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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGGGCCCTGCTGGACCTTCTGGCAATGTTGCAAATTACATGGGACAAATGGCGATGGCTATGGGAAAACTTGGCACTCTTGAGAACTTTCTACGACAGgtttgtcatgcaaaatcatggacttgctcatttcataacactgtgccatctttattttccttaatttgctggctactctttgaggccttttatatagacc...

Basic information

species Zea mays
transcript GRMZM2G125243_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G125243_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os01g59350.2 (Oryza sativa), 5'ss of exon 10
CTTGGGCCCTGCTGGACCTTCTGGCAATGTTGCAAATTACATGGGACAAATGGCGATGGCTATGGGAAAACTTGGCACTCTTGAGAACTTTCTACGACAGgtttgtcatgcaaaatcatggacttgctcatttcataacactgtgccatctttattttccttaatttgctggctactctttgaggccttttatatagacc-
  | |||||||| ||| ||||||| ||||||||||| ||||||||||||||||| ||||||||||| |||||||| || || || ||||| ||||| |||||   |  |      | |    ||   | ||  | |     |||    ||  |||| | |    |    ||   | ||| |  |||   |    |  ||  
TCTCGGCCCTGCAGGATCTTCTGGTAATGTTGCAAACTACATGGGACAAATGGCAATGGCTATGGGGAAACTTGGTACCCTAGAAAACTTCCTACGGCAGgtaacttgtatttgcttacctcctattttataacctggt-ttgtttgttcaatattgttcgagttggtttgtgcaatctatttggctcatgcattgtactt

upper sequence: GRMZM2G125243_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA20G39050.1 (Glycine max), 5'ss of exon 11
-CTTGGGCCCTGCTGGACCTTCTGGCAATGTTGCAAATTACATGGGACAAATGGCGATGGCTATGGGAAAACTTGGCACTCTTGAGAACTTTCTACGACAGgtttgtcatgcaaaatca--tggacttgctcatttcataacactgtgccatctttattttccttaatttgctggctactctttgaggccttttatatagacc-----------------------------------------------------
 |||||  ||| ||||  | || |||||||| |||||||||||||| |||||||| ||||| ||||| ||||| || || ||||||   ||  |    |||||      | |  | |||  || ||  | ||| ||     || | | |       |  | |  |    | | |  |    |   ||    || ||||  | |                                                     
ACTTGGCTCCT-CTGGTTCATCAGGCAATGTGGCAAATTACATGGGTCAAATGGCTATGGCCATGGGTAAACTAGGGACACTTGAGGGGTTCATTAAGCAGgtaaacttttcttactcacatgtacgcgatcagtttggttcatttttctcaaagaaaatgctctttcatacagcatttcatggcagattattgatatcaaacatcactattaaaataacttagctctgttcatttttgtggtggtcatttgaaag

upper sequence: GRMZM2G125243_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA10G44270.1 (Glycine max), 5'ss of exon 9
-CTTGGGCCCTGCTGGACCTTCTGGCAATGTTGCAAATTACATGGGACAAATGGCGATGGCTATGGGAAAACTTGGCACTCTTGAGAACTTTCTACGACAGgtttgtcatgcaaaatcatggacttgc--tcatttcataacactgtgccatctttattttccttaatttgctggctactctttgaggccttttatatagacc--------------------------------------------------
 |||||  ||| ||||  | || |||||||| |||||||||||||| |||||||| ||||| ||||| ||||| || || ||||||   ||  |    ||||| ||   | |  | |||      |||  ||| ||    |||   | |       |  | |  |    | | |  |    |   ||    || |||   | |                                                  
ACTTGGCTCCT-CTGGTTCATCAGGCAATGTGGCAAATTACATGGGTCAAATGGCTATGGCCATGGGTAAACTAGGGACACTTGAGGGATTCATTAAGCAGgtatgcttttcttactcacatgtgtgcgatcagtttggtacatatttctcaaagaaaatgctctttcatacagcatttcatggcagattattgataacaaacatcactattaaaataacttggctctgtttatttttgtggtcatttgaaag

upper sequence: GRMZM2G125243_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA03G28320.1 (Glycine max), 5'ss of exon 11
CTTGGGCCCTGCTGGACCTTCTGGCAATGTTGCAAATTACATGGGACAAATGGCGATGGCTATGGGAAAACTTGGCACTCTTGAGAACTTTCTACGACAGgtttgtcatgcaaaatcatggacttgctcatttcataacactgtgccatctttattttccttaatttgctggctactctttgaggccttttatatagacc------
     || |  | ||  | || || ||||| |||||||||||||| |||||||| ||||| |||||||| ||||| || ||||||   ||||| |  |||||     | ||  | |    |   |  |  | |  |  ||   | |||||||| |       |     ||    |  ||||||    | | |  |  |        
GCCCAGCTCATCAGGCTCCTCGGGAAATGTGGCAAATTACATGGGGCAAATGGCTATGGCCATGGGAAAGCTTGGTACACTTGAGGGGTTTCTTCACCAGgt-----acgctcattttccggtctaattctgttttctcaac-ttccatctttttgaaataaagagaactcaggaagctttgaattatctgagtttaatttatatg

upper sequence: GRMZM2G125243_T02 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA15G37220.1 (Glycine max), 5'ss of exon 7
CTTGGGCCCTGCTGGACCTTCTGGCAATGTTGCAAATTACATGGGACAAATGGCGATGGCTATGGGAAAACTTGGCACTCTTGAGAACTTTCTACGACAGgtttgtcatgcaaaat--catggacttgctcatttcataacactgtgccatctttattttccttaatttgctggctactctttgaggccttttatatagacc
    | | |  ||||  | || || ||||| |||||||||||||| |||||||| ||||| ||||| || || || || |||||    ||  | | ||||||   |  | |    |  ||      | |  ||    |   ||  ||     |   |       ||| |  | |     | ||||   | |  ||||     
ACCTGCCTCATCTGGTTCATCAGGGAATGTGGCAAATTACATGGGTCAAATGGCCATGGCCATGGGTAAGCTAGGGACACTTGAAGGGTTCATTCAACAGgtacttttttctttgttgcacttgtatacaaatagtttgctacattggtgaataagtgaagaagaatcttttagtccagccttgatttccta-atattatt-

upper sequence: GRMZM2G125243_T02 (Zea mays), 5'ss of exon 12
lower sequence: EFJ18699 (Selaginella moellendorffii), 5'ss of exon 2
CTTGGGCCCTGCTGGACCTTCTGGCAATGTTGCAAATTACATGGGACAAATGGCGATGGCTATGGGAAAACTTGGCACTCTTGAGAACTTTCTACGACAGgtt-tgtcatgcaaaatcatggacttgctcatttcataacactgtgccatctttattttccttaatttgctggctactctttgaggccttttatatagacc
    ||| ||   |||   ||   ||| || || || ||||||||||||||||| ||||| |||||||| || || ||||| ||||||||| | || |||||   |  |  |   ||| |   ||| |||  |  ||||  || || |                                                     
TGCCGGCTCTCTGGGAAACTCCCCCAACGTAGCGAACTACATGGGACAAATGGCCATGGCAATGGGAAAGCTCGGAACTCTCGAGAACTTTGTTCGCCAGgtaacgcgagccgcgatctt--tctttctcgctg-ataattctttggcgcag-------------------------------------------------

upper sequence: GRMZM2G125243_T02 (Zea mays), 5'ss of exon 12
lower sequence: EFJ28227 (Selaginella moellendorffii), 5'ss of exon 7
-CTTGGGCCCTGCTGGACCTTCTGGC-AATGTTGCAAATTACATGGGACAAATGGCGATGGCTATGGGAAAACTTGGCACTCTTGAGAACTTTCTACGACAGgtttgtcatgcaaaatcatggacttgctcatttcataacactgtgccatctttattttccttaatttgctggctactctttgaggccttttatatagacc
   |||  |||  ||| |  |  | | ||||| || || || |||||||||||||||||||| |||||||| || || || || |||||||||         ||| | || |  |  | ||| |  || |  |||||  |     ||   |||  | |||||||    | |  |                            
GACTGGCTCCT--TGGGCGCTGCGTCGAATGTCGCCAACTATATGGGACAAATGGCGATGGCGATGGGAAAGCTGGGAACGCTCGAGAACTTT---------GTTCGCCAGgtgatgtgatgtatctg-tggtttcacgat----tgttgtctcaactttcctt---ctaccag----------------------------

upper sequence: GRMZM2G125243_T02 (Zea mays), 5'ss of exon 12
lower sequence: EFJ29724 (Selaginella moellendorffii), 5'ss of exon 7
-CTTGGGCCCTGCTGGACCTTCTGGC-AATGTTGCAAATTACATGGGACAAATGGCGATGGCTATGGGAAAACTTGGCACTCTTGAGAACTTTCTACGACAGgtttgtcatgcaaaatcatggacttgctcatttcataacactgtgccatctttattttccttaatttgctggctactctttgaggccttttatatagacc
   |||  |||  ||| |  |  | | ||||| || || || |||||||||||||||||||| |||||||| || || || || |||||||||         ||| | || |  |  | ||| |  || |  |||||  |     ||  ||||  | |||||||    | |  |                            
GACTGGCTCCT--TGGGCGCTGCGTCGAATGTCGCCAACTATATGGGACAAATGGCGATGGCGATGGGAAAGCTGGGAACGCTCGAGAACTTT---------GTTCGCCAGgtgatgtgatgtatctg-tggtttcaccat----tgttatctcaactttcctt---ctaccag----------------------------

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|32835771|gb|CD975449.1|CD975449
EST:     TGGCGATGGCTATGGGAAAACTTGGCACTCTTGAGAACTTTCTACGACAG                         GCTGATAATCTACGGCTGCAAACACTTCAACAAATGCAACGCATCTTAACT
genomic: TGGCGATGGCTATGGGAAAACTTGGCACTCTTGAGAACTTTCTACGACAGgtttgtcatg ... tcatctgcagGCTGATAATCTACGGCTGCAAACACTTCAACAAATGCAACGCATCTTAACT
EST: gi|32929944|gb|CF034756.1|CF034756
EST:     TGGCGATGGCTATGGGAAAACTTGGCACTCTTGAGACCTTTCTACGACAG                         GCTGATAATCTACGGCTGCAAACACTTCAACAAATGCAACGCATCTTAACT
genomic: TGGCGATGGCTATGGGAAAACTTGGCACTCTTGAGAACTTTCTACGACAGgtttgtcatg ... tcatctgcagGCTGATAATCTACGGCTGCAAACACTTCAACAAATGCAACGCATCTTAACT

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: 44 (upstream exon), 44 (downstream exon)
Score: 34

CTTGGGCCCTGCTGGACCTTCTGGCAATGTTGCAAATTACATGGGACAAATGGCGATGGCTATGGGAAAACTTGGCACTCTTGAGAACTTTCTACGACAGgtttgtcatg ... tcatctgcagGCTGATAATCTACGGCTGCAAACACTTCAACAAATGCAACGCATCTTAACTACCCGACAATCAGCACGAGCCCTACTCGCAATAAGTGACTACTTCTCTC


Block sizes: 39 (upstream exon), 45 (downstream exon)
Score: 43

CTTGGGCCCTGCTGGACCTTCTGGCAATGTTGCAAATTACATGGGACAAATGGCGATGGCTATGGGAAAACTTGGCACTCTTGAGAACTTTCTACGACAGgtttgtcatg ... tcatctgcagGCTGATAATCTACGGCTGCAAACACTTCAACAAATGCAACGCATCTTAACTACCCGACAATCAGCACGAGCCCTACTCGCAATAAGTGACTACTTCTCTC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 131

CTTGGGCCCTGCTGGACCTTCTGGCAATGTTGCAAATTACATGGGACAAATGGCGATGGCTATGGGAAAACTTGGCACTCTTGAGAACTTTCTACGACAGgtttgtcatg ... tcatctgcagGCTGATAATCTACGGCTGCAAACACTTCAACAAATGCAACGCATCTTAACTACCCGACAATCAGCACGAGCCCTACTCGCAATAAGTGACTACTTCTCTC


Block sizes: 39 (upstream exon), 44 (downstream exon)
Score: 16

CTTGGGCCCTGCTGGACCTTCTGGCAATGTTGCAAATTACATGGGACAAATGGCGATGGCTATGGGAAAACTTGGCACTCTTGAGAACTTTCTACGACAGgtttgtcatg ... tcatctgcagGCTGATAATCTACGGCTGCAAACACTTCAACAAATGCAACGCATCTTAACTACCCGACAATCAGCACGAGCCCTACTCGCAATAAGTGACTACTTCTCTC