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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgattcctctgattctatctataaaaagaaactatcttatcttaatatgtgccattactgttgcttctactgcttgatttttcgaaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAG

Basic information

species Zea mays
transcript GRMZM5G829894_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G829894_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g05630.1 (Oryza sativa), 3'ss of exon 5
gtagtgattcctctgattctatctataaaaagaaactatcttatcttaatatgtgccattactgttgcttctactgcttgatttttcgaaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAG
   || ||| |  ||||||  |      |||  | |||| ||   ||  ||  ||  || |   ||| ||||       | ||   |||  |||| |||||| ||||| || ||||||||||||||||| ||||| |||||||||||||| || |||||||||||||| || ||||| || || ||||||
---gtaatttca-tgattccttt----gaaattatctattttgctttg-tacttgtaatgatcattggttctttctaacggttgaacgac-tttgcagGGACGTGGCGTGTTGGTGGTGTTCTTGCTGTTTCTCGAGCATTTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAG

upper sequence: GRMZM5G829894_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g05630.3 (Oryza sativa), 3'ss of exon 5
gtagtgattcctctgattctatctataaaaagaaactatcttatcttaatatgtgccattactgttgcttctactgcttgatttttcgaaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAG--------
   || ||| |  ||||||  |      |||  | |||| ||   ||  ||  ||  || |   ||| ||||       | ||   |||  |||| |||||| ||||| || ||||||||||||||||| ||||| |||||||||||||| || |||||||||||||| || ||||| || || ||||||        
---gtaatttca-tgattccttt----gaaattatctattttgctttg-tacttgtaatgatcattggttctttctaacggttgaacgac-tttgcagGGACGTGGCGTGTTGGTGGTGTTCTTGCTGTTTCTCGAGCATTTGGTGATAAGCTATTGAAGCAGTATGTAGTTGCTGATCCAGAGATCAAGGTTTGACT

upper sequence: GRMZM5G829894_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G33690.2 (Glycine max), 3'ss of exon 6
gtagtgattcctctgattctatctataaaaagaaactatcttatcttaatatgtgccattactgttgcttctactgcttgatttttcgaa------atttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAG
             | |    |||| || |   |   | | |||| || || | |   |||  ||||| || |     | ||  |||  ||       |||  ||| || ||| |||| ||||| ||||||||||| || || ||||||||||||| |||| |||||||||||||||| ||||| || |||||| ||
------------gtaaggtcatct-tatagttagtttttgttat-ttgatttatag-attcttgttgtttgtctctatggaaattttaaacactatgtttacagGAACTTGGAGAGTTGGTGGAGTTCTTGCTGTTTCACGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATCCAG

upper sequence: GRMZM5G829894_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 5
gtagtgattcctctgattct--atctataaaaagaaactatcttat---cttaatatgtgccattactgt----tgcttctactgcttgatttttcgaaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAG
||| ||    | || ||  |  |  ||||   ||      | ||||   ||||||       ||   | |    ||||| |     |||||        || |  ||| || ||| |||| || |||||||||||||| ||||| || |||||||||| |||| |||||||||||||||| ||||| || |||||  ||
gtaatgtcatcactcatcattaacatatagtcagctttagttttatttacttaattcaaaaaatatatatataatgcttatcactattgataacatcgcatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCGTTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG

upper sequence: GRMZM5G829894_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA14G12220.1 (Glycine max), 3'ss of exon 5
gtagtgat-tcctctgattctatctataaaaagaaactatcttatcttaatatgtgccattactgttgct-tctactgcttgatttttcgaaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAG
|||  | | || |||  ||   | | |   |      |   ||||  ||| ||    | |   |||  || |  |     | |    |  |  |||  ||| || ||| |||| ||||| ||||||||||| || || ||||||||||||| |||| |||||||||||||||| ||||| || |||||| ||
gtaaggttatcttctagttagctttttgttat----ttgatttattataagattcatcttgtttgtcactatggaaaatctaaacact--atgtttacagGAACTTGGAGAGTTGGTGGAGTTCTTGCTGTTTCACGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATCCAG

upper sequence: GRMZM5G829894_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 6
gtagtgattcctctgattctatctataaaaagaaactatcttatcttaatatgtgccattactgttgcttctactgcttgatttttcgaaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAG
||| ||    |  | |   |||    |     |   |   |||| | | | |       || |  || || |     |||||      | || |  ||| || ||| |||| || |||||||||||||| ||||| ||||||||||||| |||| |||||||||||||||| ||||| || |||||  ||
gtaatgtcatcattaaca-tatagtcagctttagttttatttatttaattctaaaaagata-taatgtttatctctgttgataacattacatatacagGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG

upper sequence: GRMZM5G829894_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT4G31750.1 (Arabidopsis thaliana), 3'ss of exon 6
gtagtgattcctctgattctatctataaaaagaaactatcttatcttaatatgtgccattactgttgcttctactgcttgatttttcgaaattt-----gtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAG
                             ||||||  || | |    ||| | |    ||| |  ||||| ||    ||| ||  | | ||||        ||| |||||| |||| || || ||||||||||| ||||| |||||||| ||||   | ||||||||||||||||| ||||| || || ||  ||
---------------------------gtaagaaaacatttaactgaaatttctcttcttatttgtgcttatataatttgcttaattggaattatactaaaagGAACATGGAGAGTTGGAGGAGTTCTTGCTGTTTCTCGTGCATTTGGCGATAGGTTGTTGAAGCAGTATGTTGTTGCTGATCCGGAGATACAG

upper sequence: GRMZM5G829894_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 3'ss of exon 6
gtagtgattcctctgattctatctataaaaagaaactatcttatcttaatatgtgccattact-----gttgcttctactgcttgatttttcgaa---atttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAG
|||  ||   |  |  ||   | | |  || | |   ||| ||    ||  | | |  | | |      ||||||  |     | ||  ||  ||    |||  ||| || ||| | || || |||||||||||||| ||||| ||||||||||||| ||||||||||||||||||||| ||||| || |||||| ||
gtaaggacatcaatcgttaggtttttccaa-gtattaatcatagaacaaagtttccagtgatttggtaattgcttgcatcttctaatgattgaaattcgtttacagGAACTTGGAGGGTTGGGGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCTTGAAGCAGTATGTTGTTGCTGATCCAGAAATCCAG

upper sequence: GRMZM5G829894_T02 (Zea mays), 3'ss of exon 3
lower sequence: PP1S17_286V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------gtagtgattcctctgattctatctataaaaagaaactatcttatcttaatatgtgcc--attactgttgcttctactgcttgatttttcgaaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAG
                               || | |     ||     ||| |   |   ||| | |  ||     ||| ||| ||  || | | ||  |       | |   | ||||   || | ||| || ||||| |||||||||||||||||||||||||| |||||||| ||    ||  ||||  | ||||| |||||||| || |||||  ||
gtgagtcacgtatctcgtctgtaccgaagattacttaagaagctcgaagtatttgggatttgaagcaaattttgtaaaatttgttccgtatgagtattcatcgcctcaccttggtgttcgctgtt-gcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAG

upper sequence: GRMZM5G829894_T02 (Zea mays), 3'ss of exon 3
lower sequence: PP1S225_37V6.2 (Physcomitrella patens), 3'ss of exon 5
---gtagtgattcctctgattctatct-ataaaaagaaactatcttatcttaatatgtgccattactgttgcttctactgcttgatttttcgaaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAG
   |||    |  || |  || ||| | ||   |    | |   |||| | | | | | |  ||   |  ||     ||   ||||   |   | | || ||| || ||||| || ||||| ||||||||||| ||||| ||||||||||||   ||  ||||  | |||||||| || || || |||||  ||
aaagtatcattctctatcgttttattttattttattttatttatttatttca-tctat-ctgtttgaggagcactgtcttagtgataagttcgattatgcagGTACTTGGCGTGTAGGTGGCGTTCTTGCTGTGTCTCGGGCATTTGGTGATCGGCTGCTGAAAAAATATGTTGTTGCCGAACCAGAAATTCAG

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|60398872|gb|DN231688.1|DN231688
EST:     AGATGAGAGACAAAGAATGGAGGACGCAGGGGGCTTTTTTATGTGGGTTG                         GGACATGGGGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGAAT
genomic: AGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattc ... aaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTG-AT
EST: gi|166421171|gb|EG149350.1|EG149350
EST:     AGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG                         GGACATGGCGAGTGGG
genomic: AGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattc ... aaatttgtagGGACATGGCGAGTGGG
EST: gi|60359012|gb|DN225985.1|DN225985
EST:     ACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG                         GGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
genomic: ACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattc ... aaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
EST: gi|60352815|gb|DN219788.1|DN219788
EST:     AGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG                         GGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
genomic: AGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattc ... aaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
EST: gi|60358897|gb|DN225870.1|DN225870
EST:     ATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG                         GGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
genomic: ATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattc ... aaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
EST: gi|71326203|gb|DR799792.1|DR799792
EST:     AGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG                         GGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
genomic: AGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattc ... aaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
EST: gi|60399036|gb|DN231852.1|DN231852
EST:     ATGAGAGACAAAGGAATTGAGGACGCAGGGGGGCTTTGTTATGTGGGCTG                         GGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
genomic: ATGAGAGACAAA-GAATTGAGGACGCA-GGGGGCTTTGTTATGTGGGCTGgtagtgattc ... aaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
EST: gi|31909593|gb|CD650996.1|CD650996
EST:     AGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTG                         GGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA
genomic: AGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattc ... aaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATA

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: 511

CTCGGAGCTGCAGCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattc ... aaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 433

CTCGGAGCTGCAGCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattc ... aaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 620

CTCGGAGCTGCAGCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattc ... aaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 389

CTCGGAGCTGCAGCGATTGCGGTTTCAAGGGATCACAAACCTGATCAGACAGATGAGAGACAAAGAATTGAGGACGCAGGGGGCTTTGTTATGTGGGCTGgtagtgattc ... aaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttaatatgtgccattactgttgcttctactgcttgatttttcgaaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAG
                                     atttttcgaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtgattcctctgattctatctataaaaagaaactatcttatcttaatatgtgccattactgttgcttctactgcttgatttttcgaaatttgtagGGACATGGCGAGTGGGTGGTGTTCTTGCTGTCTCTCGCGCATTTGGTGATAAACTCTTGAAGCAGTATGTTGTCGCTGACCCTGAAATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC