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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgcttgctttctggaacttgtttactccgttgaatttcattcttttcttggtgaattgataagagagatgtcacggtgaataattttaagaattt...

Basic information

species Glycine max
transcript GLYMA08G46860.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G46860.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os03g54860.1 (Oryza sativa), 5'ss of exon 3
GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgcttgctttctggaacttgtttactccgttgaatttcattcttttcttggtgaattgataagagagatgtcacggtgaataattttaagaattt----
|||  ||||||| |||   || ||||| ||||| |  || |||||  | ||    |||||||| |||||||||||||| ||||||||||| |||      |      |      |  ||  |||| | ||   |  |   | |     ||   |   |     | |   |  ||      |   ||||    
GGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTCCAAGGAGGTTGGCTGGAACTACTATGACACCATCAGGgtaagtttccattcctccaagg--agtagctgtgttgtaattg--ttgtgattggactgtttaccagcggtagatttataatagatcgggccattcatttagta

upper sequence: GLYMA08G46860.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os03g54890.2 (Oryza sativa), 5'ss of exon 3
GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgcttgctttctggaacttgtttactccgttgaatttcattcttttcttggtgaattgata-agagagatgtcacggtgaataattttaagaattt
|||  ||||||| |||   || ||||| ||||| |  || |||||  | ||    |||||||| |||||||||||||| ||||||||||| |||      |   |      |   |  |  | | | | |  |  ||   ||| | |   |||  |||   |||   |||   ||   ||||    || 
GGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTCCAAGGAGGTTGGCTGGAACTACTATGACACCATCAGGgtaagtttccattccttcctttctagctg-tgtggtaattgttgtgattggattgtttaccagatgtagatttatggatcgggtcattcatttagttttta

upper sequence: GLYMA08G46860.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G072315_T01 (Zea mays), 5'ss of exon 3
GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgcttgctttctggaacttgtttactccgttgaatttcattctttt-cttggtgaattgataagagagatgtcacggtgaataattttaagaattt---
|||  ||||||| ||    |||||||| ||||| |  || ||  |  | ||    ||||| |||||||||||| |||| |||||||||||||||| || |   ||   | ||  ||  ||   | | |  |||  |||| |  ||  | || |       | ||  |   ||  | | || |  ||||    
GGTCCTGAGGCTGCAACCTGGACACAAGTACTGCCTCCTTGGTGAGCTTTCTAAGGAGGTCGGATGGAACTACCATGACACCATCAGGgtgagtgttt-cccactcatattttcttgatca--taagtggcatcgttttgcacggacactttaatcacttgttgctagtttgggtgagtt-agtaattaata

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|9986841|gb|BE660949.1|BE660949
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
EST: gi|208136824|gb|GD935416.1|GD935416
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
EST: gi|208122761|gb|GD923635.1|GD923635
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
EST: gi|208204614|gb|GE007853.1|GE007853
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
EST: gi|298195955|gb|HO044346.1|HO044346
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAGAGGAAGGATAGAGC
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAGAGGAAGGATAGAGC
EST: gi|193339582|gb|FK304859.1|FK304859
EST:     GGCCAATTGTCATCTGGGGGTTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
genomic: GGCCAATTGTCATCT-GAGG-TTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
EST: gi|298189729|gb|HO038132.1|HO038132
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGA
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGA
EST: gi|298189786|gb|HO038189.1|HO038189
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGT
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGT
EST: gi|192325948|gb|FK016625.1|FK016625
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
EST: gi|18717939|gb|BM523010.1|BM523010
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
EST: gi|193632583|gb|FK580515.1|FK580515
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
EST: gi|14011338|gb|BG726260.1|BG726260
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGA
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGA
EST: gi|7042145|gb|AW472039.1|AW472039
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAGAGGAAGGATAGAGCACA-TTGTGTTACGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
EST: gi|15286024|gb|BI469915.1|BI469915
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
EST: gi|105633518|gb|DW246881.1|DW246881
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
EST: gi|163920729|gb|EH039986.1|EH039986
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
EST: gi|151407543|gb|EV277358.1|EV277358
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
EST: gi|193377070|gb|FK342707.1|FK342707
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTAC
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgcttgctttctggaacttgtttactccgttgaatttcattcttttcttggtgaattgataagagagatgtcacggtgaataattttaagaattt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA