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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctactgtactgtctgcttcgatccacagtctagtactctagtctagcagccatggcggcggcggcggcggcgggtgatcgatcagctcaacgtac...

Basic information

species Zea mays
transcript GRMZM2G071154_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G071154_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g36950.2 (Oryza sativa), 5'ss of exon 3
GCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtacc-ctactgtactgtctgcttcgatccacagtctagtactctagtctagcagccatggcggcggcggcggcggcgggtgatcgatcagctcaacgtac---
|| |||||||| ||||| || |||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||  |  | | |    | |   ||  || | | |     |    || |    |        |    |         || ||  |     |  | | |    
GCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAGgtaccattgatcttcaacttcccatgaatcagattgt----tttcgctcaaatttctgcacttccacatgttttaatatgtaattaagtgtatttaggaattag

upper sequence: GRMZM2G071154_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv02s0025g01720.t01 (Vitis vinifera), 5'ss of exon 3
GCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctactgtactgtctgcttcgatccacagtctagtact-ctagtctagcagccat-ggcggcggcggcggcggcgggtgatcgatcagctcaacgtac-
|| || ||||| || || || ||||| || || || || |||||||||||||||||||| ||||| || ||||| ||||| |||||   ||  | | |  |||   | ||||  |      ||     | | |||  || |||    |||      ||    ||||  | |   |   | | | |  
GCTGCAAGCTTTGGAGGAACAAACATTGATCCAACTGCTTGGGAGGACAAGAAGTGCCCTGGCGAATCACGCTTCCCTGCTCAGgt---ctgttctccaatcttacttgatctgccaaactgtgtagttgggctactagtcatcaaaggcaaatttggtttggggtctttgtatatggccatgaatt

upper sequence: GRMZM2G071154_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ24245 (Selaginella moellendorffii), 5'ss of exon 3
GCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctactgtactgtctgcttcgatccacagtctagtactctagtctagcagccatggcggcggcggcggcggcgggtgatcgatcagctcaacgtac
||  | || || || ||  ||||||||||  | || |||||||||||||||||||||| ||| |||||| | || || || |||||      ||    | |||      ||  | ||  |  |  | |  |  ||| || |  ||  |   ||      |   |  |    |    ||      
GCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAGgtttgtctct-cgttttctaggagaatagaaagctttttcttgttcttgagctgcaagagctacaaaggaaa--acccatcgtgatcccatacag-----

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|76018940|gb|DT946110.1|DT946110
EST:     CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG                         GTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
genomic: CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctact ... tgtgctgcagGTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
EST: gi|149002886|gb|EE038882.2|EE038882
EST:     CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG                         GTGCGGGTGGCAACGCGGAAGATTTACGACCCGCTGGAGGAGGACGCCTTC
genomic: CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctact ... tgtgctgcagGTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
EST: gi|18178271|gb|BM379481.1|BM379481
EST:     CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG                         GTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
genomic: CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctact ... tgtgctgcagGTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
EST: gi|7844641|gb|AW787863.1|AW787863
EST:     CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG                         GTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
genomic: CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctact ... tgtgctgcagGTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
EST: gi|50336543|gb|CO531669.1|CO531669
EST:     CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG                         GTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
genomic: CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctact ... tgtgctgcagGTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
EST: gi|149082668|gb|EE171878.2|EE171878
EST:     CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG                         GTGCGGGTGGCAACGCGGAAGATTTACGACCCGCTGGAGGAGGACGCCTTC
genomic: CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctact ... tgtgctgcagGTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
EST: gi|60338891|gb|DN205864.1|DN205864
EST:     CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG                         GTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
genomic: CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctact ... tgtgctgcagGTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
EST: gi|93015747|gb|EB641267.1|EB641267
EST:     CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG                         GTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
genomic: CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctact ... tgtgctgcagGTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
EST: gi|149000689|gb|EE037900.2|EE037900
EST:     CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG                         GTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
genomic: CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctact ... tgtgctgcagGTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
EST: gi|78108222|gb|DV526640.1|DV526640
EST:     GACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG                         GTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
genomic: GACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctact ... tgtgctgcagGTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
EST: gi|91871816|gb|EB401773.1|EB401773
EST:     GAGTCGCGCTTTCCTGCGCAG                         GTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
genomic: GAGTCGCGCTTTCCTGCGCAGgtaccctact ... tgtgctgcagGTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
EST: gi|211386348|gb|FL456698.1|FL456698
EST:     CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG                         GTGCGGGTGGCAACGAGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
genomic: CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctact ... tgtgctgcagGTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
EST: gi|9953961|gb|BE640544.1|BE640544
EST:     CGGCGTGGGAGGACAAGAAGTGCCCCGGTGAGTCGCGCTTTCCTGCGCAG                         GTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
genomic: CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctact ... tgtgctgcagGTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
EST: gi|110517513|gb|EE022100.1|EE022100
EST:     CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG                         GTGCGGGTGGCAACGCGGAAGATTTACGACCCGCTGGAGGAGGACGCCTTC
genomic: CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctact ... tgtgctgcagGTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
EST: gi|211074694|gb|FL076199.1|FL076199
EST:     CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG                         GTGCGGGTGGCAACGAGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
genomic: CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctact ... tgtgctgcagGTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
EST: gi|78022808|gb|DV491195.1|DV491195
EST:     CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG                         GTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
genomic: CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctact ... tgtgctgcagGTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
EST: gi|149088944|gb|EE178087.2|EE178087
EST:     CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG                         GTGCGGGTGGCAACGCGGAAGATTTACGACCCGCTGGAGGAGGACGCCTTC
genomic: CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctact ... tgtgctgcagGTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
EST: gi|4730256|gb|AI649422.1|AI649422
EST:     CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG                         GTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
genomic: CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctact ... tgtgctgcagGTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
EST: gi|149090354|gb|EE179660.2|EE179660
EST:     CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG                         GTGCGGGTGGCAACGCGGAAGATTTACGACCCGCTGGAGGAGGACGCCTTC
genomic: CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctact ... tgtgctgcagGTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
EST: gi|71444740|gb|DR825790.1|DR825790
EST:     CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAG                         GTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
genomic: CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctact ... tgtgctgcagGTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
EST: gi|211171601|gb|FL423137.1|FL423137
EST:     CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCGCAG                         GTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
genomic: CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctact ... tgtgctgcagGTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
EST: gi|9794605|gb|BE552913.1|BE552913
EST:     CGGCGTGGGAGGACAAGAAGTG-CCCGGCGAGTCGCGCTTTCCTGCGCAG                         GTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC
genomic: CGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctact ... tgtgctgcagGTGCGGGTGGCAACGCGGAAGATCTACGACCCGCTGGAGGAGGACGCCTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGCGAGCTTCGGCGGGACCAACATCGACCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTTCCTGCGCAGgtaccctactgtactgtctgcttcgatccacagtctagtactctagtctagcagccatggcggcggcggcggcggcgggtgatcgatcagctcaacgtac

- - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT