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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgcacaaaaaagtggaccttcttccatcttctcgcatagtgcactaccatccaattttcatgatctgatcaaggtttacattatcactgttatttgcagGTAGCTGTCACAGAATTAAGTGGTCAAATTTGTCAGATCTGTGGGGATGAGCTGGAGGTTACTGTGAATGGGGAGCCATTTGTTGCTTGCAATGAATGTG

Basic information

species Glycine max
transcript GLYMA02G08920.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G08920.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0072g00370.t01 (Vitis vinifera), 3'ss of exon 1
gtgcacaaaaaagtggaccttc----ttccatcttctcgcatagtgcactaccatccaattttcatgatctgatcaaggtttacattatcactgttatttgcagGTAGCT---GTCACAGAATTAAGTGGTCAAATTTGTCAGATCTGTGGGGATGAGCTGGAGGTTACTGTGAATGGGGAGCCATTTGTTGCTTGCAATGAATGTG
 |  | ||  |  ||   ||||    ||| ||||       | | |||  |  ||||| ||||||||| || ||   | || || ||    |||| |  | |||||  ||   || | |||||| ||||| || ||||||||||| |||||||||||| | ||| |||||||| ||||||||||||| ||||| || |||||||   
tttaaaaatcatatgctgcttcaatattctatctggggttgttgagcaa-aaaatccagttttcatgacctaatgccgattgactttg---ctgtgacatacagGTGACTTCCGTGAAAGAATTGAGTGGGCAGATTTGTCAGATTTGTGGGGATGAGATAGAGATTACTGTGGATGGGGAGCCATTCGTTGCCTGTAATGAAT---
















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|213605340|gb|DB966914.1|DB966914
EST:     CTCATAACAGGAATGAGTTTGTTCTTATCAATGCTGATGAAACTGCAAGA                         GTAGCTGTCACAGAATTAAGTGGTCAAATTTGTCAGATCTGTGGGGATGAG
genomic: CTCATAACAGGAATGAGTTTGTTCTTATCAATGCTGATGAAACTGCAAGAgtgagtggtc ... ttatttgcagGTAGCTGTCACAGAATTAAGTGGTCAAATTTGTCAGATCTGTGGGGATGAG
EST: gi|192328149|gb|FK022858.1|FK022858
EST:     CTCATAACAGGAATGAGTTTGTTTTTATCAATGCTGATGAAACTGCAAGA                         GTAGCTGTCACAGAATTAAGTGGTCAAATTTGTCAGATCTGTGGGGATGAG
genomic: CTCATAACAGGAATGAGTTTGTTCTTATCAATGCTGATGAAACTGCAAGAgtgagtggtc ... ttatttgcagGTAGCTGTCACAGAATTAAGTGGTCAAATTTGTCAGATCTGTGGGGATGAG
EST: gi|209719736|gb|BW669243.1|BW669243
EST:     CTCATAACAGGAATGAGTTTGTTCTTATCAATGCTGATGAAACTGCAAGA                         GTAGCTGTCACAGAATTAAGTGGTCAAATTTGTCAGATCTGTGGGGATGAG
genomic: CTCATAACAGGAATGAGTTTGTTCTTATCAATGCTGATGAAACTGCAAGAgtgagtggtc ... ttatttgcagGTAGCTGTCACAGAATTAAGTGGTCAAATTTGTCAGATCTGTGGGGATGAG
EST: gi|20814784|gb|BQ299262.1|BQ299262
EST:     CTCATAACAGGAATGAGTTTGTTCTTATCAATGCTGATGAAACTGCAAGA                         GTAGCTGTCACAGAATTAAGTGGTCAAATTTGTCAGATCTGTGGGGATGAG
genomic: CTCATAACAGGAATGAGTTTGTTCTTATCAATGCTGATGAAACTGCAAGAgtgagtggtc ... ttatttgcagGTAGCTGTCACAGAATTAAGTGGTCAAATTTGTCAGATCTGTGGGGATGAG
EST: gi|209720456|gb|BW671789.1|BW671789
EST:     CTCATAACAGGAATGAGTTTGTTCTTATCAATGCTGATGAAACTGCAAGA                         GTAGCTGTCACAGAATTAAGTGGTCAAATTTGTCAGATCTGTGGGGATGAG
genomic: CTCATAACAGGAATGAGTTTGTTCTTATCAATGCTGATGAAACTGCAAGAgtgagtggtc ... ttatttgcagGTAGCTGTCACAGAATTAAGTGGTCAAATTTGTCAGATCTGTGGGGATGAG
EST: gi|213589781|gb|DB959406.1|DB959406
EST:     CTCATAACAGGAATGAGTTTGTTCTTATCAATGCTGATGAAACTGCAAGA                         GTAGCTGTCACAGAATTAAGTGGTCAAATTTGTCAGATCTGTGGGGATGAG
genomic: CTCATAACAGGAATGAGTTTGTTCTTATCAATGCTGATGAAACTGCAAGAgtgagtggtc ... ttatttgcagGTAGCTGTCACAGAATTAAGTGGTCAAATTTGTCAGATCTGTGGGGATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccatccaattttcatgatctgatcaaggtttacattatcactgttatttgcagGTAGCTGTCACAGAATTAAGTGGTCAAATTTGTCAGATCTGTGGGGATGAGCTGGAGGTTACTGTGAATGGGGAGCCATTTGTTGCTTGCAATGAATGTG
                  atctgat  putative branch site (score: 4)
                              tttacattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcacaaaaaagtggaccttcttccatcttctcgcatagtgcactaccatccaattttcatgatctgatcaaggtttacattatcactgttatttgcagGTAGCTGTCACAGAATTAAGTGGTCAAATTTGTCAGATCTGTGGGGATGAGCTGGAGGTTACTGTGAATGGGGAGCCATTTGTTGCTTGCAATGAATGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
-tgcacaa
- - - - - - - - - -ttcttcc
- - - - - - - - - - - - - - - - - - - - tgcacta
- - - - - - - - - - - - - - - - - - - - - - - -ccatcca