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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACAAGCTCAGAGGATCACTGAAGATCGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaacttccattctaaagcttcattttgatcatgtatgcaccttatccataaacatactttgtttctgcag

Basic information

species Zea mays
transcript GRMZM2G083716_T04
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os06g02380.2 (Oryza sativa), 5'ss of exon 7
AACAAGCTCAGAGGATCACTGAAGATCGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaacttccattctaaagc-ttcattt---tgatcatgtatgcaccttatccataaacatacttt-gtttctg-cag--------------------------------------------
|||||||| ||||| ||| |||| || || || |||||||||||||||||||| ||||||||||| ||||||||||||||||||||||| || ||||||||| || |  |||| |  |||   || ||   ||   |||||||  ||||  |||||  || |  || ||   |  |||| | |                                            
AACAAGCTTAGAGGGTCATTGAAAATTGCCGCTATCAAAGCCCCTGGTTTTGGTGAGCGCAAGACCCAGTACTTGGATGATATTGCCATTCTAACTGGAGgtgaggtggacttgcgatctggtgcatttggttgggtgatcattaatgctgcttatttatgatgattctggagcatctggctggatgattaatgctgcttatttataatgattttttttctctgcag

upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA08G18760.2 (Glycine max), 5'ss of exon 6
AACAAGCTCAGAGGATCACTGAAGATCGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaacttccattctaaagcttc--attttgatcatgtatgcaccttatccataaacatactttgtttctgcag------------------------------------
||||| || ||||||||||||||||| || ||  | || |||||||| ||||||||||||||||  |||||| | ||||||||||||||| | ||||||||||    ||  |   | | | | || |   ||||||    |||||  |   | |   |        ||||||||   |                                     
AACAAACTTAGAGGATCACTGAAGATTGCAGCACTGAAGGCCCCTGGGTTTGGAGAGCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaatataaaaatttcatgcctttgattttggaagtgtatatatgcttttttttctatctttttgtttccagatgttgataagatatgtattttctcaattggtttacag

upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 6
AACAAGCTCAGAGGATCACTGAAGATCGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaacttccattctaaagcttc--attttgatcatgtatgcaccttatccataaacatactttgtttctgcag------------------------------------
||||| || |||||||||||||| || || ||  |||| |||||||| |||||||| |||||||  |||||| | ||||||||||||||| | ||||||||||    ||  ||   || |   || |   ||||||    ||| |  |     | | |  |  |  ||||||||                                         
AACAAACTTAGAGGATCACTGAAAATTGCAGCACTCAAGGCCCCTGGGTTTGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaatattaagtttttgtgcctttgattttggaagtgtgtatatgcgtttc-tctatcttttttgtttccaggtgatgataagatatgtattttctcaattgatttacag

upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 6
lower sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 7
AACAAGCTCAGAGGATCACTGAAGATCGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaacttccattctaaagcttcattttgat---catgtatgcaccttatccataaacatactttgtt-tctgcag------
|||||||| |||||  |||||||||| || ||  ||| ||| || || ||||||||||||||||  || ||| | |||||||||||||| || ||||||||| || |     | ||||    |||   || || |     || | || |  || |   |   | || |||  | ||| |        
AACAAGCTTAGAGGTACACTGAAGATAGCAGCTCTCAGAGCTCCAGGGTTTGGAGAGCGCAAGAGCCAATACCTTGATGATATTGCCATTCTAACTGGAGgtaagttctgtctgcattgatgagccctatgtttacgcatatatttgtagtttttatcttgtcctaattttctatcttcgcttgcag

upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 6
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 7
AACAAGCTCAGAGGATCACTGAAGATCGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaacttccattctaaag---cttcattttgatc---atgtatgcaccttatccat--aaacatactttgtttctgcag--------------------------------
|||||||| |||||  |||||||||| || ||  ||||||| ||||| ||||||||||||||||  || ||| | || ||||||||||| || |||||||||  |  |   ||  ||   |||    ||  || | | |    ||  |||  || |    ||    |   | || | |  |  |                                 
AACAAGCTTAGAGGCACACTGAAGATTGCAGCTCTCAAAGCTCCTGGATTTGGAGAGCGCAAGAGCCAATACCTTGACGATATTGCCATTCTAACTGGAGgtaggtcatgtttttataacaaaaaacctatatgtgggtatcaatcaatgtgccctcctgatttggaatcatttggctgttaaaaccttaccgtgttgcttctgtttttgtgtgcag

upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 6
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 7
AACAAGCTCAGAGGATCACTGAAGATCGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaacttccattctaaagcttcattttgatcatgtatgcaccttatcc-ataaacatactttgtttctgcag-----------------------
|| ||||| ||||| ||| | ||||| |||||  | ||||||||||| ||||||||||||||||  |||||| ||||||| ||||| || || ||||||||| |||  |  |  |||| | |   ||  ||||  |  | | |  |  ||||   |         ||| ||     |                        
AATAAGCTTAGAGGGTCATTAAAGATTGCTGCACTTAAAGCCCCTGGATTTGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAGgttagcatagataacattttcactatttttttttcttct-tctaaattttattttacttgagagttttattctaatattctgtcattattatatttgcaca

upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 6
lower sequence: EFJ32217 (Selaginella moellendorffii), 5'ss of exon 6
AACAAGCTCAGAGGATCACTGAAGATCGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaacttccatt-----ctaaagcttcattttgatc-atgtatgcaccttatccataaacatactttgtttctgcag
|||  |||  | || || || ||||| |  |||||||| ||||| || ||||||||| | ||||| |||||  | || |||||||||||||| ||||||||| ||   |  ||   ||     | | ||  |  |  | ||| || | | || | ||                          
AACCGGCTTCGTGGCTCTCTCAAGATTGTGGCCATCAAGGCCCCAGGATTTGGAGAGAGGAAGACGCAGTATCTCGAGGATATTGCCATCCTCACTGGAGgtaagtagagttttttttgttttccagaggcttgtgcttatcgatttgtacatcgtag-------------------------

upper sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 6
lower sequence: EFJ16507 (Selaginella moellendorffii), 5'ss of exon 6
AACAAGCTCAGAGGATCACTGAAGATCGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaacttccattctaaagcttcattttgatcatgtatgcaccttatccataaacatactttgtttctgcag
|||  |||  | || || || ||||| |  |||||||| ||||| || ||||||||| | |||||||||||  | || |||||||||||||| ||||||||| ||   |  ||            ||  ||||    | |  ||  | ||||| ||    |||   |          
AACCGGCTTCGTGGCTCTCTCAAGATTGTGGCCATCAAGGCCCCAGGATTTGGAGAGAGGAAGACTCAGTATCTCGAGGATATTGCCATCCTCACTGGAGgtaaggagagttttt----------tttgttttccagaggcttgtgc-ttatcgatttgtatatcgtag--------

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|211389169|gb|FL356628.1|FL356628
EST:     TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTATCACTTGACAAGGCAGACAAAT
genomic: TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAAAT
EST: gi|211390791|gb|FL311861.1|FL311861
EST:     TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAGGGCCGACAATT
genomic: TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAAAT
EST: gi|32825197|gb|CD964919.1|CD964919
EST:     TGGAGAGCGGAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTATCACTTGACAAGGCCGACAAGT
genomic: TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAAAT
EST: gi|33094001|gb|CF053995.1|CF053995
EST:     GTACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTATCACTTGACAAGGCCGACAAGT
genomic: GTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAAAT
EST: gi|22545503|gb|BU097862.1|BU097862
EST:     TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAATT
genomic: TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAAAT
EST: gi|87156784|gb|DY401573.1|DY401573
EST:     TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAATT
genomic: TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAAAT
EST: gi|32935129|gb|CF039941.1|CF039941
EST:     TGGAGAGCGGAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTATCACTTGACATGGCCGACAAGT
genomic: TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAAAT
EST: gi|32823357|gb|CD963079.1|CD963079
EST:     TGGAGAGCGGAAGACTCAGTACTTGGATGATATTGCCTTCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTATCACTTGACAAGGCCGACAAGT
genomic: TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAAAT
EST: gi|24934364|gb|CA452582.1|CA452582
EST:     ACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAATT
genomic: ACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAAAT
EST: gi|211390788|gb|FL311858.1|FL311858
EST:     TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCNGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAATT
genomic: TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAAAT
EST: gi|23357758|gb|BU645407.1|BU645407
EST:     TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAATT
genomic: TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAAAT
EST: gi|32837828|gb|CD977506.1|CD977506
EST:     ACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTATCACTTGACAAGGCCGACAAGT
genomic: ACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAAAT
EST: gi|211420404|gb|FL361813.1|FL361813
EST:     TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAGGGCCGACAATT
genomic: TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAAAT
EST: gi|51592649|gb|CV071795.1|CV071795
EST:     TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTATCACTTGACAAGGCCGACAAGT
genomic: TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAAAT
EST: gi|211414113|gb|FL317428.1|FL317428
EST:     TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAGGGCCGACAATT
genomic: TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAAAT
EST: gi|60343427|gb|DN210400.1|DN210400
EST:     TGGAGAGCGGAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTATCACTTGACAAGGCCGACAAGT
genomic: TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAAAT
EST: gi|26558604|gb|CA830839.1|CA830839
EST:     TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAATT
genomic: TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAAAT
EST: gi|22545873|gb|BU098247.1|BU098247
EST:     TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAG                         CAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAATT
genomic: TGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAAAT

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), 48 (downstream exon)
Score: 533

AACAAGCTCAGAGGATCACTGAAGATCGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAAATCAGTTCTTGGAACAGCTGCAAAGGTTGTCCTTACGAAAGAGTCGACAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1682

AACAAGCTCAGAGGATCACTGAAGATCGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAAATCAGTTCTTGGAACAGCTGCAAAGGTTGTCCTTACGAAAGAGTCGACAAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 230

AACAAGCTCAGAGGATCACTGAAGATCGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAAATCAGTTCTTGGAACAGCTGCAAAGGTTGTCCTTACGAAAGAGTCGACAAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 662

AACAAGCTCAGAGGATCACTGAAGATCGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaa ... gtttctgcagCAACTGTAATCAGAGATGAAGTTGGGCTGTCACTTGACAAGGCCGACAAATCAGTTCTTGGAACAGCTGCAAAGGTTGTCCTTACGAAAGAGTCGACAAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACAAGCTCAGAGGATCACTGAAGATCGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaacttccattctaaagcttcattttgatcatgtatgcaccttatccataaacatactttgtttctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA