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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgatctcagggctatgtttttatcttttattttttctgaggtctatcatgtataaaataatcagtttccattagaaatactagatctggagtgtattctgttgacgtgtgttaattcgccaaccttgttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGGACCATGGTCGCTGGTGGTGGTGCTAGTGTCATTTATGCTGATACA

Basic information

species Zea mays
transcript GRMZM2G107082_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107082_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g47330.1 (Oryza sativa), 3'ss of exon 6
----------------gtattgatctcagggctatgtttttatcttttattttttctgag---gtctatcatgtataaaataatcagt---------------ttccattagaaatactag--atctgga--------gtgtattctgttgacgtgtgtt--------aattcgccaaccttgttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGGACCATGGTCGCTGGTGGTGGTGCTAGTGTCATTTATGCTGATACA
                 ||    | |||    |      |  ||    || || | | ||   |  |  | ||||||| || ||||||               |||   ||| | | || |   |||||          | | || | ||||  | | ||         ||  |    |||| || |||||||||||||| |||||||||||||| ||||||||||| || || ||||||||||| ||||| ||||| |||||||| |||||||| ||||||||||||
gtatccacatctcaaattacacgtttcacatttcaagcctcctccccaatcttatttaagtatgagttgcctgtataatatcatcagtaggtttgcacatgaattcagataggagtgctggcagtctggctcagtactatatgtttttttgaattattttctaaatgtgatatgatgtccttattctttcagACAAGTGCATCTCTGAAGTTCACCGTTTTGAACCCAAAGGGGCGCATCTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATATATGCTGATACA

upper sequence: GRMZM2G107082_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g47120.1 (Oryza sativa), 3'ss of exon 6
----------------gtattgatctcagggctatgtttttatcttttattttttctgag---gtctatcatgtataaaataatcagt---------------ttccattagaaatactag--atctgga--------gtgtattctgttgacgtgtgt--------taattcgccaaccttgttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGGACCATGGTCGCTGGTGGTGGTGCTAGTGTCATTTATGCTGATACA
                 ||    | |||    |      |  ||    || |||| | ||   |  |  | ||||||| || ||||||               |||   ||| | | || |   |||||          | | || | ||||  | | |        | ||      ||||| || |||||||||||||| |||||||||||||| ||||||||||| || || ||||||||||| ||||| ||||| ||||                          
gtatccacatctcaaattacacgtttcacatttcaagcctcctccccaatcttttttaagtatgagttgcctgtataatatcatcagtaggtttgcacatgaattcagataggagtgctggcagtctggctcagcactatatgtttttttgaattatttgctaaatgtgatataatgaccttattctttcagACAAGTGCATCTCTGAAGTTCACCGTTTTGAACCCAAAGGGGCGCATCTGGACAATGGTTGCTGGAGGTG--------------------------

upper sequence: GRMZM2G107082_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT1G09430.1 (Arabidopsis thaliana), 3'ss of exon 7
gtattgatctcagggctatgtttttatcttttattttttctgaggtctat-catgtataaaataatcagtttccattagaaatactagatctggagtgtattctgttgacgtgtgttaattcgccaaccttgttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGGACCATGGTCGCTGGTGGTGGTGCTAGTGTCATTTATGCTGATACA
                     ||| | | |  |  |||||| |   |    | | | | |   |  |||     | | ||||     | |   ||   | |  |||    ||||||   |  |      |  ||||| ||||||||||| ||| |||||||||| |||||||| || ||||| ||||| ||||| ||||| ||||| ||||||||||| ||||| ||||||||||||
--------------------gtttaagcatccagcttttctaaaaacaccacttttgtgactcagacaggaaagacttgaaagtaatgttactgaccat-tcatgtctgtgtgtgtgtgtgtgtttgt-tacttattgcagACAAGTGCTTCTTTGAAGTTCACTGTTTTGAATCCTAAAGGCCGCATTTGGACGATGGTAGCTGGAGGTGGTGCTAGCGTCATATATGCTGATACA

upper sequence: GRMZM2G107082_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv14s0060g00550.t01 (Vitis vinifera), 3'ss of exon 7
gtattgatctcagggctatgtttttatcttttattttttctgaggtctatcatgtataaaataatcagtttccattagaaatactagatctggagtgtattctgttgacgtgtgttaattcgccaaccttgt--tatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGGACCATGGTCGCTGGTGGTGGTGCTAGTGTCATTTATGCTGATACA
                                    |||||| | | | |||  | ||| || |     ||| || | | | | | ||  |    | | | | |  ||       | || | | || |||    |  | ||||||||||| ||| |||||||||| ||||||||||| ||||| ||||||||||| ||||| ||||| |||||||| ||||| || ||||| ||||| 
------------------------------------tttctg-gttttctca-atctaagattagtctgttcaatcatagaaattggagtttacctatgtacagcagaaa----gtgatccactaatcttacactggtgcagACAAGTGCATCTTTGAAGTTCACTGTTTTGAACCCCAAAGGACGCATCTGGACTATGGTAGCTGGAGGTGGTGCAAGTGTTATATATGCCGATACT

upper sequence: GRMZM2G107082_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S63_54V6.2 (Physcomitrella patens), 3'ss of exon 9
gtattgatctcagggctatgtttttatcttttattttttctgaggt-ctatcatgtataaaataatcagtttccat---tagaaatactagatctggagtgtattctgttgacgtgtgttaattcgccaaccttgttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGGACCATGGTCGCTGGTGGTGGTGCTAGTGTCATTTATGCTGATACA
                | || ||   || ||||| |  |   ||   ||| ||  |          |||  |  |    | | ||| | |  ||  | |   |||    |   | || |||| | |       |||   | |||||  |||| |||||||| || ||| |  |||| ||||| || ||||| ||||| ||||| ||||| |||||||| ||||||||||| |||||||| 
---------------gtgtgattgattcatttatctaatacaagacactaccaaattcttccactccagactttaaccatcgcaattccacttcacgtgatcatttctatacagggtcttaagtagt-gtttatgtggctgcagACCGGTGCTTCTCTGAAATTGACGATACTGAATCCGAAGGGCCGCATTTGGACAATGGTTGCTGGAGGTGGTGCCAGTGTCATTTACGCTGATACT

upper sequence: GRMZM2G107082_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S7_156V6.1 (Physcomitrella patens), 3'ss of exon 9
gtattgatctcagggctatgtttttatcttttattttttctgaggtctatcatgta-taaaataatcagtttccat-tagaaatactagatctggagtgtattctgttgacgtgtgttaattcgccaacct---tgtt--atttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGGACCATGGTCGCTGGTGGTGGTGCTAGTGTCATTTATGCTGATACA
             |  |  |    |    |     |||   | || || ||  ||| ||  | || ||     ||| ||  |   |    |  |   ||| | | ||| | |  | ||||||  |  | ||   ||||  ||| |||||  |||||||  |||| || ||  | ||||||||  |||| || |||||||||||||||||||| || ||||| ||||| || ||  ||||||| 
-------------gtatgcggcactgctctgatagtttgaggcgggctctctggtactaccaaaaccatgccgcatgtacgagctccctgttcgtt-tgtttccagtttagggcttttaattgacatagctacatgtttgattgcagACCGGTGCCTCCTTGAAATTGACAATCTTGAACCCTGAAGGCCGAATCTGGACCATGGTCGCTGGGGGAGGTGCAAGTGTTATCTACTCTGATACG

upper sequence: GRMZM2G107082_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ27687 (Selaginella moellendorffii), 3'ss of exon 7
gtattgatctcagggctatgtttttatcttttattttttctgaggtctatcatgtataaaataatcagtttccattagaaatactagatctggagtgtattctgttgacgtgtgttaattcgccaaccttgttat-ttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGGACCATGGTCGCTGGTGGTGGTGCTAGTGTCATTTATGCTGATACA
                                                                                     |||  |         | |  | | || |  | ||    | |  ||||| | |||||||  |||| ||| | ||| | ||  |  | || |||||||||||||| ||||| ||||||||||| ||||| || ||||| || ||||| || |||
----------------------------------------------------------------------------------gtcagacttcttcctctctttcctca-gtcttctgatgactcgaatttgttttgttcagACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGGACAATGGTCGCTGGCGGTGGCGCGAGTGTGATCTATGCCGACACA

upper sequence: GRMZM2G107082_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ37257 (Selaginella moellendorffii), 3'ss of exon 7
gtattgatctcagggctatgtttttatcttttattttttctgaggtctatcatgtataaaataatcagtttccattagaaatactagatctggagtgtattctgttgacgtgtgttaattcgccaaccttgttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGGACCATGGTCGCTGGTGGTGGTGCTAGTGTCATTTATGCTGATACA
                                                                                 |   |  |||        |||  | | | | || | | |||  ||  |  ||  |||||||  |||| ||| | ||| | ||  |  | || |||||||||||||| ||||| ||||||||||| ||||| || ||||| || ||||| || |||
--------------------------------------------------------------------------------gtcagacttcttcctctctttccttagtcttctgatgactcg--aatttgttttgttcagACTGGTGCGTCTTTAAAGCTGACAATACTAAATCCGAAAGGTCGCATTTGGACAATGGTCGCTGGCGGTGGCGCGAGTGTGATCTATGCCGACACA

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|211099628|gb|FL031896.1|FL031896
EST:     GAAGAGTACTCAGCCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAG                         ACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
genomic: GAAGAGTACTCAGCCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAGgtattgatct ... gttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
EST: gi|6851489|gb|AW352499.1|AW352499
EST:     GAAGAGTACTCAGCCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAG                         ACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
genomic: GAAGAGTACTCAGCCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAGgtattgatct ... gttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
EST: gi|14243577|gb|BG841276.2|BG841276
EST:     GAAGAGTACTCAGCCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAG                         ACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
genomic: GAAGAGTACTCAGCCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAGgtattgatct ... gttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
EST: gi|60354935|gb|DN221908.1|DN221908
EST:     TACAGAAAGTTTCATCCATGAACTAGATGAGAAG                         ACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
genomic: TACAGAAAGTTTCATCCATGAACTAGATGAGAAGgtattgatct ... gttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
EST: gi|211099629|gb|FL031897.1|FL031897
EST:     GAAGAGTACTCAGCCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAG                         ACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
genomic: GAAGAGTACTCAGCCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAGgtattgatct ... gttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
EST: gi|13177932|gb|BG349115.1|BG349115
EST:     GAAGAGTACTCAGCCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAG                         ACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
genomic: GAAGAGTACTCAGCCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAGgtattgatct ... gttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
EST: gi|60398717|gb|DN231533.1|DN231533
EST:     TACAGAAAGTTTCATCCATGAACTAGATGAGAAG                         ACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
genomic: TACAGAAAGTTTCATCCATGAACTAGATGAGAAGgtattgatct ... gttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
EST: gi|32851220|gb|CD990901.1|CD990901
EST:     GAAGAGTACTCAGCCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAG                         ACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
genomic: GAAGAGTACTCAGCCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAGgtattgatct ... gttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
EST: gi|148996106|gb|EE035369.2|EE035369
EST:     GAAGAGTACTCAGCCTTACAGAAAGTTTCATCCATGAACTAGATGAGAAG                         ACAAGTGCCTCTCTGAAAGT-CACGGTTTGGACCCCGAAAGGTCGCATCTG
genomic: GAAGAGTACTCAGCCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAGgtattgatct ... gttatttcagACAAGTGCCTCTCTGAA-GTTCACGGTTTTGAACCCGAAAGGTCGCATCTG
EST: gi|211123624|gb|FL002523.1|FL002523
EST:     GAAGAGTACTCAGCCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAG                         ACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
genomic: GAAGAGTACTCAGCCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAGgtattgatct ... gttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
EST: gi|50332311|gb|CO527437.1|CO527437
EST:     GAACTAGATGAGAAG                         ACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
genomic: GAACTAGATGAGAAGgtattgatct ... gttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
EST: gi|6012698|gb|AW062135.1|AW062135
EST:     CAAGAGTACTCAGCCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAG                         ACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
genomic: GAAGAGTACTCAGCCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAGgtattgatct ... gttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
EST: gi|60395413|gb|DN228283.1|DN228283
EST:     CAGAAAGTTTCATCCATGAACTAGATGAGAAG                         ACAAGTGCCTCTTTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
genomic: CAGAAAGTTTCATCCATGAACTAGATGAGAAGgtattgatct ... gttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
EST: gi|113703355|gb|EE680859.1|EE680859
EST:     GAAAGTTTCATCCATGAACTAGATGAGAAG                         ACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
genomic: GAAAGTTTCATCCATGAACTAGATGAGAAGgtattgatct ... gttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
EST: gi|32858269|gb|CD997950.1|CD997950
EST:     GGAGAGTACTCAGCCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAG                         ACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG
genomic: GAAGAGTACTCAGCCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAGgtattgatct ... gttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGG

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: 212

GTGGGGAGGTATAGAATTTCCTCTACCTTTTGGAAGAGTACTCAGCCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAGgtattgatct ... gttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGGACCATGGTCGCTGGTGGTGGTGCTAGTGTCATTTATGCTGATACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 407

GTGGGGAGGTATAGAATTTCCTCTACCTTTTGGAAGAGTACTCAGCCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAGgtattgatct ... gttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGGACCATGGTCGCTGGTGGTGGTGCTAGTGTCATTTATGCTGATACA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 261

GTGGGGAGGTATAGAATTTCCTCTACCTTTTGGAAGAGTACTCAGCCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAGgtattgatct ... gttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGGACCATGGTCGCTGGTGGTGGTGCTAGTGTCATTTATGCTGATACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1310

GTGGGGAGGTATAGAATTTCCTCTACCTTTTGGAAGAGTACTCAGCCCTACAGAAAGTTTCATCCATGAACTAGATGAGAAGgtattgatct ... gttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGGACCATGGTCGCTGGTGGTGGTGCTAGTGTCATTTATGCTGATACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatctggagtgtattctgttgacgtgtgttaattcgccaaccttgttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGGACCATGGTCGCTGGTGGTGGTGCTAGTGTCATTTATGCTGATACA
                           tgttaat  putative branch site (score: 1310)
                                         ccttgtt  putative PPT
                                           ttgttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgatctcagggctatgtttttatcttttattttttctgaggtctatcatgtataaaataatcagtttccattagaaatactagatctggagtgtattctgttgacgtgtgttaattcgccaaccttgttatttcagACAAGTGCCTCTCTGAAGTTCACGGTTTTGAACCCGAAAGGTCGCATCTGGACCATGGTCGCTGGTGGTGGTGCTAGTGTCATTTATGCTGATACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT