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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGAACTCATGGCTCGCGTCTACGTTGGGAACCTGGATCCGCGTGTCACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcggtgcctttgctcggaagtgctcagctttgtttttttattgatagcagtagcgcgaatgtagtttttctatgatttcccctgacttgcctc...

Basic information

species Zea mays
transcript GRMZM2G027105_T07
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027105_T04 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g39720.3 (Oryza sativa), 5'ss of exon 2
--GCTGAACTCATGGCTCGCGTCTACGTTGGGAACCTGGATCCGCGTGTCACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcggtgcctttgctcggaagtgctcagctttgtttttttattgatagcagtagcgcgaatgtagtttttctatgatttcccctgacttgcctc-
     |  |||||||||||||| ||||| ||||||||||||||||| || |||||||||||||||||||||||||||||  |||||||||||||||||||||| ||     |||     ||  |    |     || | | | | ||||     |  |     |  | || || ||  ||| |  |  ||   | |  |  
CGAGCGCGCTCATGGCTCGCGTGTACGTGGGGAACCTGGATCCGCGCGTGACGGCGCGGGAGATCGAGGACGAGTTCCGCGTGTTTGGGGTTCTGAGGAGgtgtgagattctgctgactctgagctaagaatcactatatatatatattttactccctgtgttgcgtatacttgtttaatg-tgcctgcttgttcgtttga

upper sequence: GRMZM2G027105_T04 (Zea mays), 5'ss of exon 2
lower sequence: EFJ27548 (Selaginella moellendorffii), 5'ss of exon 1
GCTGAACTCATGGCTCGCGTCTACGTTGGGAACCTGGATCCGCGTGTCACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcggtgcctttgctcggaagtgctcagctttgtttttttattgatagcagtagcgcgaatgtagtttttctatgatttcccctgacttgcctc
         ||||| ||||||||||| || || |||||||||||    |||| ||||||| ||||||||||||||||||  || || || ||| | |||| ||   ||    |     |||    | |||  | |  |||||  |  |  |  |  |   | ||| |     |     |||||  | || |       
---------ATGGCGCGCGTCTACGTCGGCAATCTGGATCCGCGATCGACGGAGCGGGAGCTCGAGGACGAGTTCCGGAGCTTCGGCGTGCTGCGAAGgtaagccacg----cgcaaatcgattctcctct-cgtcctttttccagcgcca--aagaatccaaatctgaggctc----gattttgc-tggcag-----

upper sequence: GRMZM2G027105_T04 (Zea mays), 5'ss of exon 2
lower sequence: EFJ35719 (Selaginella moellendorffii), 5'ss of exon 1
GCTGAACTCATGGCTCGCGTCTACGTTGGGAACCTGGATCCGCGTGTCACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcggtgcctttgctcggaagtgctcagctttgtttttttattgatagcagtagcgcgaatgtagtttttctatgatttcccctgacttgcctc
         ||||| ||||||||||| || || |||||||||||    |||| ||||||| ||||||||||||||||||  || || || ||| | |||| ||   ||    |     |||    | |||  | |  |||||  |  |  |  |  |   | ||| | |   |     |||||  | || |       
---------ATGGCGCGCGTCTACGTCGGCAATCTGGATCCGCGATCGACGGAGCGGGAGCTCGAGGACGAGTTCCGGAGCTTCGGCGTGCTGCGAAGgtaagccacg----cgcaaatcgattctcctct-cgtcctttttccagcgcca--aagaatccaaatctggggctc----gattttgc-tggcag-----

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|15188227|gb|BI417204.1|BI417204
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGTCTTCATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|71438000|gb|DR819050.1|DR819050
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|22489522|gb|BU049445.1|BU049445
EST:     GGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
genomic: GGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|22489415|gb|BU049338.1|BU049338
EST:     CGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAANCCNCCAGGGTTTGCCTTCATTGNCTTTGATGN
genomic: CGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|71317875|gb|DR795704.1|DR795704
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|15313695|gb|BI478910.1|BI478910
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|18384819|gb|BM418018.1|BM418018
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|18053132|gb|BM318790.1|BM318790
EST:     GAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGGTTTGCCTTCATTGACTTTGATG
genomic: GAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCA-GGGTTTGCCTTCATTGACTTTGATG
EST: gi|149082345|gb|EE171527.2|EE171527
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|15177619|gb|BI398558.1|BI398558
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGTCTTTATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|15323604|gb|BI478888.1|BI478888
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGA
EST: gi|17970002|gb|BM276770.1|BM276770
EST:     GGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
genomic: GGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|211060877|gb|FK967412.1|FK967412
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|18384821|gb|BM418020.1|BM418020
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|18384989|gb|BM418188.1|BM418188
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|87298765|gb|DY470768.1|DY470768
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|15188220|gb|BI417197.1|BI417197
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGTCTTTATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|18384820|gb|BM418019.1|BM418019
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|50333998|gb|CO529124.1|CO529124
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|21331667|gb|BQ487048.1|BQ487048
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGACGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|13557662|gb|BG549018.1|BG549018
EST:     GGTCGCGGGTAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGG
genomic: GG-CGCGGG-AGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGG
EST: gi|22489184|gb|BU049107.1|BU049107
EST:     CGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGNTTTGCCTTCATTGACTTTGATG
genomic: CGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGG-TTTGCCTTCATTGACTTTGATG
EST: gi|18384999|gb|BM418198.1|BM418198
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGTCTTCATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|71438201|gb|DR819251.1|DR819251
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|71449212|gb|DR830262.1|DR830262
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGAACTCATGGCTCGCGTCTACGTTGGGAACCTGGATCCGCGTGTCACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcggtgcctttgctcggaagtgctcagctttgtttttttattgatagcagtagcgcgaatgtagtttttctatgatttcccctgacttgcctc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG