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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTTCGTCTTCTGGATCAACAGGAAATGTGGCAAACTACATGGGTCAAATGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccctcttttccaaatgcatctttgtgacatagataaagggttctgtgaatgattgtactccctcccaaaaagaatgctcatcttgcatttcag...

Basic information

species Zea mays
transcript GRMZM2G030280_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os01g17260.1 (Oryza sativa), 5'ss of exon 9
TCTTTCGTCTTCTGGATCAACAGGAAATGTGGCAAACTACATGGGTCAAATGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccctcttttccaaatgcatctttgtgacatagataaagggttctgtgaatgattgtactccctc-----ccaaaaagaatgctcatcttgcatttcag---------------------------------------------------------
||||   |||||||||||||| ||||| ||||||||||||||||| |||||||| ||||| ||||| || ||||| || ||||||||||||||||| ||||||  |    | || ||    | |   ||| |    || || | |  |        ||  | || ||         |||   || |||        | |||  ||                                                         
TCTTGGTTCTTCTGGATCAACGGGAAACGTGGCAAACTACATGGGCCAAATGGCAATGGCCATGGGGAAGCTTGGGACCCTTGAGAATTTCCTTCGCCAGgtaccatgttttttctctctct-ctcttttctagtgtaaattatgtatgtaaaccttgggtatagtcttatgatgtccatggagtatgtagtatgcggattcgagtaaactatagttcaaaattgtgtactaaatcctctttatcttttccactatatgaag

upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA20G39050.1 (Glycine max), 5'ss of exon 11
TCTTTCGTCTTCTGGATCAACAGGAAATGTGGCAAACTACATGGGTCAAATGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccctcttttccaaatgcatctttgtgacatagataaagggttctgtgaatgattgtactccctcccaaaa---------agaatgctcatcttgcatttcag------------------------------------------------
 |||   || ||||| ||| |||| ||||||||||| ||||||||||||||||| ||||| ||||| ||||| || || ||||||   ||| ||   ||||||  |    ||||   || ||| | |    | |  | | |  |   ||||   |   | ||  ||  |   ||  |         ||| |  | || |   |  |||                                                 
ACTTGGCTCCTCTGGTTCATCAGGCAATGTGGCAAATTACATGGGTCAAATGGCTATGGCCATGGGTAAACTAGGGACACTTGAGGGGTTCATTAAGCAGgtaa-acttttcttactcacatgta-cgcgatcagtttggttcatttttctcaaagaaaatgctctttcatacagcatttcatggcagattattgatatcaaacatcactattaaaataacttagctctgttcatttttgtggtggtcatttgaaag

upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA03G28400.1 (Glycine max), 5'ss of exon 5
TCTTTCGTCTTCTGGATCAACAGGAAATGTGGCAAACTACATGGGTCAAATGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtat--taaccctcttttccaaatgcatctttgtgacatagataaagggttctgtgaatgattgtactccc----tcccaaaaagaatgctcatcttgcatttcag
 |     || || || ||  | ||||||||||||||  |||||||||||||  | ||||| |||||||| ||||| || ||||||   || ||||  ||||||   | |   ||   || || |   | ||    || |  ||      || ||  |   |  | ||||           ||   | ||    |  |  ||||   
GCCCAGCTCATCAGGCTCCCCGGGAAATGTGGCAAATAACATGGGTCAAATAACTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCTCCAGgtacgctcattttccggtctaattctgttttctcaacttccatct----ttttgaaataaagagaactcaggaagctttgaattaactgagtttaatttatttg--

upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA19G31050.2 (Glycine max), 5'ss of exon 9
TCTTTCGTCTTCTGGATCAACAGGAAATGTGGCAAACTACATGGGTCAAATGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccctcttttccaaatgcatctttgtgacatagataaagggttctgtgaatgattgtactccctcccaaaaagaatgctca---tcttgcatttcag-
 |      | || || ||  | |||||||||||||  |||||||| |||||||| ||||| |||||||| ||||| || |||||    || ||||| |||||    || ||| ||| |   |  |  | |||    |  |        | | ||||  |  |   |       |   || | ||| |   |   |    | |  
ACCCAGCACATCAGGCTCCTCGGGAAATGTGGCAAGTTACATGGGGCAAATGGCTATGGCCATGGGAAAGCTTGGTACTCTTGATGGGTTTCTTCGCCAGgt----acgctcattttccggtctaattctgttttctcaacttccatctttttgaaataaagagataaagagaactcaggaagcttagaattaagtgagttaaa

upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA10G44270.1 (Glycine max), 5'ss of exon 9
TCTTTCGTCTTCTGGATCAACAGGAAATGTGGCAAACTACATGGGTCAAATGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccctcttttccaaatgcatctttgtgacatagataaagggttctgtgaatgattgtactccctcccaaaa---------agaatgctcatcttgcatttcag---------------------------------------------
 |||   || ||||| ||| |||| ||||||||||| ||||||||||||||||| ||||| ||||| ||||| || || ||||||   ||| ||   |||||||      ||||   || |||  |     | |  | | || |   ||||   |   | ||  ||  |   ||  |         ||| |  | ||     |  |||                                              
ACTTGGCTCCTCTGGTTCATCAGGCAATGTGGCAAATTACATGGGTCAAATGGCTATGGCCATGGGTAAACTAGGGACACTTGAGGGATTCATTAAGCAGgtat-gcttttcttactcacatgtgtgcg-atcagtttggtacatatttctcaaagaaaatgctctttcatacagcatttcatggcagattattgataacaaacatcactattaaaataacttggctctgtttatttttgtggtcatttgaaag

upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA03G28320.1 (Glycine max), 5'ss of exon 11
TCTTTCGTCTTCTGGATCAACAGGAAATGTGGCAAACTACATGGGTCAAATGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtat--taaccctcttttccaaatgcatctttgtgacatagataaagggttctgtgaatgattgtactccctcccaaaaagaatgctcatcttgcatttcag--
 |     || || || ||  | |||||||||||||| |||||||| |||||||| ||||| |||||||| ||||| || ||||||   || ||||  ||||||   | |   ||   || || |   | ||    || |  ||      || ||  |   |  | ||||            | |       ||  ||||     
GCCCAGCTCATCAGGCTCCTCGGGAAATGTGGCAAATTACATGGGGCAAATGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAGgtacgctcattttccggtctaattctgttttctcaacttccatct----ttttgaaataaagagaactcaggaagctttgaattatctgagtttaatttatatg

upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA13G26280.1 (Glycine max), 5'ss of exon 11
TCTTTCGTCTTCTGGATCAACAGGAAATGTGGCAAACTACATGGGTCAAATGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccctcttttccaaatgcatctttgtgaca-tagataaagggttctgtgaatgattgt--actccctcccaaaaagaatgctcatcttgcatttcag--
 | | | || ||||| ||| |||| ||||||||||  ||||||||||||||||||||||| ||||| || || || || || ||    ||| |||  ||||||   |  ||  |||     ||||  | | || || ||| |    |  |  ||||||   ||   ||         |    |    | || |   | |      
ACCTGCCTCATCTGGTTCATCAGGGAATGTGGCAAGTTACATGGGTCAAATGGCCATGGCCATGGGCAAGCTAGGGACACTAGAAGGGTTCATTCAACAGgtac--attcttctttgt---tgcacttgtatgccaatagtttgctgcattagtgaataggtgaggacgagtcttttagtccagccttgatttcctaatattatt

upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA15G37220.1 (Glycine max), 5'ss of exon 7
TCTTTCGTCTTCTGGATCAACAGGAAATGTGGCAAACTACATGGGTCAAATGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgta-ttaaccctcttttccaaatgcatctttgtgacat---agataaagggttctgtgaatgattgtactccctcccaaaaagaatgctcatcttgcatttcag
 | | | || ||||| ||| |||| ||||||||||| ||||||||||||||||||||||| ||||| || || || || |||||    ||| |||  |||||| ||    || | || ||  || ||     |    |   | ||    |  |  |||||  |   |  |     |||      ||   |   |   |||    
ACCTGCCTCATCTGGTTCATCAGGGAATGTGGCAAATTACATGGGTCAAATGGCCATGGCCATGGGTAAGCTAGGGACACTTGAAGGGTTCATTCAACAGgtacttttttctttgttgcacttgtatacaaatagtttgctacattggtgaataagtgaagaagaatcttttagtccagccttgatttcctaatattatt----

upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 8
lower sequence: AT5G06950.3 (Arabidopsis thaliana), 5'ss of exon 9
-TCTTTCGTCTTCTGGATCAACAGGAAATGTGGCAAACTACATGGGTCAAATGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccctct----tttccaaatg-catctttgtgaca--tagataaagggttctgtgaatgattgtactccctcccaaaaagaatgctcatcttgcatttcag
  || | |  |||  | ||| |||| ||||| |||| |||||||||||| ||||||||||| ||||||||  | || || || ||    ||  | || ||||||  |  | | |    |||  | |||  ||||| || |    || ||| |    ||  |   | | |   |  |             ||                 
GACTCTTGG-TTCAAGTTCATCAGGGAATGTCGCAAGCTACATGGGTCAGATGGCCATGGCAATGGGAAAGTTAGGTACACTCGAAGGATTTATCCGCCAGgtacaacacttgtgatgttttgagatgatatcttagttaagagtatatatatatatcaataggttaataatcgtctcttggttggtggtggcag-------------

upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 8
lower sequence: Vv13s0084g00660.t01 (Vitis vinifera), 5'ss of exon 11
TCTTTCGTCTTCTGGATCAACAGGAAATGTGGCAAACTACATGGGTCAAATGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccctcttttccaaatgcatctttgtgaca-tagataaagggttctgtgaatgattgtactccctcccaaaaagaatgctcatcttgcatttcag
||||   |||||||| ||| | ||||||||||||||||| |||||||||||||||||||| |||||||| || || || ||||||   ||  |||||||||||||    ||    |    ||     ||  ||||| ||   | |   |  ||   || ||| |  ||  |     |   |      |  | | |  |   
TCTTGGCTCTTCTGGTTCATCTGGAAATGTGGCAAACTATATGGGTCAAATGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAGgtattccttctaaagttttgattttctttcctgacaataagaataaaatcttgatcat-attatggtctgtttatgatcaaccagaaagttaggaaatgga

upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 8
lower sequence: Vv08s0007g05170.t01 (Vitis vinifera), 5'ss of exon 10
TCTTTCGTCTTCTGGATCAACAGGAAATGTGGCAAACTACATGGGTCAAATGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccctcttttccaaatgcatctttgtgacatagataaagggttctgtgaatgattgtactccctcccaaaaagaatgctcatcttgcatttcag------
 | |    | ||||||||| |||| |||||||||||||| ||||| || ||||||||||| ||||| || || || || ||||||   || |||||||||||| |  |||| ||     | || |  |   ||  |   || ||   ||   || || |  | | |     | || || | |  | || ||   |||         
ACCTGGCCCATCTGGATCATCAGGGAATGTGGCAAACTATATGGGCCAGATGGCCATGGCAATGGGTAAGCTAGGGACTCTTGAGGGATTTCTTCGTCAGgtaatctcccttttagtttagtggaagt---tgtaaggaatgaaaacttgaatgcatca--gcagtggtggcaaataaaattatttat-ttattttttgctatcaa

upper sequence: GRMZM2G030280_T02 (Zea mays), 5'ss of exon 8
lower sequence: EFJ18699 (Selaginella moellendorffii), 5'ss of exon 2
TCTTTCGTCTTCTGGATCAACAGGAAATGTGGCAAACTACATGGGTCAAATGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccctcttttccaaatgcatctttgtgacatagataaagggttctgtgaatgattgtactccctcccaaaaagaatgctcatcttgcatttcag
|      |||   |||    |    || || || ||||||||||| |||||||||||||| |||||||| || ||||| || ||||| ||  |||| ||||||        |    |   ||   ||||| |  |   |||||    |||| ||    |                                         
TGCCGGCTCTCTGGGAAACTCCCCCAACGTAGCGAACTACATGGGACAAATGGCCATGGCAATGGGAAAGCTCGGAACTCTCGAGAACTTTGTTCGCCAGgtaacg-----cgagccgcgatctttctttct--cgctgataa----ttctttggcgcag----------------------------------------

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|74232818|gb|DT640732.1|DT640732
EST:     TGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAG                         ACTCTACAACAGATGCAAAGGATCCTGACCACTAGACAGTCAGCTCGGGCG
genomic: TGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccc ... gcggctgcagACTCTACAACAGATGCAAAGGATCCTGACCACTAGACAGTCAGCTCGGGCG
EST: gi|211307998|gb|FL442646.1|FL442646
EST:     TGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAG                         ACTCTACAACAGATGCAAAGGATCCTGACCACTAGACAGTCAGCTCGGGCG
genomic: TGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccc ... gcggctgcagACTCTACAACAGATGCAAAGGATCCTGACCACTAGACAGTCAGCTCGGGCG

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: 122

TCTTTCGTCTTCTGGATCAACAGGAAATGTGGCAAACTACATGGGTCAAATGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccc ... gcggctgcagACTCTACAACAGATGCAAAGGATCCTGACCACTAGACAGTCAGCTCGGGCGCTACTTGTGATAAGTGATTACTCTTCACGTCTCCGTGCCCTAAGCTCTC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 34

TCTTTCGTCTTCTGGATCAACAGGAAATGTGGCAAACTACATGGGTCAAATGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccc ... gcggctgcagACTCTACAACAGATGCAAAGGATCCTGACCACTAGACAGTCAGCTCGGGCGCTACTTGTGATAAGTGATTACTCTTCACGTCTCCGTGCCCTAAGCTCTC


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 25

TCTTTCGTCTTCTGGATCAACAGGAAATGTGGCAAACTACATGGGTCAAATGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccc ... gcggctgcagACTCTACAACAGATGCAAAGGATCCTGACCACTAGACAGTCAGCTCGGGCGCTACTTGTGATAAGTGATTACTCTTCACGTCTCCGTGCCCTAAGCTCTC


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

TCTTTCGTCTTCTGGATCAACAGGAAATGTGGCAAACTACATGGGTCAAATGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccc ... gcggctgcagACTCTACAACAGATGCAAAGGATCCTGACCACTAGACAGTCAGCTCGGGCGCTACTTGTGATAAGTGATTACTCTTCACGTCTCCGTGCCCTAAGCTCTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTTCGTCTTCTGGATCAACAGGAAATGTGGCAAACTACATGGGTCAAATGGCCATGGCTATGGGAAAACTTGGAACGCTTGAGAATTTCCTTCGTCAGgtattaaccctcttttccaaatgcatctttgtgacatagataaagggttctgtgaatgattgtactccctcccaaaaagaatgctcatcttgcatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agataaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaagaa