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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcgagcttcactcttgtgattgggctccgttactttgtttttagggttaagttagagcagtggtgatggttcgcacgaattgttgtgtttttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGACCATGATCTCACCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGT

Basic information

species Zea mays
transcript GRMZM2G019267_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019267_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g72790.1 (Oryza sativa), 3'ss of exon 4
gtatgtcgagcttcactcttgtgattgggctccgttactttgtttttagggttaagttagagcagtggtgatggttcgcacgaattgttgtgtttttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGACCATGATCTCACCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGT
||||| |    || | || ||  |||           ||| |||| | ||  |   |    |  ||  ||     ||  | | |||||  | || ||||  |||| || ||||||||||||||||||||||| |||||||| |||||||| ||||| |||||||| || |||||||| ||| |||| || ||||||||||||||
gtatggcacattttattcctgcaattc----------cttggtttgtgggagtggttctaggttgtaatg-----tctgatgcattgtcatcttgttgaaatagTCGAGGGTAACAAGTACAAGGGGAGCATCTACATGGTCTTCGAGTACATGGATCATGATCTTACTGGGCTTGCAGATAGGCCTGGGATGCGGTTCACTGT

upper sequence: GRMZM2G019267_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv06s0009g01800.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------------------------------------------------------gtatgtcgagcttcactcttgtgattgg---gctccgttact-ttgtttttagggttaa-----gttagagcagtggtgatggttcgcacgaattgttgtgtttttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGACCATGATCTCACCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGT---
                                                                                  | ||   | |    || ||   ||     | | | | | | |||        | |         ||||| |      ||   |   |  || |    |  ||  | ||  |  || ||||| |||||||| ||  |||| ||||||||||| || || |||||||||||| | || || ||||||||||| || || ||| | ||  | ||   
gcaagtactttattgtcatgtgctatgttagccaatcatgatgttagtgcattgcatgctttcctatgttggttcacttatcacgtgaggatattttcatgaacttaaaaagttacataaatattgccgcataagctggtccttactagagtaccaagaatttctgatatcaacttcattacttggggtt--gcagATGGTAATAAGTACAAAGGAGGCATCTACATGGTTTTTGAATACATGGACCATGATTTGACTGGTCTTGCTGATCGTCCTGGGATGAGATTTTCAGTCCC

upper sequence: GRMZM2G019267_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S3_535V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------gtatgtcgagcttcactcttgtgattgggctccgttactt-tgtttttagggttaagttagagcagtggt--------------gatggttcgcacgaattgttgtgtttttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGACCATGATCTCACCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGT
           ||||  |  |  |||     |  |||| ||  ||  | |   |  |  |  |||   || | |||   ||               |  |  | |  |||           |  |   ||  || |  |  |||| ||| ||    ||||||||||| |||||||| |||||||||||||| || || ||                              
gcaattattacgtataactggtgtcaactgggaaattgtgcgtcgaaagtggcgcgtgaaatgttctctttgtgcaacagttggcttcttttgtgaacagGACCCGAGAAAGAGGACAACATCAAGCCAGGCGATGCGAGTAAGTTCAAAGGTTCTATTTACATGGTGTTCGAGTACATGGACCATGATCTGACTGGTCT------------------------------

upper sequence: GRMZM2G019267_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S121_162V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------------gtatgtcgagcttcactcttgtgattgggctccgttactttgtttttagggttaagttagagcagtg----------------gtgatggttcgcacgaattgttgt-gtttttgatttagTTGACGGTAACA-AGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGACCATGATCTCACCGGGCTTGCTGATCGGCCA---GGAATGCGGTTC-ACTGT---
                                                                   ||||   |||| |  |  |  || |  || |  | | |||| |||  |  |   |||  ||  | |                 |||| |   |  || ||  |  || | |||| |||||    || | | || || |  |||  | |||  |    | |   | | |||  |  ||     ||      | || || |||   |   |||    | ||  ||||    
gtgggcgctgattttatcatcgtcttatgtatgcgtacatgaactatatgtcgatagacgtctctctgtattctgagcatgtcattattgctgaggatttggttctttctttcaaatgagtagtccgatgaatatatattttttgattttgtgaggacacatactaagcgcagttgctttttatttaa---acagGACCAGAGAAGGAGGACAACATCAAGCCAGGTGAAGCGAATA-AGTTCAAAGGGTCGATTTACATGGTGTTCGAGTACATGGACCATGATTTGACTGGCCT

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|211438447|gb|FL012009.1|FL012009
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
EST: gi|29130258|gb|CB380962.1|CB380962
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
EST: gi|148931632|gb|EC874770.2|EC874770
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
EST: gi|71774594|gb|DR972472.1|DR972472
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
EST: gi|211438457|gb|FL012019.1|FL012019
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
EST: gi|211435860|gb|FL012004.1|FL012004
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
EST: gi|76914973|gb|DV165773.1|DV165773
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
EST: gi|211438453|gb|FL012015.1|FL012015
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
EST: gi|148962681|gb|EE013583.2|EE013583
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
EST: gi|148946782|gb|EC892051.2|EC892051
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
EST: gi|211438455|gb|FL012017.1|FL012017
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
EST: gi|148938174|gb|EC882457.2|EC882457
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
EST: gi|211002224|gb|FL012020.1|FL012020
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
EST: gi|211438454|gb|FL012016.1|FL012016
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
EST: gi|211435853|gb|FL011997.1|FL011997
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
EST: gi|211438445|gb|FL012007.1|FL012007
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTTCGAGTATATG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTT-CGAGTATATG
EST: gi|211438446|gb|FL012008.1|FL012008
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
EST: gi|211438452|gb|FL012014.1|FL012014
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
EST: gi|211438444|gb|FL012006.1|FL012006
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
EST: gi|211435856|gb|FL012000.1|FL012000
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
EST: gi|211435858|gb|FL012002.1|FL012002
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
EST: gi|211002225|gb|FL012021.1|FL012021
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
EST: gi|211435854|gb|FL011998.1|FL011998
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
EST: gi|148942610|gb|EC887630.2|EC887630
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
EST: gi|211438456|gb|FL012018.1|FL012018
EST:     GCCCAGAGCGGGACGAGCAAGGGAAGCCAA                         TTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG
genomic: GCCCAGAGCGGGACGAGCAAGGGAAGCCAAgtatgtcgag ... tttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttaagttagagcagtggtgatggttcgcacgaattgttgtgtttttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGACCATGATCTCACCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGT
                                            ttttgat  putative branch site (score: 4)
                                         tgttttt  CT-rich tract
                                           tttttgattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcgagcttcactcttgtgattgggctccgttactttgtttttagggttaagttagagcagtggtgatggttcgcacgaattgttgtgtttttgatttagTTGACGGTAACAAGTACAAGGGGAGCATTTACATGGTTTTCGAGTATATGGACCATGATCTCACCGGGCTTGCTGATCGGCCAGGAATGCGGTTCACTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT