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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttttctttctacttttgttttggaatttggttgttcaatcttttagatgctgaagtggtgaatgaaatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG

Basic information

species Glycine max
transcript GLYMA08G46860.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G46860.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g54890.2 (Oryza sativa), 3'ss of exon 2
----------gtgagtttttctttctacttttgttt-tggaatt-tggttgttcaatcttttagatgctgaagtggtgaatgaaatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG
           |   || || |||  | |||| ||| || |||| ||   |  | |    |   ||| ||   || |   ||     |  ||||||  ||||||| |||   || ||||| ||||| |  || |||||  | ||    |||||||| |||||||||||||| |||||||||
gtacgtcggattcgcttgttgtttggatttttttttgtgtaattgtgcgcgagcgagtagtctaatggtgtt-tgtttggtgccgaattgtagGGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTCCAAGGAGGTTGGCTGGAACTACTATGACACCATCAGG

upper sequence: GLYMA08G46860.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g54860.1 (Oryza sativa), 3'ss of exon 2
----------------------gtgagt-ttttctttctacttttgttttggaatttggttgttcaatcttttagatgctgaagtggtgaatgaaatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG
                       ||  | |||||||| |    || || |  | | ||   |  | ||   |   ||| ||   || |   ||     |  ||||||  ||||||| |||   || ||||| ||||| |  || |||||  | ||    |||||||| |||||||||||||| |||||||||
gtacgtcggattcgcttgttgtttggatattttctttttgtgattattgta-attgtgcacgagcgattggtctaatggtgtt-tgtttggtgccgaattgtagGGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTCCAAGGAGGTTGGCTGGAACTACTATGACACCATCAGG
















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:     CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
genomic: CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAAgtgagttttt ... aatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
EST: gi|208136824|gb|GD935416.1|GD935416
EST:     GGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
genomic: GGTTGTTCCTGATGCTCTCAAgtgagttttt ... aatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
EST: gi|208122761|gb|GD923635.1|GD923635
EST:     CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
genomic: CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAAgtgagttttt ... aatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
EST: gi|208204614|gb|GE007853.1|GE007853
EST:     ACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
genomic: ACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAAgtgagttttt ... aatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
EST: gi|298195955|gb|HO044346.1|HO044346
EST:     CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
genomic: CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAAgtgagttttt ... aatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
EST: gi|193730000|gb|FK667844.1|FK667844
EST:     CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAGGGAACAACAAATACTGTCATCTGGGCCA
genomic: CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAAgtgagttttt ... aatttattagGGTGTTGAGGCTTCAGAAGGGA-CA-CAAATACTGTCATCTGGGCCA
EST: gi|298189729|gb|HO038132.1|HO038132
EST:     CCTCCTCCTTGTGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
genomic: CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAAgtgagttttt ... aatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
EST: gi|298189786|gb|HO038189.1|HO038189
EST:     CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
genomic: CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAAgtgagttttt ... aatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
EST: gi|192325948|gb|FK016625.1|FK016625
EST:     CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
genomic: CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAAgtgagttttt ... aatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
EST: gi|193380148|gb|FK347854.1|FK347854
EST:     CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
genomic: CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAAgtgagttttt ... aatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
EST: gi|18717939|gb|BM523010.1|BM523010
EST:     CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
genomic: CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAAgtgagttttt ... aatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
EST: gi|193428398|gb|FK394018.1|FK394018
EST:     CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAGGGACACAAATAACTGTCATCT
genomic: CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAAgtgagttttt ... aatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATA-CTGTCATCT
EST: gi|193632583|gb|FK580515.1|FK580515
EST:     CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
genomic: CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAAgtgagttttt ... aatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
EST: gi|14011338|gb|BG726260.1|BG726260
EST:     CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
genomic: CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAAgtgagttttt ... aatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
EST: gi|7042145|gb|AW472039.1|AW472039
EST:     CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
genomic: CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAAgtgagttttt ... aatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
EST: gi|15286024|gb|BI469915.1|BI469915
EST:     CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
genomic: CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAAgtgagttttt ... aatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
EST: gi|193414001|gb|FK376595.1|FK376595
EST:     CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCT
genomic: CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAAgtgagttttt ... aatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCT
EST: gi|105633518|gb|DW246881.1|DW246881
EST:     CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
genomic: CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAAgtgagttttt ... aatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
EST: gi|163920729|gb|EH039986.1|EH039986
EST:     CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
genomic: CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAAgtgagttttt ... aatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
EST: gi|151407543|gb|EV277358.1|EV277358
EST:     CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
genomic: CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAAgtgagttttt ... aatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
EST: gi|193321509|gb|FK284049.1|FK284049
EST:     CTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTTCTCAA                         GGTGTTGAGGCTTCAGAAGGGACACAAATAACTGTCATCT
genomic: CTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCT-CTCAAgtgagttttt ... aatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATA-CTGTCATCT
EST: gi|193377070|gb|FK342707.1|FK342707
EST:     CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAA                         GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC
genomic: CCTCCTCCTTATGACAAGACCAAGAGGATGGTTGTTCCTGATGCTCTCAAgtgagttttt ... aatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaatttggttgttcaatcttttagatgctgaagtggtgaatgaaatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG
                                      tgaatgaaatttatta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttttctttctacttttgttttggaatttggttgttcaatcttttagatgctgaagtggtgaatgaaatttattagGGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG

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