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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgatctttgcgttcttcatgtttttttttgcacgttttatcgatctgctaacttgacatttgatccaacgcaagttcgttgcttttttgattgaaaatcagattttgagataccctttgtgttcccaattaatgggttttttctggtgattgtatgggtgttaatttagAAGTTGATATAGGATGGGGGCAATGATGTCGAGATTCTGGTTCATGTTATTCCCTGCAAAAGAGTATAAGATTGTTGTTGTTGGATTGGATAACGCTGGA

Basic information

species Glycine max
transcript GLYMA20G35430.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35430.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G22950.1 (Arabidopsis thaliana), 3'ss of exon 2
gttcgatctttgcgttcttcatgtttttttttgcacgttttatcgatctgctaacttgacatttgatccaacgcaagttcgttgcttttttgattgaaaatcagattttgagataccct--ttgtgttcccaattaatgggttttttctggtgattgtatgggtgttaatttagAAGTTGATATAGGATGGGGGCAATGATGTCGAGATTCTGGTTCATGTTATTCCCTGCAAAAGAGTATAAGATTGTTGTTGTTGGATTGGATAACGCTGGA
                                                     |   | || || |    | | |  ||    | ||| | ||||  |  || | || |   | |   |  | ||      |||  ||| ||||| | || | |   | | | |  | ||  |||| |||  |   |||||| ||| | |||||||| || ||||||||| | || ||||||||||||||||||||||||||||||||                
----------------------------------------------------gatgggtcaatttaaaggatgtatctttag-ggtttctcgatttcac-tctgtttgtagaacaatttgatcgtaaaagtaat-gatgtgttttatttgattagGATCTTGTTTGTGAT--AGAAATTGG-AGGAGATGGGAGCATTCATGTCGAGGTTTTGGTTCATGATGTTTCCTGCAAAAGAGTATAAGATTGTTGTTGTTGG----------------

upper sequence: GLYMA20G35430.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G22950.2 (Arabidopsis thaliana), 3'ss of exon 2
gttcgatctttgcgttcttcatgtttttttttgcacgttttatcgatctgctaacttgacatttgatccaacgcaagttcgttgcttttttgattgaaaatcagattttgagataccct--ttgtgttcccaattaatgggttttttctggtgattgtatgggtgttaatttagAAGTTGATATAGGATGGGGGCAATGATGTCGAGATTCTGGTTCATGTTATTCCCTGCAAAAGAGTATAAGATTGTTGTTGTTGGATTGGATAACGCTGGA-
                                                                      | | |  ||    | ||| | ||||  |  || | || |   | |   |  | ||      |||  ||| ||||| | || | |   | | | |  | ||  |||| |||  |   |||||| ||| | |||||||| || ||||||||| | || |||||||||||||||||||||||||||||||| |||||||| |||||  
---------------------------------------------------------------------gatgtatctttag-ggtttctcgatttcac-tctgtttgtagaacaatttgatcgtaaaagtaat-gatgtgttttatttgattaggatcttgtttgtgat--agAAATTGG-AGGAGATGGGAGCATTCATGTCGAGGTTTTGGTTCATGATGTTTCCTGCAAAAGAGTATAAGATTGTTGTTGTTGGTTTGGATAATGCTGGTA
















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|298173714|gb|HO017050.1|HO017050
EST:     TCACCCTTTCTCCCACACACTCCGATTCTCCTTGTAAACAGCGGTGCCAG                         AAGTTGATATAGGATGGGGGCAATGATGTCGAGATTCTGGTTCATGTTATT
genomic: TCACCCTTTCTCCCACACACTCCGATTCTCCTTGTAAACAGCGGTGCCAGgttcgatctt ... gttaatttagAAGTTGATATAGGATGGGGGCAATGATGTCGAGATTCTGGTTCATGTTATT
EST: gi|37996133|gb|CF807722.1|CF807722
EST:     TCACCCTTTCTCCCACACACTCCGATTCTCCTTGTAAACAGCGGTGCCAG                         AAGTTGATATAGGATGGGGGCAATGATGTCGAGATTCTGGTTCATGTTATT
genomic: TCACCCTTTCTCCCACACACTCCGATTCTCCTTGTAAACAGCGGTGCCAGgttcgatctt ... gttaatttagAAGTTGATATAGGATGGGGGCAATGATGTCGAGATTCTGGTTCATGTTATT
EST: gi|192330894|gb|FK021639.1|FK021639
EST:     TCACCCTTTCTCCCACACACTCCGATTCTCCTTGTAAACAGCGGTGCCAG                         AAGTTGATATAGGATGGGGGCAATGATGTCGAGATTCTGGTTCATGTTATT
genomic: TCACCCTTTCTCCCACACACTCCGATTCTCCTTGTAAACAGCGGTGCCAGgttcgatctt ... gttaatttagAAGTTGATATAGGATGGGGGCAATGATGTCGAGATTCTGGTTCATGTTATT
EST: gi|192330253|gb|FK020553.1|FK020553
EST:     TCACCCTTTCTCCCACACACTCCGATTCTCCTTGTAAACAGCGGTGCCAG                         AAGTTGATATAGGATGGGGGCAATGATGTCGAGATTCTGGTTCATGTTATT
genomic: TCACCCTTTCTCCCACACACTCCGATTCTCCTTGTAAACAGCGGTGCCAGgttcgatctt ... gttaatttagAAGTTGATATAGGATGGGGGCAATGATGTCGAGATTCTGGTTCATGTTATT
EST: gi|298182623|gb|HO031358.1|HO031358
EST:     TCACCCTTTCTCCCACACACTCCGATTCTCCTTGTAAACAGCGGTGCCAG                         AAGTTGATATAGGATGGGGGCAATGATGTCGAGATTCTGGTTCATGTTATT
genomic: TCACCCTTTCTCCCACACACTCCGATTCTCCTTGTAAACAGCGGTGCCAGgttcgatctt ... gttaatttagAAGTTGATATAGGATGGGGGCAATGATGTCGAGATTCTGGTTCATGTTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgtgttcccaattaatgggttttttctggtgattgtatgggtgttaatttagAAGTTGATATAGGATGGGGGCAATGATGTCGAGATTCTGGTTCATGTTATTCCCTGCAAAAGAGTATAAGATTGTTGTTGTTGGATTGGATAACGCTGGA
                                            tgttaat  putative branch site (score: 3)
                                            tgttaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgatctttgcgttcttcatgtttttttttgcacgttttatcgatctgctaacttgacatttgatccaacgcaagttcgttgcttttttgattgaaaatcagattttgagataccctttgtgttcccaattaatgggttttttctggtgattgtatgggtgttaatttagAAGTTGATATAGGATGGGGGCAATGATGTCGAGATTCTGGTTCATGTTATTCCCTGCAAAAGAGTATAAGATTGTTGTTGTTGGATTGGATAACGCTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA