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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAGgtgataatttagcttaagctaattttgtagagaaaattgcatgtgtgtatggtatcgctaatcatgtttgctattttgttttctag

Basic information

species Zea mays
transcript GRMZM5G824405_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G824405_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g18310.1 (Oryza sativa), 5'ss of exon 6
GTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAGgtgataatttagcttaagctaattttgtagagaaaattgcatgtgtgtatggtat----cgctaatcatgtttgctat--tttgttttctag
|||||| | |||||||| ||||||||||||||||| ||||| |||||||| || || |||||||||||||||||||||||||||||||||||||||||||||   | | ||||||||||  || | || |  |  ||||   | |  |||||||    | |||||||||||| ||    |||   || |||
GTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAGgtgcgcaat-agcttaagctgtttctttatatga--ttgctcatattcatggtattagccactaatcatgttttcttacgtttcaattgtag

upper sequence: GRMZM5G824405_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA02G39390.1 (Glycine max), 5'ss of exon 7
GTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAGgtgataatttagcttaagctaattttgt-agagaaaattgcatgtgtgtatggtatcgctaatcatgtttgctattttgttttctag-------------------------
||  |  | ||||||||||| ||||| |  || ||||||||||||||||||||||| ||||||||||||||| | || ||||||||||||||||| |||||  |  |    ||| |   | | || | ||  |  | |     ||| | |  |       |  |  | ||  |  ||    | ||                          
GTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAGgttgttctcattcttgactcattcttcttagtaatcagtagtcttgtatctaatggaagacaggaaatatgtcaagtttgaatttaacaaaacttatgtttcaatgttgcag

upper sequence: GRMZM5G824405_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA18G06770.1 (Glycine max), 5'ss of exon 9
GTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAGgtgataa-----tttagcttaagctaattttgtagagaaaat-tgcatgtgtgtatggtatcgctaatcatgtttgctattttgttttctag-------------------------------
|| || || ||||| |||||||| || || || ||||||||||||||||||||||| ||||||||||||||| | || ||||||||||||||||| |||||  |        ||| | | |   |  | | ||   ||||| | | |     ||  |     ||    || | | | | | ||   | |                                 
GTGGGTCTGCCAGCCCGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAGgttgttcacattcttaacatcattcatctgtttaatcaaaatatacttcgacctagtgcgaaactggaaatatgt-caagtatgaactatgaagattaacccacttatttttggatgtcacag

upper sequence: GRMZM5G824405_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA14G37520.3 (Glycine max), 5'ss of exon 7
GTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAGgtgataatttagcttaagctaattttgtagagaa--aattgcatgtgtgtatggtatcgctaatcatgtttgctattttgttt---tctag------------------------
||  |  | ||||||||||| ||||| |  || ||||||||||| ||||||||||| ||||||||||||||| | || ||||||||||||||||| |||||  |       ||| |   | | || |    ||  |||    |   |||||  || ||  |  || |     | |   ||||   | ||                         
GTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTAACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAGgttgttcacattcttgactcattcttcttagtaatcaatcatcttgttgtatc-taacgaaaggcaggaaatatgtcaagtttgaatttaacacacttatgtttcaatgttgcag

upper sequence: GRMZM5G824405_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA11G27410.1 (Glycine max), 5'ss of exon 13
GTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAGgtg---------------ataattta---gcttaagcta---attttg---tagag-aaaattgcatgtgtgtatggtatcgctaatcatgtttgctattttgttttctag---------
|| || || |||||  ||||||| || || || ||||||||||||||||||||||| |  |||||||||||| | || ||||||||||||||||| |||||                || ||| |   | |||| | |   | || |   ||| | |||| || |  | |||   ||||     || | | ||       |  ||| | |         
GTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCATTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAGgttgtttacattcttaacatcattcatctgtttaatcaatatacttcgacctagtgcaaaactggaaatatgtcaagtatgaactatgaagattaacccacttatttttggatgtcacag

upper sequence: GRMZM5G824405_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA11G27870.1 (Glycine max), 5'ss of exon 8
GTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAGgtg---------------ataattta---gcttaagcta---attttg---tagag-aaaattgcatgtgtgtatggtatcgctaatcatgtttgctattttgttttctag---------
|| || || |||||  ||||||| || || || ||||||||||||||||||||||| || |||||||||||| | || ||||||||||||||||| |||||                || ||| |   | |||| | |   | ||||   ||| | |||| || |  | |||   ||||     || | | ||       |  ||| | |         
GTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGTTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAGgttgtttacattcttaacatcattcatctgtttaatcaatatactttgacctagtgcaaaactggaaatatgtcaagtatgaactatgaagattaacccacttatttttggatgtcacag

upper sequence: GRMZM5G824405_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 5'ss of exon 7
GTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAGgtgataatttagcttaagctaattttgtagagaaaattgcatgtgtgtatggtatcgctaatcatgtttgctattttgttttctag--------------------
|||||  | || |||||||| ||||| ||||| ||||| ||  | ||||||||||| || ||||| || ||||| || ||||| || |||||||||||||| |    ||   ||    | ||| |  |       | || | |   | |  |  ||| |  | |||| |  |  |||  |   |                     
GTTGGCTTGCCTGCTCGAGGAAAGACTTTTACTGCAGCAAAGTTGACAAGATATCTACGCTGGTTGGGACATGATACTAAACATTTTAATGTTGGAAAGgttagctattttgttgcaatgattcttgattttttttagcttat-cctgtcattacgcgacccttgttggaaagattgactcaaacattgctccgtttctttgcag

upper sequence: GRMZM5G824405_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 5'ss of exon 7
GTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAGgtgataatttagcttaagctaatt--ttgtagagaaaattgcatgtgtgtatggtatcgctaatcatgtttgctattttgttttctag
|||||  | |||||||||||||| || ||||| ||||||||||||||||||||||| || ||||| |||||||| || ||||||||||||||||||||||||||   |    ||||  | |||  |   ||    |||       |||      || | ||    | || | | |            
GTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAGgtgatttatatttttaaagttattcatcacagctctaatcattgaagtgaggaagattgatatgacttttggttgtaacag-------

upper sequence: GRMZM5G824405_T01 (Zea mays), 5'ss of exon 7
lower sequence: PP1S414_24V6.1 (Physcomitrella patens), 5'ss of exon 7
GTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAGgtga---taatttagc-ttaagctaa----ttttgtagagaaaattgcatgtgtgtatggtatcgctaatcatgtttgctatttt------gttttctag------------------------------------
|||||| |||| || ||||| ||||| ||||| ||||| ||| | || ||||||||  | ||| |||| ||||| || |||||||||||||||||||| || |   || | |||| || ||| |     ||||        | | |||    || ||  |||      |  ||||| |  |  |      |||    ||                                    
GTTGGGTTACCTGCACGAGGCAAGACGTTTACGGCAGCAAAATTGACGAGATATCTTAGGTGGCTAGGCCATGATACTAAACACTTCAATGTTGGAAAAgtaagcttattctagcatttagccacgggcttttcctataggattcgcaatgttggatcttatgaagggtgttgtttccggtcctctaaatgttacgcagggctatttgactgacttctttgttgtgatgaactag

upper sequence: GRMZM5G824405_T01 (Zea mays), 5'ss of exon 7
lower sequence: PP1S235_92V6.1 (Physcomitrella patens), 5'ss of exon 6
GTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAGgtga--taatttagctta--agctaattttgtagagaaaattgcatgtgtg------tatggtatcgctaatcat-gtttgct--attttgttttctag-
||||| ||||| |||||||| ||||| |||||||||||||| || || ||||||||| | ||| | || ||||| || ||||||||||||||||||||||| |  | | |  ||| |  ||   |   || |   |  |||    |  |       | ||     |  | |||| || | ||   || || | | ||| 
GTTGGCCTACCTGCTCGAGGGAAGACTTTTACAGCAGCTAAGCTGACGAGATATCTCAGGTGGCTTGGCCATGATACCAAACACTTCAATGTTGGAAAGgtaagcttagtctgctcattagtagacagtgaaagtagtattttgagctttaactattgtgagggggacagtcattgtctacttggttctggtgtttagt

upper sequence: GRMZM5G824405_T01 (Zea mays), 5'ss of exon 7
lower sequence: PP1S215_89V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAGgt---------gataattt-------agcttaagctaattttgtagagaaaattgca----tgtgtgtatggtatcgc--taatcatgtttgctat-tttgttttctag------------------------------------------------------------------------------------
|||||| |||| ||||| || ||||| || || ||||||||||| || |||||| | || |||||||||||||| || || |||||||||||||| |||||         || || ||       ||||   |  ||| || |  |   | ||       ||  || ||| | | |   | || || |||  | |      | ||||                                                                                     
GTTGGGTTACCGGCTCGTGGAAAGACATTCACTGCAGCTAAACTGACCAGATATTTGCGGTGGTTAGGTCATGACACCAAGCACTTCAATGTTGGCAAGgtatgtttttagaaaactttgtacgcagctggtgtcaatcttctcaacttatttcttgttttggttgcatgattttgggatgattatattttgtgtacccaatatctaaggtgctctttcaggttttagccttagagtgcacactttttgcagtggagtattttgatgcgattgtgcttttgatgtttcacag

upper sequence: GRMZM5G824405_T01 (Zea mays), 5'ss of exon 7
lower sequence: EFJ07288 (Selaginella moellendorffii), 5'ss of exon 3
GTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAGgtga-taatttagcttaagctaattttgtagagaaaattgcatgtgtgtatggtatcgctaatcatgtttgctattttgttttctag
|| ||  |||||||  | || || || || || || |  || || ||||||||||| || ||| | |||||||| || ||||||||||| |||||||| || | | | | |  ||  | |  | ||| || |      |  | |  || || | |  || | ||                      
GTGGGCTTACCAGCAAGGGGGAAAACTTTCACTGCTGTCAAGCTAACAAGATATCTTCGTTGGCTTGGTCATGACACTAAACACTTCAACGTTGGAAAAgtcagtcagtcacttt--gtttgtcttgaagggctctcaggtttttggtgtgatttttcttaccag---------------------

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|19437252|gb|BM953662.1|BM953662
EST:     GATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG                         TACCGCCGGCTCAAGCATGGAACTAATCAG
genomic: GATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAGgtgataattt ... tgttttctagTACCGCCGGCTCAAGCATGGAACTAATCAG
EST: gi|22491067|gb|BU050990.1|BU050990
EST:     GATATCTCCGATGGTTAGGTCATGAAACAAACCTCTTCAATGTTGGAAAG                         TCCCGCCGGCTCAAGCATGGAACTAATCAG
genomic: GATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAGgtgataattt ... tgttttctagTACCGCCGGCTCAAGCATGGAACTAATCAG
EST: gi|148957598|gb|EC903699.2|EC903699
EST:     GATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAA-G                         TACCGCCGGCTCAAGCATGGAACTAATCAG
genomic: GATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAGgtgataattt ... tgttttctagTACCGCCGGCTCAAGCATGGAACTAATCAG

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), 30 (downstream exon)
Score: 86

GTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAGgtgataattt ... tgttttctagTACCGCCGGCTCAAGCATGGAACTAATCAG


Block sizes: 47 (upstream exon), 30 (downstream exon)
Score: 80

GTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAGgtgataattt ... tgttttctagTACCGCCGGCTCAAGCATGGAACTAATCAG


Block sizes: 49 (upstream exon), 30 (downstream exon)
Score: 63

GTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAGgtgataattt ... tgttttctagTACCGCCGGCTCAAGCATGGAACTAATCAG


Block sizes: 49 (upstream exon), 30 (downstream exon)
Score: 276

GTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAGgtgataattt ... tgttttctagTACCGCCGGCTCAAGCATGGAACTAATCAG