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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggacccttaaactagacgaggcttgacatcggttttgtgattccagactttcttcttaaagatgctgatcaccacggttctattcgttttatgtttcagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCAGGTAGCACCTACCGCACAAGGGATGAGATCGCTGGCATAAGGCAG

Basic information

species Zea mays
transcript GRMZM2G027627_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027627_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g13720.1 (Oryza sativa), 3'ss of exon 3
aggacccttaaactagacgaggcttgacatcggt--tttgtg--attccagactttcttcttaaagatgctgatcaccacggttctattcgttttatgtttcagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCAGGTAGCACCTACCGCACAAGGGATGAGATCGCTGGCATAAGGCAG
    | | ||   |     ||  |      || |  |  ||   |  |   |   |  ||||  ||||||   | ||      | ||| |  |   ||||  |||| ||||||||||||||||||||||||||||| ||||| |||||||||||||| ||||| |||||||| || ||||| || || |||||||| |||
---gctcatattgttcgatagattcagtgccgctaatcagtagaaaacacaatcctgctcttggagatgcatgtaactttt-ctatatcctctcggtgttgtagATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCAGGGAGCACTTACCGCACCAGAGATGAAATTGCAGGCATAAGACAG

upper sequence: GRMZM2G027627_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 3
aggacccttaaactagacgaggcttg----acatcggttttgtgattccagactttcttct--taaagatgctgatcaccacggttctattcgttttatgtttcagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCAGGTAGCACCTACCGCACAAGGGATGAGATCGCTGGCATAAGGCAG
       |||   |||  |    |||       | | ||   | ||   ||  | |  |||  || |  || |      | |  |  ||||  || |    | ||||| ||||| |||||||| ||||||||||| || ||||| ||||| ||||| || ||||| ||||| ||| | ||||| ||  ||||  | || |||
------tttatcatagctgtcatttgtgtagttttgattgaattatcatagtttattctctgttagatttgattgatttctctatcttattgattattctgtccagATTCTTGAAATGGACACTTACAGATACCATGGACACTCTATGTCTGATCCTGGCAGCACATACCGGACACGTGATGAAATTTCTGGTGTGAGACAG

upper sequence: GRMZM2G027627_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G40380.1 (Glycine max), 3'ss of exon 3
--------------------aggacccttaaactagacgaggcttgacatcggttttgtgattccagactttcttcttaaagatgctgatcaccacggttctattcgttttatgtt--tcagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCAGGTAGCACCTACCGCACAAGGGATGAGATCGCTGGCATAAGGCAG
                          |||| | |     ||  ||    | | ||||  || |      ||| ||||     ||  |       |    |||||     |||| ||   ||||| ||||| |||||||| ||||||||||| || ||||| ||||| ||||| || ||||| ||||| ||| | ||||||||  ||||  | || |||
gtaagtaaattaacctctcatttgtacttatattttttaagaatttttttagcttttaggaatgattcttttattctctgttatattataattgatttctctatcttaattattttgtccagATTCTTGAAATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTGAGACAG

upper sequence: GRMZM2G027627_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G17240.1 (Glycine max), 3'ss of exon 3
--------------------aggacccttaaactagacgaggcttgacatcggttttgtgattccagactttcttcttaaagatgctgatcaccacggttctattcgttttatgtt--tcagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCAGGTAGCACCTACCGCACAAGGGATGAGATCGCTGGCATAAGGCAG
                          |||| | |     |   |     | | ||||  || |      ||| ||||     ||  |       |    |||||     |||| ||   ||||| || ||||||||||| ||||||||||| || ||||| ||||| ||||| || ||||| ||||| ||| | ||||||||  ||||  |||| |||
gtaagtaaatttacttcttttttgtacttatatttcttaaatttgtgtttagattttaggaatgattcttttattctctgttatattacaattgatttctctatcttaattattttgtccagATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTAAGACAG

upper sequence: GRMZM2G027627_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G24180.1 (Arabidopsis thaliana), 3'ss of exon 3
aggacccttaaactagacgaggcttgacatcggttttgtgattccagactttcttcttaaagatgctgatcaccacggttctattcgttttatgttt-cagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCAGGTAGCACCTACCGCACAAGGGATGAGATCGCTGGCATAAGGCAG
  |    || ||  | |  ||  |||||||   |  | |  ||  |  |  |  |||      || | || ||||   | | |||    |||| |   |||||||||||||||||||| |||||||||||||| ||||| ||||| || ||||| ||||| ||||| ||  | ||||| ||| ||||| | || |||
ttgtgaattcaatcacat-agcgttgacatttatcgtatttttataatccattctctacctagtgattatgaccaacataccattgccattatttgcgcagATCCTTGAGATGGACACTTACAGATACCACGGTCACTCTATGTCTGACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAG

upper sequence: GRMZM2G027627_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 3
aggacccttaaactagacgaggcttgacatcggttttgtgattccagactt--tcttcttaaagatgctgatcaccacggttctatt----cgttttatgttt-cagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCAGGTAGCACCTACCGCACAAGGGATGAGATCGCTGGCATAAGGCAG
     | |  || |||   ||  |||   ||   ||| |  | |     ||  ||||    |  ||   ||| ||    |   || |    |||||  | | | ||||| |||||||||||||| ||||| |||||||| ||||| ||||| ||||| || ||||| ||||| ||  | ||||||||  ||||  | ||||||
-----catataagtag--tagctttggtttccaatttattttcctgtgtttattctttcctatcatatggattacagaagcattaatacatcgtttcttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCTGGGAGCACATACCGTACCCGAGATGAGATATCTGGTGTGAGGCAG

upper sequence: GRMZM2G027627_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 3
aggacccttaaactagacgaggcttgaca-tcggttttgtgattccagactttcttcttaaagatg-ctgatcaccacggttctattc---gttttatgtttcagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCAGGTAGCACCTACCGCACAAGGGATGAGATCGCTGGCATAAGGCAG
     | ||||  | |  |    |      ||  |||||  |||     | || |   | |   || || ||  |     || | |||    |  |    ||||||| ||||| |||||||| || || ||||| || ||||| ||||| ||||| || ||||||||||| ||| | ||||||||  ||||  | || |||
-----ctttaatgttgttgctagtaatttctctcttttggcattgtcatcattttatgtgagattgactaattgctttatttttcttctaaatgctggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGCACCTACCGTACACGTGATGAGATTTCTGGTGTGAGACAG

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|101391487|gb|EB817679.1|EB817679
EST:     AGCAAGCTTGCAAATTTGCCAAAGAACATGCCCTTGAAAATGGGCCAATC                         ATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCA
genomic: AGCAAGCTTGCAAATTTGCCAAAGAACATGCCCTTGAAAATGGGCCAATTgtaagtattt ... tatgtttcagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCA
EST: gi|76019405|gb|DT946575.1|DT946575
EST:     AGCAAGCTTGCAAATTTGCCAAAGAACATGCCCTTGAAAATGGGCCAATT                         ATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCA
genomic: AGCAAGCTTGCAAATTTGCCAAAGAACATGCCCTTGAAAATGGGCCAATTgtaagtattt ... tatgtttcagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCA
EST: gi|91876001|gb|EB405958.1|EB405958
EST:     AGCAAGCTTGCAAATTTGCCAAAGAACATGCCCTTGAAAATGGGCCAATT                         ATCTTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCA
genomic: AGCAAGCTTGCAAATTTGCCAAAGAACATGCCCTTGAAAATGGGCCAATTgtaagtattt ... tatgtttcagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCA
EST: gi|211508254|gb|FL470985.1|FL470985
EST:     AGCAAGCTTGCAAATTTGCCAAAGAACATGCCCTTGAAAATGGGCCAATT                         ATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCA
genomic: AGCAAGCTTGCAAATTTGCCAAAGAACATGCCCTTGAAAATGGGCCAATTgtaagtattt ... tatgtttcagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCA
EST: gi|78117770|gb|DV536157.1|DV536157
EST:     GCAAGCTTGCAAATTTGCCAAAGAACATGCCCTTGAAAATGGGCCAATT                         ATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCA
genomic: GCAAGCTTGCAAATTTGCCAAAGAACATGCCCTTGAAAATGGGCCAATTgtaagtattt ... tatgtttcagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCA
EST: gi|31349079|gb|CD433436.1|CD433436
EST:     AGCAAGCTTGCAAATTTGCCAAAGAACATGCCCTTGAAAATGGGCCAATT                         ATCCTCGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCA
genomic: AGCAAGCTTGCAAATTTGCCAAAGAACATGCCCTTGAAAATGGGCCAATTgtaagtattt ... tatgtttcagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCA
EST: gi|211508252|gb|FL470983.1|FL470983
EST:     AGCAAGCTTGCAAATTTGCCAAAGAACATGCCCTTGAAAATGGGCCAATT                         ATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCA
genomic: AGCAAGCTTGCAAATTTGCCAAAGAACATGCCCTTGAAAATGGGCCAATTgtaagtattt ... tatgtttcagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCA

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 3 RNA-Seq libraries.


Block sizes: 28 (upstream exon), 46 (downstream exon)
Score: 5

GTCGATGGAATGGATGTTCTTGCTGTGAAGCAAGCTTGCAAATTTGCCAAAGAACATGCCCTTGAAAATGGGCCAATTgtaagtattt ... tatgtttcagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCAGGTAGCACCTACCGCACAAGGGATGAGATCGCTGGCATAAGGCAG


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 10

GTCGATGGAATGGATGTTCTTGCTGTGAAGCAAGCTTGCAAATTTGCCAAAGAACATGCCCTTGAAAATGGGCCAATTgtaagtattt ... tatgtttcagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCAGGTAGCACCTACCGCACAAGGGATGAGATCGCTGGCATAAGGCAG


Block sizes: 41 (upstream exon), 46 (downstream exon)
Score: 11

GTCGATGGAATGGATGTTCTTGCTGTGAAGCAAGCTTGCAAATTTGCCAAAGAACATGCCCTTGAAAATGGGCCAATTgtaagtattt ... tatgtttcagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCAGGTAGCACCTACCGCACAAGGGATGAGATCGCTGGCATAAGGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agactttcttcttaaagatgctgatcaccacggttctattcgttttatgtttcagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCAGGTAGCACCTACCGCACAAGGGATGAGATCGCTGGCATAAGGCAG
                  tgctgat  putative branch site (score: 11)
                                      ttcgtttt  putative PPT
                                          ttttatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggacccttaaactagacgaggcttgacatcggttttgtgattccagactttcttcttaaagatgctgatcaccacggttctattcgttttatgtttcagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCAGGTAGCACCTACCGCACAAGGGATGAGATCGCTGGCATAAGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - tgtgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caccacg