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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgattactaccttcaatgattctgttcaaagcaccagatttccatttaaacttgtctggttgcactgaacgtgtttaatcctctgtgctctcttttatagGCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAGCCATGTACATGAAACTAACG

Basic information

species Zea mays
transcript GRMZM2G031107_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031107_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g38840.2 (Oryza sativa), 3'ss of exon 12
tgattactaccttcaatgattctgttcaaagcaccagatttccatttaaacttgtct-ggttgcactgaacgtgtttaatcctctgtgctctcttt-------tatagGCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAGCCATGTACATGAAACTAACG
        | | ||  | |  || ||  || ||  | | |||  | |    |||| | | ||   |  |  |||| |||  ||||||  |   ||        || ||||||||| ||||| |||||||| || || |||||  |||||||||| ||||||||||| |||||| |||| 
-------aaacatccgtaac-ctatttgaatcaatacagttctgtctgctattgttttgcttctgccaatggtgtctaaaactctgtttttatttcaccctgataaagGCAAGAAGCAAGGAAGGAATGAATTCGTTATACGGTTGCAGCCATCGGAAGCCATGTATATGAAATTAACT

upper sequence: GRMZM2G031107_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA19G22690.1 (Glycine max), 3'ss of exon 12
tgattactaccttcaatgattctgt-tcaaagcaccagatttccatttaa--acttgtctggttgcactgaacgtgtttaatcctctgtgctctcttttatagGCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAGCCATGTACATGAAACTAACG
|  |  |||   |  ||| |||  | ||       ||  |  | ||| |   |  | ||   ||    | ||      | |   |        || | | ||||  | || || || || ||||||||||| ||||||||||| || |||||||| ||||||||||| || || 
tattagctagagtgtatgtttccttatcttgatggcaagtgcctattaatctaaatatcaacttatgtttaa---accttactgtaaacttattcctgtttagGTCAAAAGCAGGGGAGAAATGAGTTTGTTATACGCCTGCAACCTTCAGAAGCTATGTACATGAAGCTTACA

upper sequence: GRMZM2G031107_T02 (Zea mays), 3'ss of exon 12
lower sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 12
-tgattactaccttcaatgattctgttcaaagcaccagatttccatttaaacttgtctggttgcactga----acgtgtttaatcctctgtgctctctttta-tagGCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAGCCATGTACATGAAACTAACG
 |  |  ||  |    |        ||  || |  |   |  |  ||| || ||   |   || |  ||    | || |    |  |||   |||||||  |  |||  | || ||||| ||||| |||||||| |||||| |||| || ||||| || ||||||||||||||||| 
gtattgtcttgccctgacatcgtgttttgaatcttcttttagctttttgaatttaaatatatgtaaagacacaatgtatcgctttgtctaaactctcttgcaacagGTCAAAAGCAAGGAAGGAACGAGTTTGTGATACGCTTGCAACCTTCAGAGGCAATGTACATGAAACTAACT

upper sequence: GRMZM2G031107_T02 (Zea mays), 3'ss of exon 12
lower sequence: AT3G27300.2 (Arabidopsis thaliana), 3'ss of exon 13
tgattactaccttcaatgattctgttcaaagca--ccagatttccatttaaacttgtctggttgcactgaacgtgtttaatcctctgtgctctcttttatagGCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAGCCATGTACATGAAACTAACG
                 | || | |  | | ||   || |  | |    | |||||         | |      || ||| |     |||  |     | |||  | || ||||| ||||| |||||||| |||||| ||||||| ||||| |||||||||||||| ||||| 
-----------------gtttgtatcgagaccaaatcaaaccttcccaaatacttg-------aaatttggttggtctaacctctcatgcaatgc--aacagGTCAAAACCAAGGGAGGAACGAGTTTGTTATACGCTTGCAGCCTTCAGAGGCCATGTACATGAAGCTAACT

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|14203621|gb|BG837298.1|BG837298
EST:     AGCAGAGATACGTGTACAGTTCAAGGATGCTCCTGGTGACATTTTTAGAT                         GCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAG
genomic: AGCAGAGATACGTGTACAGTTCAAGGATGCTCCTGGTGACATTTTTAGATgtaggtaccc ... tcttttatagGCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAG
EST: gi|6031397|gb|AW076299.1|AW076299
EST:     AGCAGAGATACGTGTACAGTTCAAGGATGCTCCTGGTGACATTTTTAGAT                         GCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAG
genomic: AGCAGAGATACGTGTACAGTTCAAGGATGCTCCTGGTGACATTTTTAGATgtaggtaccc ... tcttttatagGCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAG
EST: gi|71596396|gb|DR907147.1|DR907147
EST:     AGCAGAGATACGTGTACAGTTCAAGGATGCACCTGGTGACATTTTTAGAT                         GCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAG
genomic: AGCAGAGATACGTGTACAGTTCAAGGATGCTCCTGGTGACATTTTTAGATgtaggtaccc ... tcttttatagGCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAG
EST: gi|78077421|gb|DV505855.1|DV505855
EST:     AGCAGAGATACGTGTACAGTTCAAGGATGCTCCTGGTGACATTTTTAGAT                         GCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAG
genomic: AGCAGAGATACGTGTACAGTTCAAGGATGCTCCTGGTGACATTTTTAGATgtaggtaccc ... tcttttatagGCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAG
EST: gi|22521339|gb|BU080150.1|BU080150
EST:     CCTGGTGACATTTTTAGAT                         GCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAG
genomic: CCTGGTGACATTTTTAGATgtaggtaccc ... tcttttatagGCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAG
EST: gi|78119963|gb|DV538347.1|DV538347
EST:     AGCAGAGATTCGTGTCCAGTTCAAGGATGCTCCTGGTGACATTTTTAGTT                         GCAAGAAACAAGACAGGAATGAGTTTGTCATTCGCCTGCAGCCATCAGAAG
genomic: AGCAGAGATACGTGTACAGTTCAAGGATGCTCCTGGTGACATTTTTAGATgtaggtaccc ... tcttttatagGCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAG
EST: gi|76281884|gb|DV021452.1|DV021452
EST:     AGCAGAGATACGTGTACAGTTCAAGGATGCTCCTGGTGACATTTTTAGAT                         GCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAG
genomic: AGCAGAGATACGTGTACAGTTCAAGGATGCTCCTGGTGACATTTTTAGATgtaggtaccc ... tcttttatagGCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAG
EST: gi|78544145|gb|DV621643.1|DV621643
EST:     AGCAGAGATACGTGTACAGTTCAAGGATGCTCCTGGTGACATTTTTAGAT                         GCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAG
genomic: AGCAGAGATACGTGTACAGTTCAAGGATGCTCCTGGTGACATTTTTAGATgtaggtaccc ... tcttttatagGCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAG
EST: gi|78109019|gb|DV527436.1|DV527436
EST:     AGCAGAGATACGTGTACAGTTCAAGGATGCTCCTGGTGACATTTTTAGAT                         GCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAG
genomic: AGCAGAGATACGTGTACAGTTCAAGGATGCTCCTGGTGACATTTTTAGATgtaggtaccc ... tcttttatagGCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAG

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), 48 (downstream exon)
Score: 133

GGGTTCCATTCATCCTCAAGGCTGGCAAAGCACTAAATTCGAGGAAAGCAGAGATACGTGTACAGTTCAAGGATGCTCCTGGTGACATTTTTAGATgtaggtaccc ... tcttttatagGCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAGCCATGTACATGAAACTAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 601

GGGTTCCATTCATCCTCAAGGCTGGCAAAGCACTAAATTCGAGGAAAGCAGAGATACGTGTACAGTTCAAGGATGCTCCTGGTGACATTTTTAGATgtaggtaccc ... tcttttatagGCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAGCCATGTACATGAAACTAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 834

GGGTTCCATTCATCCTCAAGGCTGGCAAAGCACTAAATTCGAGGAAAGCAGAGATACGTGTACAGTTCAAGGATGCTCCTGGTGACATTTTTAGATgtaggtaccc ... tcttttatagGCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAGCCATGTACATGAAACTAACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 264

GGGTTCCATTCATCCTCAAGGCTGGCAAAGCACTAAATTCGAGGAAAGCAGAGATACGTGTACAGTTCAAGGATGCTCCTGGTGACATTTTTAGATgtaggtaccc ... tcttttatagGCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAGCCATGTACATGAAACTAACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaacttgtctggttgcactgaacgtgtttaatcctctgtgctctcttttatagGCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAGCCATGTACATGAAACTAACG
                           gtttaat  putative branch site (score: 264)
                                 tcctctgtgctctctt  CT-rich tract
                                             tcttttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgattactaccttcaatgattctgttcaaagcaccagatttccatttaaacttgtctggttgcactgaacgtgtttaatcctctgtgctctcttttatagGCAAGAAACAAGGCAGGAATGAGTTTGTCATACGCCTGCAGCCATCAGAAGCCATGTACATGAAACTAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC