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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAAGAATTTCATCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaatctcatcagtcattatttccaatcactatgtggttttttaatgccatgttttgactaataattcgatgatatggtgacaagtttgtgtagt...

Basic information

species Zea mays
transcript GRMZM2G374779_T03
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G374779_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g01150.1 (Oryza sativa), 5'ss of exon 7
GTCAAGAATTTCATCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaatctcatcagtcattatttccaatcactatgtggttttttaatgccatgttttgact-aataattc--gatgatatggtgacaagtttgtgtagt-----
|||||||||||||| || || || || |||||||||||||| ||||||||||| |||||||||||||||| |||||||       | |||||||    ||  | |||| |  |||  | |||   | | |||||| |  |||  |     ||     |    |        
GTCAAGAATTTCATTTCACTCGGTGGCCCTCATGCTGGTACTGCTTCAGTGCCACTTTGTGGTgtaagttcatctcat-------tgtttccaagtgatacctagtttgt-gatgaaaagttaaaatttaataatccaagattgtgcatggatcttctcagatgacacata

upper sequence: GRMZM2G374779_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv02s0488g00020.t01 (Vitis vinifera), 5'ss of exon 6
GTCAAGAATTTCATCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaatctcatcagtcattatttcca-atcac-tatgtggttttttaatgccatgttttgactaataattcgatgatatggtgacaagtttgtgtagt------
|| ||||| ||  ||||  ||| ||| |||||||||||||||||||| || ||||||||||| ||||||     |      |||| |||  || ||||   |||  |  || |||  |      |||  | |  ||| |   ||| ||| |   || | |  |        
GTTAAGAACTTTGTCTCATTAGCAGGACCTCATGCTGGTACCGCTTCTGTCCCTCTTTGTGGGgtaagt--gcttttgtgatcatcattatcatatcatgcatgatgaattctaaaactgc---ttggtttaagattgggaaataaggtta---gtctatccaaaaaaggg

upper sequence: GRMZM2G374779_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv15s0021g01760.t01 (Vitis vinifera), 5'ss of exon 7
GTCAAGAATTTCATCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaatctcatcagtcattat-ttccaatcactatgtggttttttaatgccatgttttgactaataattcgatgatatggtgacaagtttgtgtagt---
|| ||||||||||| || || |||||||||||||||||||| ||||| || || |||||||| |||||||  |||  | || | ||   ||    ||||| | ||  ||    || |  |  ||   ||  |  ||  |  | |     ||  || |  ||  |   
GTTAAGAATTTCATATCACTTGGAGGTCCTCATGCTGGTACAGCTTCCGTTCCACTTTGTGGAgtaagttcttct--ttagccttttcattatgttcactttatgtgttgcacatactttacttgtgctt-tgttttcacaaaactcc-actggtctaagttttgaa

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|211340859|gb|FL372915.1|FL372915
EST:     TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGT                         TCTGGANNNNNNNGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
genomic: TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaat ... atatatgcagTCTGGATTTTTTTGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
EST: gi|211357926|gb|FL387018.1|FL387018
EST:     TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGT                         TCTGGANNNNNNNGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
genomic: TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaat ... atatatgcagTCTGGATTTTTTTGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
EST: gi|211458917|gb|FL402420.1|FL402420
EST:     TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGT                         TCTGGANNNNNNNGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
genomic: TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaat ... atatatgcagTCTGGATTTTTTTGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
EST: gi|211319230|gb|FL384888.1|FL384888
EST:     TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGT                         TCTGGATTTTT
genomic: TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaat ... atatatgcagTCTGGATTTTT
EST: gi|101397865|gb|EB820809.1|EB820809
EST:     TCTCTCTAGGAGGTCCTCATGCTGGGACCGCTTCAGTGCCTCTTTGTGGT                         TCTGGATTTTT
genomic: TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaat ... atatatgcagTCTGGATTTTT
EST: gi|211298857|gb|FL392428.1|FL392428
EST:     TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGT                         TCTGGANNNNNNNGCATTATTGTTGATGCTCTGATCNAATTGGAGATCTAC
genomic: TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaat ... atatatgcagTCTGGATTTTTTTGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
EST: gi|211533538|gb|FL409967.1|FL409967
EST:     TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGT                         TCTGGANNNNNNNGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
genomic: TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaat ... atatatgcagTCTGGATTTTTTTGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
EST: gi|211487556|gb|FL382361.1|FL382361
EST:     TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGT                         TCTGGANNNNNNNGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
genomic: TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaat ... atatatgcagTCTGGATTTTTTTGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
EST: gi|32868245|gb|CF007927.1|CF007927
EST:     TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGT                         TCTGGANNNNNNNGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC
genomic: TCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaat ... atatatgcagTCTGGATTTTTTTGCATTATTGTTGATGCTCTGATCAAATTGGAGATCTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAAGAATTTCATCTCTCTAGGAGGTCCTCATGCTGGTACCGCTTCAGTGCCTCTTTGTGGTgtaagttaatctcatcagtcattatttccaatcactatgtggttttttaatgccatgttttgactaataattcgatgatatggtgacaagtttgtgtagt

- - - - - - - - - - - - - - -  ATGCTG