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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgaaaatatattatcgcacacatccttttttattcctaacaagagagaatatcaagttatcgacgattgacgaccaaccaaattggtttcgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCTGCAAGAAGGACACAAGGGGGGAGCCGAGGCAGGTTGACAAGCTAGGAAG

Basic information

species Zea mays
transcript GRMZM2G027478_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027478_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g60830.1 (Oryza sativa), 3'ss of exon 2
--------ctgaaaatatatta-tcgcacacatccttttttattcctaa-caagagagaatatcaagttatcgacgattgacgacc--aaccaaat-tggtttcgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCTGCAAGAAGGACACAAGGGGGGAGCCGAGGCAGGTTGACAAGCTAGGAAG
            | ||   ||| | ||| |   |     ||| | || | | | | ||| |||     ||          ||   |  |||    | ||  |||   || |||| |||||| ||||||| ||||| |||||||| || |||||||||||  | |||||||||||||| || ||||| || |||||||| ||||||||||||||
gtactacctcatatatgctttacttgcagaatcctaaaattacttctgatccaaaaagattatactagtaggagtatcgcacagtcctaactgtttctgaattctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTTGCAAGAAGGACACTAGAGGGGAACCCAGGCAGGTCGACAAGCTAGGAAG

upper sequence: GRMZM2G027478_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT3G56290.1 (Arabidopsis thaliana), 3'ss of exon 2
-------ctgaaaatatatta----tcgcacacatccttttttattcctaacaagagagaatatcaagttatcgacgattgacgaccaaccaaattggtttcgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCTGCAAGAAGGACACAAGGGGGGAGCCGAGGCAGGTTGACAAGCTAGGAAG
       ||  | |  ||||     | | | | |   |  |  |||  |        |  | |  | || |   |  |      ||| |     ||   | |   ||  ||| || |||||||| ||||||||||| ||||| ||||| || || ||||| ||||| |||||||||| ||| ||| | || || || |||||| |||| ||
gtaaagtctagagaactatttaaattggaagaaagaatgatgaatttatttgttataattaaactatgtga--aataaactgtaacctattgttttaaatacatgttatagTGGATGGGCAATATGTGGAGGAGGGATGGGTGGACAAAACATGTAAGATATGCAAAAAGGACACAAAGGGTGAGGCAAGACAAGTGGACAAGTTAGGGAG

upper sequence: GRMZM2G027478_T02 (Zea mays), 3'ss of exon 2
lower sequence: Vv13s0067g02560.t01 (Vitis vinifera), 3'ss of exon 2
---------ctgaaaatatattatcgcacacatccttttttattcctaacaagagagaatatcaagttatcgacgattgacgaccaaccaaattggtttcgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCTGCAAGAAGGACACAAGGGGGGAGCCGAGGCAGGTTGACAAGCTAGGAAG
          |||   |  |||| |   |    | | ||| |||     |||     | | ||    |    ||   |   || |||   | |     | ||| | |||| || || |||||||| ||||||||||||||||| || ||||||||  | |||||| ||||||| || ||||| || |||||||| |||||| | |||||
gctatgcaaatgagcctgcattaccaatctttccatgtttgattttcctcaa-----agtttc---ctgcaaaccggttttgatcaattcagtcttgcttgaaat-cagTGGATGGACAATACGTCGAGGAGGGTTGGGTCGATAAAACCTGCAAAGTATGCAAGGAGGACACCAGAGGGGAACCCAGGCAGGTGGACAAGTTTGGAAG

upper sequence: GRMZM2G027478_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S20_237V6.1 (Physcomitrella patens), 3'ss of exon 2
---------ctgaaa-atatattatcgcacacatccttttttattcctaacaagagagaatatcaagttatcgacgattgacgaccaaccaaattggtttcgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCTGCAAGAAGGACACAAGGGGGGAGCCGAGGCAGGTTGACAAGCTAGGAAG
         | | |   ||| |||    | | ||| | |   ||| || | | ||  |||   | | |  |     |   || |    || | |||  |      | |||| || |||   |||||||| || |||||||||||||| ||||||||   ||||||||||||||| |  || |  ||  |       |||      ||| |
caacagtcacagtagcgtatgttacaata-atatcatatccgattactca-acgattgaa---cgactcgtttcatacctacaattgcccga-ttgact----gctgcagTTGATGGGGCGTACGTGGACGAAGGTTGGGTCGACAAAACCTGCAAATACTGCAAGAAGGACACGAAAGGTGCTCCCCGAACTAAGGACTCAAGTGGACG

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|211173965|gb|FL006047.1|FL006047
EST:     GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAG                         TCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCT
genomic: GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAGgtatcttatc ... cgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCT
EST: gi|211175637|gb|FL006055.1|FL006055
EST:     GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAG                         TCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCT
genomic: GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAGgtatcttatc ... cgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCT
EST: gi|18178672|gb|BM379882.1|BM379882
EST:     GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAG                         TCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCT
genomic: GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAGgtatcttatc ... cgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCT
EST: gi|211304348|gb|FL459467.1|FL459467
EST:     GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAG                         TCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCT
genomic: GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAGgtatcttatc ... cgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCT
EST: gi|211175633|gb|FL006051.1|FL006051
EST:     GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAG                         TCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCT
genomic: GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAGgtatcttatc ... cgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCT
EST: gi|211321918|gb|FL078167.1|FL078167
EST:     GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAG                         TCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCT
genomic: GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAGgtatcttatc ... cgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCT
EST: gi|211173966|gb|FL006048.1|FL006048
EST:     GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAG                         TCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGAC
genomic: GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAGgtatcttatc ... cgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGAC
EST: gi|211173963|gb|FL006045.1|FL006045
EST:     GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAG                         TCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCT
genomic: GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAGgtatcttatc ... cgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCT
EST: gi|211175535|gb|FL450620.1|FL450620
EST:     GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAG                         TCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCT
genomic: GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAGgtatcttatc ... cgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCT
EST: gi|211173967|gb|FL006049.1|FL006049
EST:     GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAG                         TCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCT
genomic: GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAGgtatcttatc ... cgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCT
EST: gi|211175634|gb|FL006052.1|FL006052
EST:     GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAG                         TCGACGGGCAATACGTGGAAGGAGGGTTGGGTCGACAAGACCTGCAAGATC
genomic: GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAGgtatcttatc ... cgaatttcagTCGACGGGCAATACGTGGA-GGAGGGTTGGGTCGACAAGACCTGCAAGATC
EST: gi|211100909|gb|FL435529.1|FL435529
EST:     GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAG                         TCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCT
genomic: GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAGgtatcttatc ... cgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCT
EST: gi|211175638|gb|FL006056.1|FL006056
EST:     GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAG                         TCGACGGGCAATACGTGGAGGAGAGTTGGGTCGACAAGACCTGCAAGATCT
genomic: GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAGgtatcttatc ... cgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCT
EST: gi|211173964|gb|FL006046.1|FL006046
EST:     GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAG                         TCGACGGGCAATACGTGGAGGAGGGTTNGGTCGACAAGACCTGCAAGATCT
genomic: GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAGgtatcttatc ... cgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCT
EST: gi|12968215|gb|BG265161.1|BG265161
EST:     GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAG                         TCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCT
genomic: GCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAGgtatcttatc ... cgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCT

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: 43 (upstream exon), 43 (downstream exon)
Score: 12

TACGGAGCACTTAGGCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAGgtatcttatc ... cgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCTGCAAGAAGGACACAAGGGGGGAGCCGAGGCAGGTTGACAAGCTAGGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 56

TACGGAGCACTTAGGCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAGgtatcttatc ... cgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCTGCAAGAAGGACACAAGGGGGGAGCCGAGGCAGGTTGACAAGCTAGGAAG


Block sizes: 39 (upstream exon), 46 (downstream exon)
Score: 15

TACGGAGCACTTAGGCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAGgtatcttatc ... cgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCTGCAAGAAGGACACAAGGGGGGAGCCGAGGCAGGTTGACAAGCTAGGAAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 26

TACGGAGCACTTAGGCGGAAGATTGGTGGCACCTACCAGGATTTCTTCAAGTCATATGTTGAAGgtatcttatc ... cgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCTGCAAGAAGGACACAAGGGGGGAGCCGAGGCAGGTTGACAAGCTAGGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagaatatcaagttatcgacgattgacgaccaaccaaattggtttcgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCTGCAAGAAGGACACAAGGGGGGAGCCGAGGCAGGTTGACAAGCTAGGAAG
                    gattgac  putative branch site (score: 26)
         aagttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgaaaatatattatcgcacacatccttttttattcctaacaagagagaatatcaagttatcgacgattgacgaccaaccaaattggtttcgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCTGCAAGAAGGACACAAGGGGGGAGCCGAGGCAGGTTGACAAGCTAGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - -cacatcc
- - - - - - - - - - - - - - - - - - - aacaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaccaa