     |||  |  ||    |||||   |    |   | |       ||| |   ||| ||   | || | |     ||||    |  |   |                                                                  
AATGCTACCCAGAAAAGCCAACAGGTTTTTGTACACGTGCCTACAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgta-----tgtctacatggggaaacaaatcctttgatagtttgatttccttatttcagagcataagaatgatgagggaatttttttttttgtaaatgcttccgaggaaactcaatggagtccttcttgcttcgcttacgccagttggttggtcttgaacag

upper sequence: GRMZM2G061745_T03 (Zea mays), 5'ss of exon 5
lower sequence: Vv08s0007g01980.t01 (Vitis vinifera), 5'ss of exon 5
AATGCAACTCAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttgtt-----gatctgcatgaacaacaaccaaaaa-gttatatggattttactatcgagatggtattgtta-aaattgttttcaagtcggacgacttgct---------------------------------------------
||||| || |||||||| |||||||| ||||||||||| || || |||||||| ||||||||||||||||||||||||| | | ||        | || | |      |    |  || | | | |   |||   |||   ||   |   | |  ||||||  || |    | |  | || |                                              
AATGCTACCCAGAAAAGCCAGAAGGTTTTTGTCCATGTCCCATCTGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtatgtcatgagccgaaaagcttcttattttcctcttagcaatgctttttccctttccgtattctgaacttgaagatgcaaattgactttatcatgaattatttacctttttgaaccttcagtaattaacttcatgtgtcacctttccctag

upper sequence: GRMZM2G061745_T03 (Zea mays), 5'ss of exon 5
lower sequence: Vv02s0025g01490.t01 (Vitis vinifera), 5'ss of exon 5
AATGCAACTCAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttgttgat---ctgcatgaacaacaaccaaaaag--ttatatggattttactatcgagatggtattgttaaaattgttttcaagt-cggacgacttgct-------------------------------------------
||||| ||||||||||| ||||| || ||||||||  | ||||| |||||||| ||||||||||||||||||||||||| | |  | |||    || | |      |    | ||    |  | |   |||| ||||   ||    |  |  | |||||  || |  |  |||    ||                                              
AATGCCACTCAGAAAAGCCAGAAAGTTTTTGTCCACATACCTTCTGAAATTGCTGCTCATGAAGTTGAGGAAATTGgtatgtcaagctgaaaaactacttattttcctcttagaagtgttcctttcccttttcctattctgaactcaaagacacaattgaatttatatatggattgtttaactttgaatctttaatgataaacttcctacatcacctgccaatag

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|60348273|gb|DN215246.1|DN215246
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
EST: gi|20811186|gb|BQ295664.1|BQ295664
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
EST: gi|211385219|gb|FK956040.1|FK956040
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTCCYAAGGGATGTCAAGGACACAACAATAAGCACACTT
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCT-AAGGGATGTCAAGGACACAACAATAAGCACACTT
EST: gi|149014660|gb|EE044326.2|EE044326
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
EST: gi|148958380|gb|EC904610.2|EC904610
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
EST: gi|148960678|gb|EE011309.2|EE011309
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
EST: gi|149013823|gb|EE043297.2|EE043297
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
EST: gi|50325946|gb|CO521072.1|CO521072
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
EST: gi|76015327|gb|DT942497.1|DT942497
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
EST: gi|149081616|gb|EE170759.2|EE170759
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
EST: gi|211382590|gb|FK956032.1|FK956032
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
EST: gi|44681759|gb|CK786807.1|CK786807
EST:     ATTTGTCCATGTTCCTTCAAAAATTGCAGCTCATGAAGTTGAGGAAATTG                         GAAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATA
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGA-GTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATA
EST: gi|91055801|gb|EB166219.1|EB166219
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
EST: gi|211382594|gb|FK956036.1|FK956036
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTCMTAAGGGATGTCAAGGACACAACAATAAGCACACTT
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTC-TAAGGGATGTCAAGGACACAACAATAAGCACACTT
EST: gi|78081122|gb|DV509534.1|DV509534
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTCTAAGGGATGTCAGGGACACAACAATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
EST: gi|26456947|gb|CA828530.1|CA828530
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
EST: gi|148943844|gb|EC888923.2|EC888923
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
EST: gi|148935087|gb|EC879128.2|EC879128
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
EST: gi|148971131|gb|EE021979.2|EE021979
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
EST: gi|62525906|gb|DN828554.1|DN828554
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGAAAATTG                         GAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
EST: gi|211385222|gb|FK956043.1|FK956043
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
EST: gi|149072304|gb|EE160567.2|EE160567
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
EST: gi|149107089|gb|EE188981.2|EE188981
EST:     ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTG                         GAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG
genomic: ATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTG

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: 260

AATGCAACTCAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 323

AATGCAACTCAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 282

AATGCAACTCAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 256

AATGCAACTCAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttg ... caaccatcagGAGTTGAACACCTTCTAAGGGATGTCAAGGACACAACAATAAGCACACTTGCTACAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGCAACTCAGAAAAGTCAGAAGGTATTTGTCCATGTTCCTTCAGAAATTGCAGCTCATGAAGTTGAGGAAATTGgtaagacttgttgatctgcatgaacaacaaccaaaaagttatatggattttactatcgagatggtattgttaaaattgttttcaagtcggacgacttgct

- - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA