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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgaactgaaacgagacaaataaaaaagaactgggggagtatctgacaccgttacgacttacgtttataagtaaaatattgcaacttctgtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGTGACTGTGAATATGCATATATGATGGACAGCTTAACTGCATACCAACATG

Basic information

species Zea mays
transcript GRMZM2G158872_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158872_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os11g43950.1 (Oryza sativa), 3'ss of exon 7
tttgaactgaaacgagacaaataaaaaagaactgggggagtatctgacaccgttacgacttacgtttataagtaaaatattgcaacttctgtgttaa-cagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGTGACTGTGAATATGCATATATGATGGACAGCTTAACTGCATACCAACATG---------
  |    |     |      ||   |  |   |     ||| |   |     ||| ||  |  |    | | | |  |    |  | | ||  | || |||||||||||||||||||||||||||||||||||||| | || || || || |     |||||    ||| ||| |   |||| |||||  ||||| |||||         
cattgtttctcttgctcatcatgctattgctgtttataagtcttatattttatta-gatgtctgccgttcacttatcttccaccgcatttgcataaaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTTTAAACCATCCACCATA----TGAATGGATATAAATGTT---CAGCCTAACT--ATACCCACATGAAGAACTGG

upper sequence: GRMZM2G158872_T01 (Zea mays), 3'ss of exon 7
lower sequence: AT4G12770.1 (Arabidopsis thaliana), 3'ss of exon 7
------------------------------------------------------------------------tttgaactgaaacgagacaaataaaaaagaactgggggagtatctgacaccgttacgacttacgtttataag--taaaatattgcaacttctgtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGTGACTGTGAATATGCATATATGATGGACAGCTTAACTGCATACCAACATG--
                                                                         |  |  |  |  | | |   | |   |  ||| |  ||    |  |       |  |   |  || |   |  | || | ||    | |     | ||||||| |||||||||||||||||||| || || ||||| ||||  |||||  | ||   ||  | ||    | || ||  |  ||  |  ||  |  |  | |  
gtatgattcaacatctttctggaactaaatccatcactgctactttcagatgccaccaaaggaaccaaaaaaatccacttagactgcgtctcctcatggatgactagaagaaccgcacaattgtacaaaatccatattaactggcttgaactcttttctcatgacaataaacagGAAGCATGGAACAAATTCAACTCAGAGGAACTCTTTTGAAAAAACCT--GAGATAATGTTTTTGAGAGTGTGTTGTTCGTCTCTAGCGCGAAAGATGAAGCA
















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|6227229|gb|AW155828.1|AW155828
EST:     CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAN                         GAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCC
genomic: CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAGgtacgtgaac ... gtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCC
EST: gi|32863076|gb|CF002758.1|CF002758
EST:     CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAG                         GAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGT
genomic: CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAGgtacgtgaac ... gtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGT
EST: gi|5847361|gb|AW000440.1|AW000440
EST:     CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAG                         GAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGT
genomic: CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAGgtacgtgaac ... gtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGT
EST: gi|5860429|gb|AW011651.1|AW011651
EST:     CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAG                         GAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACC
genomic: CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAGgtacgtgaac ... gtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACC
EST: gi|5325205|gb|AI783396.1|AI783396
EST:     CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAG                         GAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCC
genomic: CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAGgtacgtgaac ... gtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCC
EST: gi|116816443|gb|EC859181.1|EC859181
EST:     CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAG                         GAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGT
genomic: CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAGgtacgtgaac ... gtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGT
EST: gi|32836578|gb|CD976256.1|CD976256
EST:     CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAG                         GAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGT
genomic: CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAGgtacgtgaac ... gtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGT
EST: gi|5895879|gb|AW037125.1|AW037125
EST:     CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAG                         GAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGN
genomic: CAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAGgtacgtgaac ... gtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGT

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), 46 (downstream exon)
Score: 76

CAGGAAGGCAACACTGTGCATTCATCCTGATAAGGTGCAACAGAAAGGTGCAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAGgtacgtgaac ... gtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGTGACTGTGAATATGCATATATGATGGACAGCTTAACTGCATACCAACATG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 87

CAGGAAGGCAACACTGTGCATTCATCCTGATAAGGTGCAACAGAAAGGTGCAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAGgtacgtgaac ... gtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGTGACTGTGAATATGCATATATGATGGACAGCTTAACTGCATACCAACATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

CAGGAAGGCAACACTGTGCATTCATCCTGATAAGGTGCAACAGAAAGGTGCAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAGgtacgtgaac ... gtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGTGACTGTGAATATGCATATATGATGGACAGCTTAACTGCATACCAACATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 74

CAGGAAGGCAACACTGTGCATTCATCCTGATAAGGTGCAACAGAAAGGTGCAACACTTCAGCAGAAATATATTGCCGAAAAAGTCTTTGACATTCTTAAGgtacgtgaac ... gtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGTGACTGTGAATATGCATATATGATGGACAGCTTAACTGCATACCAACATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacaccgttacgacttacgtttataagtaaaatattgcaacttctgtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGTGACTGTGAATATGCATATATGATGGACAGCTTAACTGCATACCAACATG
           gacttac  putative branch site (score: 74)
                                        cttctgt  putative PPT
              ttacgtttataagtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgaactgaaacgagacaaataaaaaagaactgggggagtatctgacaccgttacgacttacgtttataagtaaaatattgcaacttctgtgttaacagGAGGCATGGAACAAATTCAACTCTGAAGAGCTCTTCTGAAGCAACCTCCGTGACTGTGAATATGCATATATGATGGACAGCTTAACTGCATACCAACATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- tgaactg
- - - - - - - agacaaa
- - - - - - - - - - -taaaaaa
- - - - - - - - - - - - - - - - - - - - - -ctgacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagtaaaa