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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgcttccccttctctaagctatctccattattttttgttgcaatcaccatgtgcatcatctgttgtgtaccctcatgcggttctccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCTGGCCGAACTGGCCGTGCTGGGAAGAAGGGCACTGCAATTGTGATGTACA

Basic information

species Zea mays
transcript GRMZM2G565140_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G565140_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g41715.1 (Oryza sativa), 3'ss of exon 5
----------------------------------------------------------gtttgtgcttccccttctctaagctatctccattattttttgttgcaatcaccatgtgcatcatctgttgtgta-ccctcatgcggttctccttgtt----cagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCTGGCCGAACTGGCCGTGCTGGGAAGAAGGGCACTGCAATTGTGATGTACA
                                                          | |||   |||     || |    ||  |   || |||||   |  ||  | ||  | ||   | |||||   |   ||   | |  |  ||||  |    |||||||||||||| ||||||||||| || || ||  | || |||||||| ||||||||||||||||||||||| |||||||| |  |||||||| ||| |||
gttagtgttttccttgattattctgctcttctaattttgtatgaaatagctgtttctaggttggttttctttcgctgtgttttaggttgtttttttttaaataaaaatagcaactacactttgtgttgaacagtgcttgagtgacttcccttccttttacagGTGATACATTTTGAATTGCCAAACTCCTCGGAATTGTTTGTTCACAGGTCTGGCCGAACTGGCCGTGCTGGAAAGAAGGGTAAGGCAATTGTTATGCACA

upper sequence: GRMZM2G565140_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G41510.1 (Glycine max), 3'ss of exon 6
gtttgtgcttccccttctctaagctatctccattattttttgttgcaat-caccatgtgcatcatctgttgtgtac---cctcatgcggttctccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCTGGCCGAACTGGCCGTGCTGGGAAGAAGGGCACTGCAATTGTGATGTACA
|  | |   |    |    |  |  || || |     ||    | || | |||  |||   |    |  | ||||      | |   |||| ||  | | ||||| ||||||| |||  | || ||||| || |||||||| |||||  ||||||| ||||||||||||||||||||||| || | ||| ||| |  | ||||
gcctttatgtaatatatatt--gtcatttcaaacccattgacatacacttcactttgtttgttgatttgtatgtaaatattttacttggttttctct-tacagGTAATACATTACGATCTTCCCAATTCATCTGAGATATTTGTTCATCGATCTGGACGAACTGGCCGTGCTGGGAAGAAAGGAAGTGCGATTCTTGTTTACA

upper sequence: GRMZM2G565140_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA18G14670.1 (Glycine max), 3'ss of exon 5
gtttgtgcttccccttctctaagctatctccatt----attttttgttgca-atcaccatgtgcatcatctgt-tgtgtaccctcatgcggttctccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCTGGCCGAACTGGCCGTGCTGGGAAGAAGGGCACTGCAATTGTGATGTACA
  || ||| |     | | |||  |||   ||||    |    |||    | |     ||     |  | ||| |||  |   | |   |||| ||||  | ||||| |||||||  ||  | || ||||| ||||||||||| |||||  ||||||| ||||||||||||||||||||||| || | ||| ||| |  | | ||
--ttatgccttta--tgtgtaatatattgtcatttcaaacccattgacatacactgttattcaatttgtttgtatgtaaatttttacttggtt-tcctcttacagGTAATACATTATGATCTTCCCAATTCATCAGAGATATTTGTTCATCGATCTGGACGAACTGGCCGTGCTGGGAAGAAAGGAAGTGCCATTCTTTTTTTCA

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|32842833|gb|CD982514.1|CD982514
EST:     TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTG                         GTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
genomic: TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
EST: gi|32842842|gb|CD982523.1|CD982523
EST:     TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTG                         GTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
genomic: TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
EST: gi|32842824|gb|CD982505.1|CD982505
EST:     TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTG                         GTGATACATCTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
genomic: TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
EST: gi|32842589|gb|CD982270.1|CD982270
EST:     TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTG                         GTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
genomic: TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
EST: gi|32842460|gb|CD982141.1|CD982141
EST:     TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCCAATGTAGATCTG                         GTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
genomic: TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
EST: gi|32842456|gb|CD982137.1|CD982137
EST:     TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTG                         GTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
genomic: TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
EST: gi|32842583|gb|CD982264.1|CD982264
EST:     TTGCTCCTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTG                         GTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
genomic: TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
EST: gi|32842809|gb|CD982490.1|CD982490
EST:     TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTG                         GTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
genomic: TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
EST: gi|32842651|gb|CD982332.1|CD982332
EST:     TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTG                         GTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
genomic: TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
EST: gi|32842391|gb|CD982072.1|CD982072
EST:     TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCC-AAATGTAGATCTG                         GTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
genomic: TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
EST: gi|32842806|gb|CD982487.1|CD982487
EST:     TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTG                         GTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
genomic: TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
EST: gi|32842737|gb|CD982418.1|CD982418
EST:     TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTG                         GTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
genomic: TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
EST: gi|22543120|gb|BU093558.1|BU093558
EST:     TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTG                         GTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
genomic: TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
EST: gi|32842485|gb|CD982166.1|CD982166
EST:     TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTG                         GTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
genomic: TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
EST: gi|32842761|gb|CD982442.1|CD982442
EST:     TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTG                         GTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
genomic: TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
EST: gi|32842566|gb|CD982247.1|CD982247
EST:     TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTG                         GTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
genomic: TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
EST: gi|32842771|gb|CD982452.1|CD982452
EST:     TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTG                         GTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
genomic: TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
EST: gi|32842765|gb|CD982446.1|CD982446
EST:     TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTG                         GTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
genomic: TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
EST: gi|32842619|gb|CD982300.1|CD982300
EST:     TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTG                         GTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
genomic: TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
EST: gi|32842579|gb|CD982260.1|CD982260
EST:     TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTG                         GTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
genomic: TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
EST: gi|32842750|gb|CD982431.1|CD982431
EST:     TTGCTCCTGCTGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTG                         GTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
genomic: TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
EST: gi|32842646|gb|CD982327.1|CD982327
EST:     TTGCTCCTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTG                         GTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
genomic: TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
EST: gi|32841848|gb|CD981529.1|CD981529
EST:     TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTG                         GTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
genomic: TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
EST: gi|32842834|gb|CD982515.1|CD982515
EST:     TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTG                         GTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT
genomic: TTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCT

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: 122

AAGAGAGAGGACACTGGCAGGATTTCGGGATGGGCGGTTTAATATATTGATTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCTGGCCGAACTGGCCGTGCTGGGAAGAAGGGCACTGCAATTGTGATGTACA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 66

AAGAGAGAGGACACTGGCAGGATTTCGGGATGGGCGGTTTAATATATTGATTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCTGGCCGAACTGGCCGTGCTGGGAAGAAGGGCACTGCAATTGTGATGTACA


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

AAGAGAGAGGACACTGGCAGGATTTCGGGATGGGCGGTTTAATATATTGATTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCTGGCCGAACTGGCCGTGCTGGGAAGAAGGGCACTGCAATTGTGATGTACA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 40

AAGAGAGAGGACACTGGCAGGATTTCGGGATGGGCGGTTTAATATATTGATTGCTACTGATGTCGCTTCTCGTGGATTGGATATCCCAAATGTAGATCTGgtttgtgctt ... ccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCTGGCCGAACTGGCCGTGCTGGGAAGAAGGGCACTGCAATTGTGATGTACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaatcaccatgtgcatcatctgttgtgtaccctcatgcggttctccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCTGGCCGAACTGGCCGTGCTGGGAAGAAGGGCACTGCAATTGTGATGTACA
                                         ttctccttgttc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgcttccccttctctaagctatctccattattttttgttgcaatcaccatgtgcatcatctgttgtgtaccctcatgcggttctccttgttcagGTGATACATTTCGAATTGCCAAATTCGTCAGAGATATTCGTTCACAGATCTGGCCGAACTGGCCGTGCTGGGAAGAAGGGCACTGCAATTGTGATGTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG