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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTAGGTTAAAGAGATACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGGgtttgtgatctgctttcctttgactttgttttgtatttctgtgcactgccactgacagccacaagttaatatcaatatggtctctctgcggtagtagtttatttctagtttttgctggaagttttaatcagaattttgtttatgtctacag

Basic information

species Zea mays
transcript GRMZM2G020096_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020096_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os05g03820.3 (Oryza sativa), 5'ss of exon 12
GTTAGGTTAAAGAGATACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGGgtttgtgatctgctttcctttgactttgttttgtatttctgtgcact----------gccactga---cagccacaagttaatatcaata---tggtc-tctctgcggtagtagtttat---ttctagtttttgctggaag---ttttaatcag-----aattttgtttatgtctacag
|||||| | ||| |||| || ||||||||||||||||||||||||||||||||||||||||||||  |||| | ||||||||||||| | ||    |||||||   || |||||||||||||| || |          | || ||    ||   | |||| ||    |  |   ||| | |   | | |||||| | |||   ||| |  || |   |||||   ||| || |||      | || || | ||| |||||
GTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGTATTTTGGgtttgttagct-tactcctttgcacttcttttgtatttctgtacagtttgcagtgtggtcattggtgtcaagtagaagtaaacgcaaggagtttggacatgggtactgtagtaatgtatatcttccatgttctataggaagaattttgaaccagttttggaattggtatttgtatacag

upper sequence: GRMZM2G020096_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os07g27790.1 (Oryza sativa), 5'ss of exon 12
GTTAGGTTAAAGAGATACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGGgtttgtgatctgctttcctttgactttgttttgtatttctgtgcactgc------------cactgacagccacaagttaatatcaata---tggtc-tctctgcggtagtagtttat---ttctagtttttgctggaag---ttttaatcag-----aattttgtttatgtctacag
|| ||| | ||| |||| || ||||||||||||||||||||||||||||||||||||||||||||  |||| |||||||||||| || | ||    |||||||   || |||||||||||||| ||||                 || ||   | |||| || |  || |   ||| | |   | | |||||| |||||   ||| |  || |   |||||   ||| || |||      | || ||   ||| |||||
GTCAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGGgttcgttagct-tactcctttgcacttcttttgtatttctgtacactttgcagtgtggtcttggtgtcaagtagaagtaaacacaaagagtttggacatgggtactgtagtaatttatatcttccatgttctataggaagaattttgaaccagttttggaattggtacttgtatacag

upper sequence: GRMZM2G020096_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA05G37850.3 (Glycine max), 5'ss of exon 12
GTTAGGTTAAAGAGATACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGGgtttgtgatctgctttcctttgactttgttttgtatttctgtgcact--gccactgacagccacaagttaatatcaatatggtctctctgcggtagtagtttatttctagtttttgctggaagttttaatcagaattttgtttatgtctacag
|| ||| | ||||| ||  | |||||||||||||||||||| || || ||||| |||||||||||  | || |||||||||||  |||  |   |||    |   | ||  |  | ||| ||  ||||  ||| ||||||        ||  |  |  |||  | | ||  |   |  |   | |                                                 
GTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGGgtgagtggcc---tttttactacttctgcatgatgtttgtggtcacttagcctctgacattt--ggattgttcactgtattatttgtcaacatcaaaatggtgtc------------------------------------------------

upper sequence: GRMZM2G020096_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT4G23100.3 (Arabidopsis thaliana), 5'ss of exon 12
GTTAGGTTAAAGAGATACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGGgtttgtg-atctgctttcctttgactttgttttgtatttctgtgcactgccactgacagccacaagt-taatatcaatatggtctctctgcggtagtagtttatttctagtttttgctggaagttttaatcagaattttgtttatgtctacag
||| |||| ||||||||| | |||||||||||||||||||| || || ||||||||  ||||||| ||||| || || |||||   |  ||||  |  |   |   | | ||| ||  ||      | ||   |  | ||     | | |  | |  || |  |||         ||                                                         
GTTCGGTTGAAGAGATACTTGGAGATGAGAGGTGCTGATGGAGGTCCCTGGAGGAGGCTGTGTGCCCTGCCAGCTTTCTGGgtaactacatctattagcacata--tatatttcgtgcttaatgagaatgtttcaaaaagtattgactgttgttttgattttatctacaaatttcag---------------------------------------------------------

upper sequence: GRMZM2G020096_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv02s0025g03530.t01 (Vitis vinifera), 5'ss of exon 12
GTTAGGTTAAAGAGATACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGGgtttgtgatctgctttcctttgactttgttttgtatttctgtgcactgccactgacagccacaagttaatatcaatatggtctctctgcggtagtagtttatttctagtttttgctggaagttttaatcagaattttgtttatgtctacag
|| ||| | ||||||||| | || ||||| ||||||||||| || || |||||||| || |||||  |||| |||||||||||   |   ||      |||  |  |   | | |||| |   || | |    | |||      ||| |  |||| ||     ||| |  || |  ||| ||| | |                                             
GTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGGgtagttagcct------cttcaatctgtatatttattacaaagc-cagtttgt-acatgattcagtaatcatcagtact-catctgtatggaataagtgtatcttttcc------------------------------------------

upper sequence: GRMZM2G020096_T01 (Zea mays), 5'ss of exon 11
lower sequence: PP1S479_14V6.1 (Physcomitrella patens), 5'ss of exon 11
GTTAGGTTAAAGAGATACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGGgtttgtgatctgctttcctttgactttgttttgtatttctgtgcactgccactga-cagccacaagttaatatcaatatggtctctctgcggtagtagtttatttctagtttttgctggaagt--------tttaatca-gaattttgtttat-gtctacag
|| ||| ||||  | ||  | |||||||| || ||||||||||| |||||| |  ||||||||||  ||||||||||||||||  ||   |     || ||  | | |  |    |   | ||| |  |  ||||| || |  |     ||  | |||||  |     |   | || ||| || |   |    | |  | |||         |||| ||| ||| |  |||| | || |  ||
GTGAGGCTAAAACGTTATTTGGAGATGAGGGGAGCTGATGGTGGTCCATGGCGACGATTGTGTGCATTGCCTGCATTTTGGgtacgttgacgaagctcatt--attcttataacgaaaacggtggatag--actgagcaacttccgaccaac-tgaatatacttgtcataacg-agcagtgtactcagacgagtggtagcaagcctgctttgtttactcaagaaatgcgtttgttgtttgtag

upper sequence: GRMZM2G020096_T01 (Zea mays), 5'ss of exon 11
lower sequence: PP1S28_268V6.1 (Physcomitrella patens), 5'ss of exon 11
GTTAGGTTAAAGAGATACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGGgtttgtgatctgctttcctttgactttgttttgtatttc---tgtgcactgccactgacagcca--caagttaatatc-aatatggtctctctgcggt-agtagtttatttctagtttttgctggaagttttaatc-----------agaattttgtttatgtctacag-------
|| || || ||  | ||| | |||||||| || ||||||||||| |||||| |  ||||||||||  |||||||||| |||||  || ||   ||| | ||  |          |||      |   |   || |||   |   |   |  | | ||   ||||   |       |  | |||||||  |   |     ||| ||| |   || ||              ||  || | | ||| |   |       
GTGAGATTGAAACGGTACTTAGAGATGAGGGGAGCTGATGGTGGTCCATGGCGCCGATTGTGTGCTTTGCCTGCATTCTGGgtacgttattcacttacattccatgaaaacgaatatgggaaatagacctggcaactcgaacttaagtacttcactactgaatacacttcactcacaatgagtagttcgtgcgtgaaaattgatggcaaacttgattttgttacccatgtaagattttctgtgtttgtcgattgtag

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|211306283|gb|FL001396.1|FL001396
EST:     GTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGG                         GTTGGGCTGCTGTACGAT
genomic: GTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGGgtttgtgatc ... atgtctacagGTTGGGCTGCTGTACGAT
EST: gi|22543186|gb|BU093624.1|BU093624
EST:     CTGCATTTTGG                         GTTGGGCTGCTGTACGATGAGGAATCATTACAAAGCATTTTAGACATGACT
genomic: CTGCATTTTGGgtttgtgatc ... atgtctacagGTTGGGCTGCTGTACGATGAGGAATCATTACAAAGCATTTTAGACATGACT
EST: gi|89251366|gb|DY623152.1|DY623152
EST:     GTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGG                         GTTGGGCTGCTGTACGATGAGGAATCATTACAAAGCATTTTAGACATGACT
genomic: GTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGGgtttgtgatc ... atgtctacagGTTGGGCTGCTGTACGATGAGGAATCATTACAAAGCATTTTAGACATGACT
EST: gi|78544507|gb|DV622005.1|DV622005
EST:     GTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGG                         GTTGGGCTGCTGTACGATGAGGAATCATTACAAAGCATTTTAGACATGACT
genomic: GTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGGgtttgtgatc ... atgtctacagGTTGGGCTGCTGTACGATGAGGAATCATTACAAAGCATTTTAGACATGACT
EST: gi|211306280|gb|FL001393.1|FL001393
EST:     GTGCTGATGGTGGCCCATGGAGGAGAT-GTGTGCGCTGCCTGCATTTTGG                         GTTGGGCTGCTGT
genomic: GTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGGgtttgtgatc ... atgtctacagGTTGGGCTGCTGT
EST: gi|91048671|gb|EB159089.1|EB159089
EST:     GTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGG                         GTTGGGGCTGCTGTACGATGAGGAATCATTACAAAGCATTTTAGACATGAC
genomic: GTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGGgtttgtgatc ... atgtctacagGTT-GGGCTGCTGTACGATGAGGAATCATTACAAAGCATTTTAGACATGAC
EST: gi|211306279|gb|FL001392.1|FL001392
EST:     GTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGG                         GTTGGGCTGCTGTACGATGAGGAATCATTACAAAGCATTTTAGACATGACT
genomic: GTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGGgtttgtgatc ... atgtctacagGTTGGGCTGCTGTACGATGAGGAATCATTACAAAGCATTTTAGACATGACT
EST: gi|211306282|gb|FL001395.1|FL001395
EST:     GTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGG                         GTTGGGCTGCTGTACGATGAGGAATCAT
genomic: GTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGGgtttgtgatc ... atgtctacagGTTGGGCTGCTGTACGATGAGGAATCAT

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), 49 (downstream exon)
Score: 299

GTTAGGTTAAAGAGATACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGGgtttgtgatc ... atgtctacagGTTGGGCTGCTGTACGATGAGGAATCATTACAAAGCATTTTAGACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 964

GTTAGGTTAAAGAGATACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGGgtttgtgatc ... atgtctacagGTTGGGCTGCTGTACGATGAGGAATCATTACAAAGCATTTTAGACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 2612

GTTAGGTTAAAGAGATACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGGgtttgtgatc ... atgtctacagGTTGGGCTGCTGTACGATGAGGAATCATTACAAAGCATTTTAGACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 186

GTTAGGTTAAAGAGATACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGGgtttgtgatc ... atgtctacagGTTGGGCTGCTGTACGATGAGGAATCATTACAAAGCATTTTAGACATGACTTTTGACTGGACACAGGAGGAAAGAGAGATGCTAAGACATAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTAGGTTAAAGAGATACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGCTGCCTGCATTTTGGgtttgtgatctgctttcctttgactttgttttgtatttctgtgcactgccactgacagccacaagttaatatcaatatggtctctctgcggtagtagtttatttctagtttttgctggaagttttaatcagaattttgtttatgtctacag

- - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT