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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGTGGCTGCCAATCAGGATGTGGCTGTGAACCTGATCATCACAGACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactgaactactccggcatgatcactgaacattctgtatagtgcttgctttctggcatgatcactgaagataacaaggcctaaagatgcatgtttggtttggtttgctctaccag

Basic information

species Zea mays
transcript GRMZM2G129954_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G129954_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os12g04500.1 (Oryza sativa), 5'ss of exon 3
GATGTGGCTGCCAATCAGGATGTGGCTGTGAACCTGATCATCACAGACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactgaactactccggcatgatc--actgaacattctgtatagtgcttgctttctggcatgatcactgaagataacaaggcctaaagatgcatgtttg--gtttggtttgctctaccag
                  || || |  |||||||||||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||||| | |||          |    ||||   ||  | ||||   | |  |     ||       |||| || ||| |  |      ||| || |    | |||    ||||||||| || | |||
------------------GAGGTTGGAGTGAACCTGATCATCACAGACTACTGCATGCCTGGCATGACAGGATATGATCTTCTCAAGAAGATCAAGgtaattaccatctctgctctatttgattgtaccaaccatttgatttgat-----ctactcaagatga-cagtgaggtcagtt---cctgaatacagttttttcccttttggtttgttcaatcag

upper sequence: GRMZM2G129954_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os11g04720.1 (Oryza sativa), 5'ss of exon 3
GATGTGGCTGCCAATCAGGATGTGGCTGTGAACCTGATCATCACAGACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactgaactactccggcatgatc--actgaacattctgtatagtgcttgctttctggcatgatcactgaagataacaaggcctaaagatgcatgtttg--gtttggtttgctctaccag
                  || || || |||||||||||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||||| | |||          |    ||||   ||  | ||||   | |  |     ||       |||| || ||| |  |      ||| || |    | |||    ||||||||| || | |||
------------------GAGGTTGCAGTGAACCTGATCATCACAGACTACTGCATGCCTGGCATGACAGGATATGATCTTCTCAAGAAGATCAAGgtaattaccatctctgctctatttgattgtaccaaccatttgatttgat-----ctactcaagatga-cagtgaggtcagtt---cctgaatacagttttttcccttttggtttgttcaatcag

upper sequence: GRMZM2G129954_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA19G31320.2 (Glycine max), 5'ss of exon 3
GATGTGGCTGCCAATCAGGATGTGGCTGTGAACCTGATCATCACAGACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactgaactactccggcatgatcactgaacattctgtatagtgcttgctttctggcatgatcactgaagataacaaggcctaaagatgcatgtttggtttggtttgctctaccag
                  || ||||  ||||| ||  | || ||||| ||||| ||||||||||||||||| |||||| |||| ||||| ||||||||   | ||    | ||  | | || |  ||     | |||| |  ||  | ||||    |||  | | |    |  ||    | |     |   ||  |||    | ||| |       
------------------GAGGTGGAGGTGAATCTTGTTATAACAGATTACTGTATGCCTGGCATGACAGGCTATGACTTGCTTAAGAAAATCAAGgta--tgct----tgctttgccttggtttcta---ttcctgtctcatgtct-cttttaaccatt-ttattctccaccacttttcttctcagtttttg--tggccaagattgtt-------

upper sequence: GRMZM2G129954_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA03G28570.1 (Glycine max), 5'ss of exon 3
GATGTGGCTGCCAATCAGGATGTGGCTGTGAACCTGATCATCACAGACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactgaactactccggcatgatcactgaacattctgtatagtgcttgctttctggcatgatcactgaagataacaaggcctaaagatgcatgtttggtttggtttgctctaccag-
                  || ||||  ||||| ||  | || ||||| ||||| ||||||||||||||||| |||||| |||| ||||| ||||||||   | ||    | ||  |   || |  ||     | |||| |  |   |  ||| |    | | || |  |     ||   | |           ||    |  ||||      |||  
------------------GAGGTGGAGGTGAATCTTGTTATAACAGATTACTGTATGCCTGGCATGACAGGCTATGACTTGCTTAAGAAAATCAAGgta--tgcttc-ttgctttgctttggtttcta---ttcctgtctcatctctcttttat----taaccattttattctccaccactt-----------ttcttctcagtttttgtagccaag

upper sequence: GRMZM2G129954_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ26364 (Selaginella moellendorffii), 5'ss of exon 3
---GATGTGGCTGCCAAT-CAGGATGTGGCTGTGAACCTGATCATCACAGACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactgaactactccggcatgatcactgaacattctgtatagtgcttgctttctggcatgatcactgaagataacaaggcctaaagatgcatgtttggtttggtttgctctaccag
   | | | |||     | ||||   |     | ||| |||||||||| ||||| || ||||| |  |||||||| ||||| |||||||||||| |||||||     ||  | ||    |   ||||  | |    |  || || |  |    | |||  |   ||| |||   | |                                           
CTGGCTTTTGCTTTTGTTGCAGGCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAGgtacacgctttaataaattg-tttgatgccag---ttgatgcatgg-acacagtatctatctgcatcgctgtcaacag------------------------------------------

upper sequence: GRMZM2G129954_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ14702 (Selaginella moellendorffii), 5'ss of exon 3
GATGTGGCTGCCAATCAGGATGTGGCTGTGAACCTGATCATCACAGACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactgaactactccggcatgatcactgaacattctgtatagtgcttgctttctggcatgatcactgaagataacaaggcctaaagatgcatgtttggtttggtttgctctaccag
                  |   |     | ||| |||||||||| ||||| || ||||| |  |||||||| ||||| |||||||||||| |||||||     ||  | ||    |   ||||  | |    |  || || |  |    | |||  |   ||| |||   | |                                           
------------------GCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAGgtacacgctttaataaattg-tttgatgccag---ttgatgcatgg-acacagtatctatctgcatcgctgtcaacag------------------------------------------

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|211009674|gb|FL207158.1|FL207158
EST:     ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAG                         GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGAT
genomic: ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGAT
EST: gi|211399019|gb|FL440142.1|FL440142
EST:     ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAG                         GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
genomic: ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
EST: gi|91878635|gb|EB408592.1|EB408592
EST:     ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAG                         GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
genomic: ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
EST: gi|40303893|gb|CK348280.1|CK348280
EST:     ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAG                         GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
genomic: ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
EST: gi|211009671|gb|FL207155.1|FL207155
EST:     ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAG                         GAGTCGTCGTCTCTCAGAGATATCC
genomic: ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGATATCC
EST: gi|211213579|gb|FL456137.1|FL456137
EST:     ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAG                         GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
genomic: ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
EST: gi|5895964|gb|AW037210.1|AW037210
EST:     ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAG                         GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
genomic: ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
EST: gi|19822364|gb|BQ048388.1|BQ048388
EST:     ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAG                         GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
genomic: ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
EST: gi|211009672|gb|FL207156.1|FL207156
EST:     ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAG                         GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
genomic: ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
EST: gi|76933672|gb|DV173539.1|DV173539
EST:     TGCTCAGGAAGATCAAG                         GAGTCGTTGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGACC
genomic: TGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
EST: gi|37382649|gb|CF628283.1|CF628283
EST:     ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAG                         GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
genomic: ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
EST: gi|76933673|gb|DV173540.1|DV173540
EST:     ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAG                         GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
genomic: ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
EST: gi|211009677|gb|FL207161.1|FL207161
EST:     ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAG                         GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
genomic: ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
EST: gi|5597298|gb|AI891396.1|AI891396
EST:     ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAG                         GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
genomic: ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
EST: gi|40335323|gb|CK369393.1|CK369393
EST:     ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAG                         GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
genomic: ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
EST: gi|91869452|gb|EB400392.1|EB400392
EST:     ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAG                         GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
genomic: ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
EST: gi|113704219|gb|EE681723.1|EE681723
EST:     ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAG                         GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
genomic: ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
EST: gi|211012454|gb|FL207172.1|FL207172
EST:     ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAG                         GAGTCGTCGTCTCTCA
genomic: ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCA
EST: gi|74237752|gb|DT645666.1|DT645666
EST:     ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAG                         GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
genomic: ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
EST: gi|211012453|gb|FL207171.1|FL207171
EST:     ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAG                         GAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCCGAGAAC
genomic: ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAAC
EST: gi|211012452|gb|FL207170.1|FL207170
EST:     ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAG                         GAGTCGTCGTCTCTCAGAGATATCCCGGT
genomic: ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGATATCCCGGT
EST: gi|211009670|gb|FL207154.1|FL207154
EST:     ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAG                         GAGTCGTCGTCTCTCAGAGA
genomic: ACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGA

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: 47 (upstream exon), 42 (downstream exon)
Score: 19

GATGTGGCTGCCAATCAGGATGTGGCTGTGAACCTGATCATCACAGACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 108

GATGTGGCTGCCAATCAGGATGTGGCTGTGAACCTGATCATCACAGACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

GATGTGGCTGCCAATCAGGATGTGGCTGTGAACCTGATCATCACAGACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAG


Block sizes: 43 (upstream exon), 42 (downstream exon)
Score: 7

GATGTGGCTGCCAATCAGGATGTGGCTGTGAACCTGATCATCACAGACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactg ... gctctaccagGAGTCGTCGTCTCTCAGAGATATCCCGGTGGTGATCATGTCCTCTGAGAACATTCCTTCAAGGATCAATAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGTGGCTGCCAATCAGGATGTGGCTGTGAACCTGATCATCACAGACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAGgtgactactgaactactccggcatgatcactgaacattctgtatagtgcttgctttctggcatgatcactgaagataacaaggcctaaagatgcatgtttggtttggtttgctctaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA