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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctaattccttatttatttcagttacttagcagttcattggcatgaacttctttgcatataccgtgttgcgtagcatctggacctggacgggtgccaaaatttcgtctcttgcctaacgcgattctttttcttctctcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA

Basic information

species Zea mays
transcript GRMZM2G333433_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G333433_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g47180.1 (Oryza sativa), 3'ss of exon 6
--gtatgctaattccttatttatttcagttacttagcagttcattggcatgaacttctttgcatataccgtgttgcgtagcatctggacctggacgggtgccaaaatttcgtctcttgcctaacgcgattctttttcttctctcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA
   | ||||  ||  |   | ||||||||| || |   ||||||| |||||| |             ||    |  | | |||     ||| ||    ||  ||  |  |  |||       || ||||  |    |||          |||||||||||  | ||||| ||||||||||| ||||||||||| |||||||||||||| || |||||||| ||||| || || | ||| ||||| ||||| |
gtatgtgcttttttttggctgatttcagttgctcatttgttcatttgcatgatcc-----------gccacaatcagaaacatact--cctagaacaatgttaagctcacagctc-------actcgatcgtacaactt---------gcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA

upper sequence: GRMZM2G333433_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g47180.2 (Oryza sativa), 3'ss of exon 6
gtatgctaattccttatttatttcagttacttagcagttcattggcatgaacttctttgcatataccgtgttgcgtagcatctggacctggacgggtgccaaaatttcgtctcttgcctaacgcgattctttttcttctctcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA
   ||||  ||  |   | ||||||||| || |   ||||||| |||||| |             ||    |  | | |||     ||| ||    ||  ||  |  |  |||       || ||||  |    |||          |||||||||||  | ||||| ||||||||||| ||||||||||| |||||||||||||| || |||||||| ||||| || || | ||| ||||| ||||| |
--gtgcttttttttggctgatttcagttgctcatttgttcatttgcatgatcc-----------gccacaatcagaaacatact--cctagaacaatgttaagctcacagctc-------actcgatcgtacaactt---------gcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA

upper sequence: GRMZM2G333433_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G38140.1 (Glycine max), 3'ss of exon 6
gtatgctaattccttatttatttcagttacttagcagttcattggcatgaacttctttgcatataccgtgttgcgtagcatctggacctggacgggtgccaaaatttcgtctcttgcctaacgcgattctttttcttctctcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA
                                        ||    ||  |  | | |  ||| |  | ||||  |   ||||   | |       || |  ||| | ||            |  ||  ||  |   ||||  | |||||| | |  |  || |||| |||||||||||||||||||||||||| ||||| ||||| || ||| | || ||  | || |||| ||| ||||| | |||  
--------------------------------------atatatatatatatatatatatatacatggggttggttcatatctcagcttacttttatgtcttaatcttgta-----------gtaatggttgcttaactcttat-tacagAGATGGCGACTGGTAACACATGCAAATGCTAAGAGCAAGAGCGAGAAGTTTCCTCCTCCTCATGAAGATGGAACTCTAGGCTATCCTTTGGGTTCTTCAC

upper sequence: GRMZM2G333433_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G28650.1 (Glycine max), 3'ss of exon 6
gtatgctaattccttatttatttcagttacttagcagttcattggcatgaacttctttgcatataccgtgttgcgtagcatctggacctggacgggtgccaaaatttcgtctcttgcctaacgcgattctttttcttctctcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA
                                            | ||   || | | | |  |   | |||    |  ||    |  ||      |   | |  ||    |  ||   |||    ||  | |||  ||||   || |||| | |  || |||| || ||||||||||||||||||||||| || ||||| ||||| || || || || || || || |||| ||| ||||| | |||  
--------------------------------------------gtatattctacgtggaaattttggggttatccaagat----aattgtgtta-tattacagcttttcttagtgtagaacagtgttaatgttcagctctta-ctgcagAGACGGCGGCTGATCACACATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCCCACCAAGATGGAGCTCTAGGCTATCCTTTGGGTTCTTCAC

upper sequence: GRMZM2G333433_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA20G37360.1 (Glycine max), 3'ss of exon 6
gtatgctaa------ttccttatttatttcagttacttagcagt-------tcattggcatgaacttc-tttgcatataccgtgttgcgtagcatctggacctg-gacgggtgccaaaatttcgtctcttgcctaacgcgattctttttcttctctcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA
||||| |||      || ||| | |  ||   |  ||| | | |       || ||   || || ||| |||   | |    |  |    |   | |  |  || ||  |     | ||  |      |     ||      |    |  ||   |     ||||| |||  | || || |||||||||||||||||||||||||| |||||||| |||||||| ||| | || ||   ||| |||||||| ||||| | ||| |
gtatgttaaagaaatttacttctattgtttgatgcctttgtactgcttctatccttctaataaaattcatttttgttttttataattgaaaatctgtataattgtgattgaaagtataaaattaatgttgattaaaatttgctgcaatgatttcatgtgtaacagAGAAGGCGTTTAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTACCTCCACCACATGAAGATGGACAGCTTGGCTTTCCTTTGGGATCTTCTA

upper sequence: GRMZM2G333433_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA03G40330.1 (Glycine max), 3'ss of exon 6
gtatgctaattccttatttatttcagttacttagcagttcattggcatgaacttctttgca-tataccgtgt-tgcgtagcatctggacctggacgggtgccaaaatttcgtctcttgcctaacgcgattctttttcttctctcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA
                                               |||  |  ||| || || |  || | ||| |   |  || | |  | |      ||||| |         |  |||     ||  | |  ||   ||    ||||| |||| |  | || |||||||||||||| ||||||||||| ||||||||||||||||| ||||| || ||     | || ||||| ||||| | |||  
---------------------------------------------actgatttattttacaatacaaagtatctgcatgataa-tgcatccagtcaaaactcaaaagtaaa------gattaaatttgttactatgatttcttctgtaacagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTCCCTCCACCACATCAAGATGGACAAGTTGGTTTTCCTTTGGGATCTTCAC

upper sequence: GRMZM2G333433_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA19G42960.1 (Glycine max), 3'ss of exon 5
gtatgctaattccttatttatttcagttacttagcagttcattggcatgaacttct---ttgca-tataccgtgt-tgcgtagcatctggacctggacgggtgccaaaatttcgtctcttgcctaacgcgattctttttcttctctcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA
                                         ||   |||||||  |   || || || |  || | ||| | | || || | |  | |    |  || |||   | | || |       ||||  || | |          ||||| |||| |  | || |||||||||||||| |||||||||||||||||||| |||||||| ||||| || ||     | || ||||| || || | |||  
-----------------------------------------ttctaatgaactcttattttacaatagaaagtatatgcat-gaatatgcatccagtcaaaagtaaagattaaatttgttac----tatgatttcttgtgta---------acagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTTCCTCCACCACATCAAGATGGACAAGTTGGTTTTCCTTTAGGATCTTCAC

upper sequence: GRMZM2G333433_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G02580.1 (Glycine max), 3'ss of exon 6
gtatgctaattccttatttatttcagttacttagcagttcattggcatgaacttctttgcatataccgtgttgcgtagcatctggacctggacgggtgccaaaatttcgtctcttgcctaacgcgattctttttcttctctcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA
                                     |  | |||||| ||  | | |  ||| |  | ||||  |   ||||  || |             | |||  | ||||   ||  |   |  |  ||   ||||  | |||||| | |  |  || |||| ||||||||||||||||||||||| || ||||| ||||| || ||  | || ||  | || |||| ||| ||||| | |||  
-----------------------------------cataaagtggcatcaatatatatatatacatggagttggttcatatctcaactt-------------acttttatgtcttaa-tattgtagtaatggtttaactcttat-tacagAGATGGCGACTGGTAACGCATGCAAATGCTAAGAGCAAGAGTGAGAAGTTTCCTCCTCCTCACGAAGATGGAACTCTTGGCTATCCTTTGGGTTCTTCAC

upper sequence: GRMZM2G333433_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA10G30030.1 (Glycine max), 3'ss of exon 6
gtatgctaa------ttccttat-ttatttca-gttacttagcag-----ttcattggcatgaacttctttg-catataccgtgttgcgtagc-atctggacctggacgggtgccaaaatttcgtctcttgcctaacgcgattctttttcttctctcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA
||||| |||      || ||| | || ||| | |    | | | |     ||| ||   || || ||| ||  ||| |    | |||   | |  | | |   ||   |   |   |||  |   |  |     ||      |    |  ||   |     ||||| |||  | || || |||||||||||||||||||||||||| ||||||||||||||||| ||| | || ||   ||| |||||||| ||||| | ||| |
gtatgttaaagaaatttacttctattgttttatgcctttgaactgctgctttccttctaataaaattcattatcatttttattattgaaaatctgtatagttgtgattgaaagtataaaactaa-cgttgattaaaatttgctgcaatgatttcatgtgtaacagAGAAGGCGTTTAATCACTCATGCAAATGCTAAGAGCAAGAGTGAAAAGTTCCCTCCACCACATGAAGATGGACAGCTTGGCTTTCCTTTGGGATCTTCTA

upper sequence: GRMZM2G333433_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT3G05050.1 (Arabidopsis thaliana), 3'ss of exon 7
gtatgctaattccttatttatttcagttacttagcagttcattggcatgaacttctttgcatataccgtgttgcgta-gcatctggacctggacgggtgccaaaatttcgtctcttgcctaacgcgattctttttcttctctcctct----acagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA
                                                                          ||| | || |  | |   |   |     ||  || |  |  |   |  |  || |  |||     | | ||||    |||||  |   |  |||| || || || ||||| |||||||||||||| ||||| |||||||||||||| |||||  | ||||| ||||   |||| | ||| |
--------------------------------------------------------------------------gtaagaatttaaaacaaaaaaagaagtgaatctttgattggttaatgtcttgagtactttgaacttgttctcttaaaacagAGGATGCGTATGATCACACACGCGAATGCAAAGAGCAAGAGCGAGAAGTTTCCTCCACCGCATCAAGACGGGTCACTCGGTTTTCAGGTGGGATCTTCAA

upper sequence: GRMZM2G333433_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv05s0020g01890.t01 (Vitis vinifera), 3'ss of exon 6
gtatgctaattccttatttatttcagttacttagcagttcattggcatgaacttctttgcatataccgtgttgcgtagcatctggacctggacgggtgccaaaatttcgtctcttgcctaacgcgattctttttcttctctcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA
                                         |   ||||    ||    ||||||   | |||   | ||  | |     ||    ||   |  ||     | |||  |   ||  |  | | ||| |  | ||  |||||   || |  | ||||||||||||||||| ||||||||||| |||||||| ||||| || || ||||| ||  | || ||||  || ||||| | |||  
---------------------------------------tttcatcatgtggctc----catata--attttgttgatcaagttggttctgatacttgt--agtttgtagattttgatt---gctgtcttatatctccatttctaaacagAGGCGACGTCTAATAACTCATGCAAATGCCAAGAGCAAGAGTGAAAAGTTTCCTCCCCCACACCAGGATGGAACCCTTGGCTACCCATTGGGTTCTTCAC

upper sequence: GRMZM2G333433_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv14s0030g01260.t01 (Vitis vinifera), 3'ss of exon 9
gtatgctaattccttatttatttcagttacttagcagttcattggcatgaacttctttgcatataccgtgttgcgtagcatctggacctggacgggtgccaaaatttcgtctcttgcctaacgcgattctttttcttctctcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA
                                                || ||| | |   | |    ||||    | || | |   |    |     ||| | ||   |   |||   ||   | ||    |  |||| ||    ||||  |||| |  | ||  | ||||||||||| ||||| ||||| |||||||| |||||||| || |||||||| ||  | ||||| ||||||||   |||  
--------------------------------------------ttgagagcttttgtttcttttttatgtttgcaatcacccgagtccttgca---accagagttcgattgtttg---aatttgttttccgtgtttctttctgaaacagCGAAGACGCCTAATCTCCCATGCAAATGCAAAGAGTAAGAGTGAAAAGTTTCCTCCACCTCACCAGGACGGAGCAGTTGGCTTCCCCTTGGGTGCTTCAC

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|211438201|gb|FL348381.1|FL348381
EST:     GGGCTGTTCCAGCGCCAGAGGCAAACGCCGAACTGCAAGCAAACATTGAT                         AAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTC
genomic: GGGCTGTTCCAGCGCCAGAGGCAAACGCCGAACTGCAAGCAAACATTGATgtatgctaat ... tcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTC
EST: gi|149106632|gb|EE188525.2|EE188525
EST:     GGGCTGTTCCAGCGCCAGAGGCAAACGCCGAACTGCAAGCAAACATTGAT                         AAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTC
genomic: GGGCTGTTCCAGCGCCAGAGGCAAACGCCGAACTGCAAGCAAACATTGATgtatgctaat ... tcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTC

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: 60

TAGAGGTAACGGAGATGGAACAAGGAAGACAAGGACACGGGATCGGCCTAGGGCTGTTCCAGCGCCAGAGGCAAACGCCGAACTGCAAGCAAACATTGATgtatgctaat ... tcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 30

TAGAGGTAACGGAGATGGAACAAGGAAGACAAGGACACGGGATCGGCCTAGGGCTGTTCCAGCGCCAGAGGCAAACGCCGAACTGCAAGCAAACATTGATgtatgctaat ... tcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 32

TAGAGGTAACGGAGATGGAACAAGGAAGACAAGGACACGGGATCGGCCTAGGGCTGTTCCAGCGCCAGAGGCAAACGCCGAACTGCAAGCAAACATTGATgtatgctaat ... tcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 62

TAGAGGTAACGGAGATGGAACAAGGAAGACAAGGACACGGGATCGGCCTAGGGCTGTTCCAGCGCCAGAGGCAAACGCCGAACTGCAAGCAAACATTGATgtatgctaat ... tcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgccaaaatttcgtctcttgcctaacgcgattctttttcttctctcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA
                    gcctaac  putative branch site (score: 62)
                          cgcgattctttttctt  CT-rich tract
                              attcttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctaattccttatttatttcagttacttagcagttcattggcatgaacttctttgcatataccgtgttgcgtagcatctggacctggacgggtgccaaaatttcgtctcttgcctaacgcgattctttttcttctctcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT