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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTTCATTCACAAGCTCTAACAGAGAAAGTTGGGGCAGATGTTCATCTTTAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAGgtgacacattgcttcaattgcttgacaatttagttatccagtgtctgatacgaataccttaatcaaagctattgttgttactagttggcttctttctaacatgtgatatttaccacttcgatatcatcaatgaaaaaagattgtctgatctggttattggttcgtgcatcatag

Basic information

species Zea mays
transcript GRMZM2G081642_T04
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081642_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os02g10440.1 (Oryza sativa), 5'ss of exon 13
ATTTTCATTCACAAGCTCTAACAGAGAAAGTTGGGGCAGATGTTCATCTTTAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAGgtgacacattgcttcaattgcttgacaatttagttatccagtgtctgatacgaataccttaatcaaagctattgttgttactagttggcttctttctaacatgtgatatttaccacttcgatatcatcaatgaaaaaagattgtctgatctggttattggttcgtgcatcatag
    ||||  |||||||||||||||||||||||||| |||||||| |||||||| | ||| ||||| || |||||| | ||||||| || ||||||||| | |  |  |||| ||  || |||  |  || ||||     |||| |  ||  |||||  | |    ||  |   | | |   || |   || |    || || |                                                                      
---CTCATGTACAAGCTCTAACAGAGAAAGTTGGGGTAGATGTTCCTCTTTAGGGGGAGCTAGTGACGACTCATTCCCTGGCGATATTAGTGATAAGCAAGAGgtaagttgcctctcttacttccct-ttcagtttagttgtgtgtactaaaaatactatgaaagcaggcacattggatgtgaggtaa-ttatgataaatatttt---------------------------------------------------------------------

upper sequence: GRMZM2G081642_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA17G00770.1 (Glycine max), 5'ss of exon 13
---ATTTTCATTCACAAGCTCTAACAGAGAAAGTTGGGGCAGATGTTCATCTTTAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAGgtgacacattgcttcaattgcttgacaatttagttatccagtgtctgatacgaataccttaatcaaagctattgttgttactagttggcttctttctaacatgtgatatttaccacttcgatatcatcaatgaaaaaagattgtctgatctggttattggttcgtgcatcatag
    |  || | ||| ||||| ||||||||||||||||| |||||||| || |||||||    ||||||||||  ||  |  |  ||| |||        |||||     | |  |||   ||  |    |||  |  || |    | |  |   ||||      ||| |  || |  ||| |                                                                                              
TTGTTGCTCGTACACGAGCTCAAACAGAGAAAGTTGGGGAAGATGTTCTTCGTTAGGAG---GCAGTGATGAAGAATCTTGTGCAGATGATACCCTCTCTCAGgtacacaacttgttctgctgtattgtcatt--ggcatgcttcattt--tgtaaataataatgtcagaa-tactactgtgaag--------------------------------------------------------------------------------------------

upper sequence: GRMZM2G081642_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA07G40050.1 (Glycine max), 5'ss of exon 13
---ATTTTCATTCACAAGCTCTAACAGAGAAAGTTGGGGCAGATGTTCATCTTTAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAGgtgacacattgcttcaattgcttgacaatttagttatccagtgtctgatacgaataccttaatcaaagctattgttgttactagttggcttctttctaacatgtgatatttaccacttcgatatcatcaatgaaaaaagattgtctgatctggttattggttcgtgcatcatag
    |  ||||  || ||||| |||||||||||||||||||||||||| ||||||||||    ||||||||||   ||    |  ||| |||     |  ||||| |||| |    |  |   ||||      |   | ||  |||  |   | | |||  | |   |     |||||  ||  |                                                                                            
TTGTTGCTCATATACGAGCTCAAACAGAGAAAGTTGGGGCAGATGTTCTTCTTTAGGAG---GCAGTGATGAAGATTTAAGGGCTGATGATACCCTCACTCAGgt-acac-taaagtacacaacttgttctgctgtatgtct-gtgcttctcatggatatttcatctat--tcattgtcatttgtgaag----------------------------------------------------------------------------------------

upper sequence: GRMZM2G081642_T01 (Zea mays), 5'ss of exon 13
lower sequence: Vv00s0475g00050.t01 (Vitis vinifera), 5'ss of exon 6
ATTTTCATTCACAAGCTCTAACAGAGAAAGTTGGGGCAGATGTTCATCTTTAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAGgtgacacattgcttcaattgcttgacaatttagttatccagtgtctgatacgaataccttaatcaaagctattgttgttactagttggcttctttctaacatgtgatatttaccacttcgatatcatcaatgaaaaaagattgtctgatctggttattggttcgtgcatcatag
          |||||||| || ||||| |||||||| ||||| |||||||||||||    ||||||||||  |   || |  |||     ||   ||| | | |||     | |||  |   |  |  | |    |  ||     | |||    |  || ||| ||     || |||||  |  ||    |||   | | || |   |  |     || | | |                                                  
---------TACAAGCTCAAATAGAGAGAGTTGGGGAAGATGCTCATCTTTAGGAG---GCAGTGATGAAGAAACTTCTGCTGAT-----TGTGCAGCTGCTAACAATAGCCATCAGgtctctctctctct---cacacacatgttcataaagttttctaaataaa-----tttttgttgatcattcatatctcgtttatatatataagctttgggttgggtctg-------------------------------------------------

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|149069964|gb|EE158363.2|EE158363
EST:     TAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAG                         AATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
genomic: TAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAGgtgacacatt ... tgcatcatagAATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
EST: gi|211442455|gb|FL443592.1|FL443592
EST:     ATGAATCATTCTCAGGCGATAATAATGATAASCAG                         AATTTGMCAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
genomic: ATGAATCATTCTCAGGCGATAATAATGATAAGCAGgtgacacatt ... tgcatcatagAATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
EST: gi|32858949|gb|CD998630.1|CD998630
EST:     TAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAG                         AATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
genomic: TAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAGgtgacacatt ... tgcatcatagAATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
EST: gi|21480872|gb|BQ577555.1|BQ577555
EST:     CTCAGGCGATAATAATGATAAGCAG                         AATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
genomic: CTCAGGCGATAATAATGATAAGCAGgtgacacatt ... tgcatcatagAATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
EST: gi|71757857|gb|DR955794.1|DR955794
EST:     TAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAG                         AATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
genomic: TAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAGgtgacacatt ... tgcatcatagAATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
EST: gi|5915152|gb|AW052793.1|AW052793
EST:     TAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAG                         AATTTGACAG-CAAGG
genomic: TAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAGgtgacacatt ... tgcatcatagAATTTGACAGTCAAGG
EST: gi|21480742|gb|BQ577425.1|BQ577425
EST:     CTCAGGCGATAATAATGATAAGCAG                         AATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
genomic: CTCAGGCGATAATAATGATAAGCAGgtgacacatt ... tgcatcatagAATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
EST: gi|21481154|gb|BQ577837.1|BQ577837
EST:     TAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAG                         AATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
genomic: TAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAGgtgacacatt ... tgcatcatagAATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
EST: gi|32870183|gb|CF009865.1|CF009865
EST:     TAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAG                         AATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
genomic: TAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAGgtgacacatt ... tgcatcatagAATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
EST: gi|21236632|gb|BQ442044.1|BQ442044
EST:     TAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAG                         AATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
genomic: TAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAGgtgacacatt ... tgcatcatagAATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
EST: gi|17932105|gb|BM269065.1|BM269065
EST:     AGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAG                         AATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
genomic: AGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAGgtgacacatt ... tgcatcatagAATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
EST: gi|5804604|gb|AI979574.1|AI979574
EST:     TAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAG                         AATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
genomic: TAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAGgtgacacatt ... tgcatcatagAATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
EST: gi|21481331|gb|BQ578014.1|BQ578014
EST:     CTCAGGCGATAATAATGATAAGCAG                         AATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
genomic: CTCAGGCGATAATAATGATAAGCAGgtgacacatt ... tgcatcatagAATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
EST: gi|21329781|gb|BQ485162.1|BQ485162
EST:     TAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAG                         AATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
genomic: TAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAGgtgacacatt ... tgcatcatagAATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
EST: gi|211442456|gb|FL443593.1|FL443593
EST:     CAGGCGATAATAATGATAAGCAG                         AATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
genomic: CAGGCGATAATAATGATAAGCAGgtgacacatt ... tgcatcatagAATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
EST: gi|78125549|gb|DV543933.1|DV543933
EST:     TAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAG                         AATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
genomic: TAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAGgtgacacatt ... tgcatcatagAATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
EST: gi|211126998|gb|FL461335.1|FL461335
EST:     TAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAG                         AATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
genomic: TAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAGgtgacacatt ... tgcatcatagAATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
EST: gi|32870184|gb|CF009866.1|CF009866
EST:     TAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAG                         AATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA
genomic: TAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAGgtgacacatt ... tgcatcatagAATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAA

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: 47 (upstream exon), 45 (downstream exon)
Score: 100

ATTTTCATTCACAAGCTCTAACAGAGAAAGTTGGGGCAGATGTTCATCTTTAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAGgtgacacatt ... tgcatcatagAATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAAAGCCAGAGGAAACCGATTGAGAAAGCTAAGCAGAAGAAGATTCAAGCCC


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 55

ATTTTCATTCACAAGCTCTAACAGAGAAAGTTGGGGCAGATGTTCATCTTTAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAGgtgacacatt ... tgcatcatagAATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAAAGCCAGAGGAAACCGATTGAGAAAGCTAAGCAGAAGAAGATTCAAGCCC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 33

ATTTTCATTCACAAGCTCTAACAGAGAAAGTTGGGGCAGATGTTCATCTTTAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAGgtgacacatt ... tgcatcatagAATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAAAGCCAGAGGAAACCGATTGAGAAAGCTAAGCAGAAGAAGATTCAAGCCC


Block sizes: 46 (upstream exon), 43 (downstream exon)
Score: 51

ATTTTCATTCACAAGCTCTAACAGAGAAAGTTGGGGCAGATGTTCATCTTTAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAGgtgacacatt ... tgcatcatagAATTTGACAGTCAAGGCTTTGGCTACGCCTGTAAGACAAAACCAGAGGCAAAGCCAGAGGAAACCGATTGAGAAAGCTAAGCAGAAGAAGATTCAAGCCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTTCATTCACAAGCTCTAACAGAGAAAGTTGGGGCAGATGTTCATCTTTAGGAGCAGCCAGTGATGAATCATTCTCAGGCGATAATAATGATAAGCAGgtgacacattgcttcaattgcttgacaatttagttatccagtgtctgatacgaataccttaatcaaagctattgttgttactagttggcttctttctaacatgtgatatttaccacttcgatatcatcaatgaaaaaagattgtctgatctggttattggttcgtgcatcatag

- - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG