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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagaacaaacacaattacaactaaaaatataacatattcttaacttcaggggaactttcttattgaatattgtttcattactaaatttgatctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA

Basic information

species Zea mays
transcript GRMZM2G113592_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113592_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os10g02630.1 (Oryza sativa), 3'ss of exon 6
aaagaacaaacacaattacaactaaaaatataacatattcttaacttcaggggaactttcttattgaatattgtttcattactaaatttga--tctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA
 ||  | | | ||||||  ||  | ||     | | |||||||| ||||| | |  |||||| ||| | |    || ||   || ||||||  | ||| ||||| || ||||| || || || || |||| |||||||||||||||||||||||| |||||| ||||||| || ||||||||||
-aaacaaacaaacaattgtaatgacaaccggca-acattcttaagttcagtgcatatttctttttggaaagaccttaatgggtacatttgagctttttgcagGTACGGCTTGTGACCGACAAGGAAACAAATAAACCTAGAGGATATGCATTCATCGAGTATATGCACACCCGGGACATGAAAA

upper sequence: GRMZM2G113592_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA01G38120.1 (Glycine max), 3'ss of exon 6
aaagaacaaacacaattacaactaaaaatataacatattcttaacttcagg--ggaactttct-tattgaatattgtttcattactaaatttgatctt--tccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA
   |||   |   | ||     ||    | ||   | ||   | ||  ||    ||| ||||| |  ||| || | |||| ||  |||||||  |  |  |  |||||||  | ||  |||| |||||||||| ||| || || || ||||| |||||||||||| |||| ||| ||||||||||| 
--tgaaatgagggagttttgttta---ttttattttctttgcagctgaagaccagaattttctgttctgactagtttttcttttttaaattttcttgtgatttagGTTCGATTAGTTGCTGACAAAGATACAAATAAGCCCAGGGGTTATGCTTTCATTGAGTATCTGCATACAAGAGACATGAAAG

upper sequence: GRMZM2G113592_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv04s0023g01580.t01 (Vitis vinifera), 3'ss of exon 6
aaagaacaaacacaattacaactaaaaatataacatattcttaacttcaggggaactttcttattgaatattgtttcattactaaatttgatctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA
 |||| ||||||  ||       || |   |  | |  |    |  | |    |  ||| ||| |  |  || ||| |    |   ||||| |||| ||||| || ||  | || || ||||| || |||||||||||||| ||||| |||||||| ||| |||| ||||| || |||||| 
taagatcaaacatcatctgtttcaatatgttttcttgattcagatatgaatctacttttattactttagtttatttaacctttttctttgagctttgcagGTCCGACTCATTACCGACAAAGAGACTAGTAAACCTAGAGGTTATGCTTTCATTGAATATATGCATACACGGGATATGAAAG

upper sequence: GRMZM2G113592_T02 (Zea mays), 3'ss of exon 6
lower sequence: PP1S42_265V6.1 (Physcomitrella patens), 3'ss of exon 6
-----aaagaacaaacacaattacaactaaaaatataacatattcttaacttcaggggaactttcttattgaatattgtttcattactaaatttgatctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA
     |    ||| | | | ||  |  | |  |||   |  |||  |||   ||  ||||        |||       ||  | | ||       |||||  ||||| || ||||||  ||| |||  | |||     ||  ||||||||||||| |||||||||  |||||| || ||||||||||
ttcgcattttacagagatacttgtagatgatgata---cgcatttgtaag--cattggaagcagagggttgggctgacttgaactccttctgcctatcttctcagGTCCGACTTGTACATGATAAAACTTCAAAGGCTCCCCGAGGATATGCATTTATTGAGTATCAGCACACTCGGGACATGAAAA

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|148969418|gb|EE020215.2|EE020215
EST:     CTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGG                         GTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTC
genomic: CTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGGgtaagtaatg ... atctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTC
EST: gi|30087143|gb|CB885351.1|CB885351
EST:     CTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGG                         GTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTC
genomic: CTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGGgtaagtaatg ... atctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTC
EST: gi|149078708|gb|EE167506.2|EE167506
EST:     CTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTTAAAGG                         GTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTC
genomic: CTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGGgtaagtaatg ... atctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTC
EST: gi|71312602|gb|DR792823.1|DR792823
EST:     CTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGG                         GTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTC
genomic: CTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGGgtaagtaatg ... atctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTC
EST: gi|91873232|gb|EB403189.1|EB403189
EST:     CTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGG                         GTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTC
genomic: CTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGGgtaagtaatg ... atctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTC
EST: gi|31358158|gb|CD442515.1|CD442515
EST:     CTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGG                         GTTCGTCTTGTAACTGAGAAAGATACCAGTAAACCTAGAGGATATGCATTC
genomic: CTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGGgtaagtaatg ... atctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTC
EST: gi|91052321|gb|EB162739.1|EB162739
EST:     CTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGG                         GTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTC
genomic: CTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGGgtaagtaatg ... atctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTC
EST: gi|149072504|gb|EE160783.2|EE160783
EST:     CTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGG                         GTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTC
genomic: CTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGGgtaagtaatg ... atctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTC
EST: gi|30307225|gb|CD001898.1|CD001898
EST:     CTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGG                         GTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTC
genomic: CTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGGgtaagtaatg ... atctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTC
EST: gi|211227312|gb|FL251473.1|FL251473
EST:     CTGAGCAGAGGATCAAATGCGAGTTTGAAGGTTATGGTCCTATTAAAAGG                         GTTCGTCTTGTAACTGAGAAAGATCCAAGTAAACCTAGAGGATATGCATTC
genomic: CTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGGgtaagtaatg ... atctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTC
EST: gi|211227315|gb|FL251476.1|FL251476
EST:     TGAGCAGAGGATCAAACGCGAGTTTGAAGGGTATGGTCCCTATTAAA-GG                         GTTCGTCTTGNTA-CTGANGAA-GATACAAGTAAACCTAGAGGATATGCAT
genomic: TGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCC-TATTAAAAGGgtaagtaatg ... atctttccagGTTCGTCTTG-TAACTGA-GAAAGATACAAGTAAACCTAGAGGATATGCAT
EST: gi|71310643|gb|DR791619.1|DR791619
EST:     CTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGG                         GTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTC
genomic: CTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGGgtaagtaatg ... atctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTC
EST: gi|91051679|gb|EB162097.1|EB162097
EST:     CTGAGCAGAGGATCAAACGCGAGTTTGAAGGGTATGGTCCTATTAAAAGG                         GTTCGTCTTGTAACTGAGAAAGATACAAGTA
genomic: CTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGGgtaagtaatg ... atctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTA

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: 48 (upstream exon), 49 (downstream exon)
Score: 790

AACTATGAGACATCTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGGgtaagtaatg ... atctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 445

AACTATGAGACATCTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGGgtaagtaatg ... atctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 421

AACTATGAGACATCTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGGgtaagtaatg ... atctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 461

AACTATGAGACATCTGAGCAGAGGATCAAACGCGAGTTTGAAGGTTATGGTCCTATTAAAAGGgtaagtaatg ... atctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaggggaactttcttattgaatattgtttcattactaaatttgatctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA
                                              tctttcc  CT-rich tract
               ttattgaatattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagaacaaacacaattacaactaaaaatataacatattcttaacttcaggggaactttcttattgaatattgtttcattactaaatttgatctttccagGTTCGTCTTGTAACTGAGAAAGATACAAGTAAACCTAGAGGATATGCATTCATTGAGTATGTGCACACACGAGACATGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- -gaacaaa
- - - - - - - - - - - -aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttca