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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgaaatttatttatcatgttatatcattgaatggtagaaaacttaaactaaaatacctttgctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT

Basic information

species Zea mays
transcript GRMZM2G121790_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121790_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g14130.1 (Oryza sativa), 3'ss of exon 9
--------------------gtatgtgaaatttatttatcatgtt-atatcattgaa-tggtagaaaacttaaactaaaatacctttgctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT
                       |  | | |  |||| |    || || | ||   | | ||  | |    || ||  ||  ||| ||||   ||||||||||||||||||||||||||||||||| || || || || |||||  | ||||||||| ||||||||||| |||||||||| 
gtattagaattgttttgtttactttagcattccatttttttaattgatgttatgatactagtgcatattacaacctgcaaatcctatgct---gcagATTTTCCACAAGCGGATGCCTCCAGAAGCAATTGACCTTGCATCACGTCTTCTCCAGTATGCACCAAATCTACGATGCACTGCC

upper sequence: GRMZM2G121790_T01 (Zea mays), 3'ss of exon 9
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 8
------------------------gtatgtgaaatttatttatcatgttatatcattgaatggtagaaaacttaa-actaaaatacctttgctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT
                        ||||    | |  |   ||   ||| | |          ||   ||| |   ||     |    | |   | |||| ||||||||||||| ||||||||||||||  ||||||| | |||| |  | || ||||| || || |||||  | |||| ||||
atgccagtagatcgaggctcctttgtatcgtgattgcaagaatggggttctttgggatttgcctaaccaacgtggtacggggttggtgtcgtgatggcagGTTTTCCACAAGCGCATGCCTCCAGAAGCAGTAGATCTGGTTTCAAGGCTACTTCAGTACTCTCCGAATCTGCGGTGCAATGCT
















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|19770441|gb|BQ035162.1|BQ035162
EST:     ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG                         ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
genomic: ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAGgtatgtgaaa ... gctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
EST: gi|211251114|gb|FL353291.1|FL353291
EST:     ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG                         ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
genomic: ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAGgtatgtgaaa ... gctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
EST: gi|32855414|gb|CD995095.1|CD995095
EST:     ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG                         ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
genomic: ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAGgtatgtgaaa ... gctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
EST: gi|211298028|gb|FL233897.1|FL233897
EST:     ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG                         ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
genomic: ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAGgtatgtgaaa ... gctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
EST: gi|71430637|gb|DR811687.1|DR811687
EST:     ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG                         ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
genomic: ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAGgtatgtgaaa ... gctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
EST: gi|149107144|gb|EE189033.2|EE189033
EST:     GAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG                         ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
genomic: GAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAGgtatgtgaaa ... gctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
EST: gi|110961978|gb|EE182030.1|EE182030
EST:     ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG                         ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
genomic: ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAGgtatgtgaaa ... gctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
EST: gi|211326797|gb|FL341548.1|FL341548
EST:     ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG                         ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTTCGCTTCACGCTT
genomic: ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAGgtatgtgaaa ... gctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCT-CGCTTCACGCTT
EST: gi|76922776|gb|DV169168.1|DV169168
EST:     TTCCTCAGATCAAAGCTCACCCATGGCAC-AG                         ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
genomic: TTCCTCAGATCAAAGCTCACCCATGGCACAAGgtatgtgaaa ... gctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
EST: gi|60338092|gb|DN205065.1|DN205065
EST:     ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG                         ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
genomic: ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAGgtatgtgaaa ... gctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
EST: gi|110194431|gb|EC876329.1|EC876329
EST:     CGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG                         ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
genomic: CGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAGgtatgtgaaa ... gctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
EST: gi|87153591|gb|DY398380.1|DY398380
EST:     ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG                         ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
genomic: ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAGgtatgtgaaa ... gctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
EST: gi|76287881|gb|DV027449.1|DV027449
EST:     ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG                         ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
genomic: ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAGgtatgtgaaa ... gctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
EST: gi|60350723|gb|DN217696.1|DN217696
EST:     ATCAAAGCTCACCCATGGCACAAG                         ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
genomic: ATCAAAGCTCACCCATGGCACAAGgtatgtgaaa ... gctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
EST: gi|60358944|gb|DN225917.1|DN225917
EST:     ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG                         ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
genomic: ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAGgtatgtgaaa ... gctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
EST: gi|148952786|gb|EC898772.2|EC898772
EST:     TCAGATCAAAGCTCACCCATGGCACAAG                         ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
genomic: TCAGATCAAAGCTCACCCATGGCACAAGgtatgtgaaa ... gctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
EST: gi|31352553|gb|CD436910.1|CD436910
EST:     ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG                         ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
genomic: ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAGgtatgtgaaa ... gctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
EST: gi|20300401|gb|BQ163344.1|BQ163344
EST:     ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAG                         ATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG
genomic: ACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAGgtatgtgaaa ... gctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTG

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), 47 (downstream exon)
Score: 334

GTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAGgtatgtgaaa ... gctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 388

GTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAGgtatgtgaaa ... gctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 385

GTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAGgtatgtgaaa ... gctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 246

GTTCTTGGTACCCCAACGCGCGAGGAAATCCGATGTATGAATCCAAACTACACCGAGTTTAGATTTCCTCAGATCAAAGCTCACCCATGGCACAAGgtatgtgaaa ... gctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttatatcattgaatggtagaaaacttaaactaaaatacctttgctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT
                              aactaaa  putative branch site (score: 246)
                                        cctttgctctt  putative PPT
                   tagaaaacttaaacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgaaatttatttatcatgttatatcattgaatggtagaaaacttaaactaaaatacctttgctcttgcagATTTTCCACAAGCGGATGCCTCCAGAAGCTATAGATCTCGCTTCACGCTTGCTCCAGTATTCACCAAATCTAAGATGCACTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG