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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccacagacaactaacgggacgagggtttgttcgtttgagttgtcttggctacaatattatgcagttgcttatgtctgcaaggcgcatctcaatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG

Basic information

species Zea mays
transcript GRMZM2G375002_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G375002_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g58730.2 (Oryza sativa), 3'ss of exon 1
----ccacagacaactaacgggacgagggtttgttcgtttgagttgtcttggctacaatattatgcagttgcttatgtctgcaaggcgcatctcaatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG
         |  ||  ||     | |  || | | | | |  |   | ||   |   | | | |    ||  |      |        |||||| ||| | |||||||||||||||||||| || || ||||||||||| ||||||||||| || ||||||||||| ||||||||  |||||||||||||||
tcgttttgtgcgaaaaaataaatctaatgtat-tgcatctttgcatttttaattggcagactgtatgtttaatgggacatttc---ttcatctctatgttacagGACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAG

upper sequence: GRMZM2G375002_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT4G35020.3 (Arabidopsis thaliana), 3'ss of exon 3
-ccacagacaactaacgggacgagggtttgttc-gtttgagttgtcttggctacaatattatgcagttgcttatgtctgcaaggcgcatctcaatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG
      |   |        | ||   |       || | || |  |||  ||  ||    ||   || ||| |||| |  |  |    | || |||   ||||| ||||| |||||||||||||| || ||||||||||||||  | ||||| || | |||| ||||||||||  |||||||||| ||||
aatgttgttgatctgtttaatgatcttagaaagagtgttaggtaacttt-ctgtaaggagattttgtagctgatgttt-tagtggaattttctatgtgacagGATTATGTGCCAACTGTGTTCGATAATTTCAGTGCCAATGTGATTGTTGATGGCAACACTATCAACTTGGGATTGTGGGATACTGCAG

upper sequence: GRMZM2G375002_T03 (Zea mays), 3'ss of exon 1
lower sequence: PP1S257_74V6.1 (Physcomitrella patens), 3'ss of exon 1
-----ccacagacaactaacgggacgagggtttgttcgtttgagttgtcttggctacaatattatgcagttgcttatgtctgcaaggcgcatctcaatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG
      || || |    |   |   || | | ||  | | |   |||| | | | ||  |    |||| || | |  |     ||   | |  |   |    ||||| || || || ||||| |||||||||||||| || ||||| ||||| || ||||  || |||||| |||| || |||||||||||||
ttctaacagaggcgtggacacgcgtgatgatatgg-catgttctttgtatggaccactgt----tgcattttccttggctgaaaaatggaactttcgtctcacagGATTACGTCCCTACTGTATTCGACAACTTCAGCGCGAATGTCGTGGTCGATGGGAATACCGTCAACCTGGGACTATGGGATACAGCAG

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|211163176|gb|FK955403.1|FK955403
EST:     TCGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTYNCCCACT                         GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGAC
genomic: TCGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACTgtgagttgag ... aatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGAC
EST: gi|211163177|gb|FK955404.1|FK955404
EST:     TCGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACT                         GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGAC
genomic: TCGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACTgtgagttgag ... aatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGAC
EST: gi|32909548|gb|CF014360.1|CF014360
EST:     TCGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACT                         GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGAC
genomic: TCGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACTgtgagttgag ... aatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGAC
EST: gi|211236584|gb|FK955431.1|FK955431
EST:     CGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTT-CGCCCACT                         GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGA
genomic: CGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTC-CCCACTgtgagttgag ... aatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGA
EST: gi|211520026|gb|FL347002.1|FL347002
EST:     CGGAAAGACCTGCATGCTCATCTCCTACACATCCGAACAC-TTYCCCACT                         GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGAC
genomic: CGGAAAGACCTGCATGCTCATCTCCTACACATCC-AACACTTTCCCCACTgtgagttgag ... aatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGAC
EST: gi|32936373|gb|CF041192.1|CF041192
EST:     TCGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACT                         GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGAC
genomic: TCGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACTgtgagttgag ... aatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGAC
EST: gi|32827834|gb|CD967512.1|CD967512
EST:     TCGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACT                         GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGAC
genomic: TCGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACTgtgagttgag ... aatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGAC
EST: gi|211356949|gb|FL222513.1|FL222513
EST:     TCAGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACT                         GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGAC
genomic: TCGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACTgtgagttgag ... aatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGAC
EST: gi|78107806|gb|DV526224.1|DV526224
EST:     TCGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACT                         GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGAC
genomic: TCGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACTgtgagttgag ... aatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGAC
EST: gi|16918068|gb|BM073562.1|BM073562
EST:     TCGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACT                         GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGAC
genomic: TCGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACTgtgagttgag ... aatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGAC
EST: gi|12047201|gb|BF729340.1|BF729340
EST:     TCGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACT                         GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGAC
genomic: TCGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACTgtgagttgag ... aatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGAC
EST: gi|32858427|gb|CD998108.1|CD998108
EST:     TCGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACT                         GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGAC
genomic: TCGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACTgtgagttgag ... aatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGAC
EST: gi|33467050|gb|CF244099.1|CF244099
EST:     GAAAGACCTGCATGCTCATCTCCTACACATCCAACACGTTCCCCACT                         GACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGAC
genomic: GAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACTgtgagttgag ... aatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGAC

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: 271

GATGAGCGCGTCTCGGTTCATCAAGTGCGTCACCGTGGGGGACGGTGCCGTCGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACTgtgagttgag ... aatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 322

GATGAGCGCGTCTCGGTTCATCAAGTGCGTCACCGTGGGGGACGGTGCCGTCGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACTgtgagttgag ... aatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 312

GATGAGCGCGTCTCGGTTCATCAAGTGCGTCACCGTGGGGGACGGTGCCGTCGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACTgtgagttgag ... aatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 344

GATGAGCGCGTCTCGGTTCATCAAGTGCGTCACCGTGGGGGACGGTGCCGTCGGAAAGACCTGCATGCTCATCTCCTACACATCCAACACTTTCCCCACTgtgagttgag ... aatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggctacaatattatgcagttgcttatgtctgcaaggcgcatctcaatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG
     acaatattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccacagacaactaacgggacgagggtttgttcgtttgagttgtcttggctacaatattatgcagttgcttatgtctgcaaggcgcatctcaatgctgcagGACTATGTTCCAACTGTGTTCGACAACTTCAGTGCCAATGTTGTGGTTGACGGGAGCACTGTCAACTTGGGTCTGTGGGATACAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA