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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAGgtatgataaatgatgctttcaatttatgggaacagataaaaagatgtattccctcccccgatactgtcttgaacacgttaccttattggcatgtgccttatttactactttggttttgcag

Basic information

species Glycine max
transcript GLYMA14G39890.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G39890.2 (Glycine max), 5'ss of exon 13
lower sequence: GRMZM2G101383_T01 (Zea mays), 5'ss of exon 14
GCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAGgtatgataaatgatgctttcaatttatgggaacagataaaaag-atgtattccctcccccgatactgtcttgaacacgttaccttattggcatgtgccttatttactactttggttttgcag------------------------------------------------------------------------------
||||| || ||||||||||||||||| ||||| |||||||||||||| ||||| |||||   |   ||   || |  |    ||  |  ||  |||    |  | |    | | |  ||  | || |||| |    ||   || |  | || ||| |      | |||||| |                                                                                   
GCTGGAACATACATCAAGGAATTTGTGCATGGTGATCTTGGACGCACGCATCCCAGgtagcgt---tgtctctatttagccttgtcactagccaaattccaactgtcaaatacacaaatcttttcatgaaaaaaaaactgcat-gttaagt-cctcaccagtcattttggtataaagattgaactgatgaccttgctttacactttacagtaacactacaatcctgataggcctcgttccactttgcctattgcag

upper sequence: GLYMA14G39890.2 (Glycine max), 5'ss of exon 13
lower sequence: Vv18s0001g00500.t01 (Vitis vinifera), 5'ss of exon 14
GCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAGgtatgataaatg---atgctttcaatttatgggaacagataaaaagatgtattccctcccccgatactgtcttgaacacgttaccttattggcatgtgccttatttactactttggttttgcag
||||| || || ||||||||||||||||| || ||||||||||||||||||||||||||| |   |||   ||   || ||||  ||  ||  |     |   | ||||          ||  | | |     |   ||  ||  |  || | |||                        
GCTGGAACATATATCAAGGAATTTGTTCACGGTGATCTTGGACGCACCCATCCTAGgtataaattatgcccatctctttaattc-tgtaaattgtagggagcttctattaggattttacatcttatttcctttattctatgttcatcacaagggcca-----------------------
















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|51343704|gb|CO984437.1|CO984437
EST:     CTTGGACGCACCCATCCTAG                         CATTGGATCAATTTTGGGTTGCAGAGCTGAAATTTTGCAACTTGATGTCAC
genomic: CTTGGACGCACCCATCCTAGgtatgataaa ... ggttttgcagCATTGGATCAATTTTGGGTTGCAGAGCTGAAATTTTGCAACTTGATGTCAC
EST: gi|209721756|gb|BW682597.1|BW682597
EST:     TGGACGCACCCATCCTAG                         CATTGGATCAATTTTGGGTTGCAGAGCTGAAATTTTGCAACTTGATGTCAC
genomic: TGGACGCACCCATCCTAGgtatgataaa ... ggttttgcagCATTGGATCAATTTTGGGTTGCAGAGCTGAAATTTTGCAACTTGATGTCAC
EST: gi|51342518|gb|CO983503.1|CO983503
EST:     ACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAG                         CATTGGATCAATTTTGGGTTGCAGAGCTGAAATTTTGCAACTTGATGTCAC
genomic: ACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAGgtatgataaa ... ggttttgcagCATTGGATCAATTTTGGGTTGCAGAGCTGAAATTTTGCAACTTGATGTCAC
EST: gi|58017398|gb|CX704140.1|CX704140
EST:     ACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAG                         CATTGGATCAATTTTGGGTTGCAGAGCTGAAATTTTGCAACTTGATGTCAC
genomic: ACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAGgtatgataaa ... ggttttgcagCATTGGATCAATTTTGGGTTGCAGAGCTGAAATTTTGCAACTTGATGTCAC
EST: gi|208221094|gb|GE020764.1|GE020764
EST:     ACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAG                         CATTGGATCAATTTTGGGTTGCAGAGCTGAAATTTTGCAACTTGATGTCAC
genomic: ACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAGgtatgataaa ... ggttttgcagCATTGGATCAATTTTGGGTTGCAGAGCTGAAATTTTGCAACTTGATGTCAC
EST: gi|58017203|gb|CX703945.1|CX703945
EST:     ACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAG                         CATTGGATCAATTTTGGGTTGCAGAGCTGAAATTTTGCAACTTGATGTCAC
genomic: ACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAGgtatgataaa ... ggttttgcagCATTGGATCAATTTTGGGTTGCAGAGCTGAAATTTTGCAACTTGATGTCAC
EST: gi|163922935|gb|EH039556.1|EH039556
EST:     ACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAG                         CATTGGATCAATTTTGGGTTGCAGAGCTGAAATTTTGCAACTTGATGTCAC
genomic: ACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAGgtatgataaa ... ggttttgcagCATTGGATCAATTTTGGGTTGCAGAGCTGAAATTTTGCAACTTGATGTCAC
EST: gi|51342063|gb|CO983330.1|CO983330
EST:     ACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAG                         CATTGGATCAATTTTGGGTTGCAGAGCTGAAATTTTGCAACTTGATGTCAC
genomic: ACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAGgtatgataaa ... ggttttgcagCATTGGATCAATTTTGGGTTGCAGAGCTGAAATTTTGCAACTTGATGTCAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGGGACCTACATCAAGGAATTTGTTCATGGGGATCTTGGACGCACCCATCCTAGgtatgataaatgatgctttcaatttatgggaacagataaaaagatgtattccctcccccgatactgtcttgaacacgttaccttattggcatgtgccttatttactactttggttttgcag

- - - - - - -  AAGGAA