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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ggtattaatgttctcatattatgcttgttttaaccacattttgtgaatgtgttttttccttcctttatattgcatcaaggtcccatttacgccttactgcttatatgtttcaGTTCTTCTGTTATTCATGATACTGAACTCTCACCAGATGTCCCCAAACTTTCT

Basic information

species Glycine max
transcript GLYMA18G04160.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G04160.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g16570.1 (Oryza sativa), 3'ss of exon 2
ggtattaatgttctcatattatgcttgttttaaccacattttgtgaatgtgttttttccttcctttatattgcatcaaggtcccatttacgccttactgcttatatgtttcaGTTCTTCTGTTATTCATGATACTGAACTCTCACCAGATGTCCCCAAACTTTCT-
     ||||||   |||    |  ||||  || | | ||| |     |||      |      ||| ||     | || |  | || ||    ||| |  || |  |   |||||||| |||| |||||| |||||||||| ||||||||||| || |||||| | 
----gtaatgtgggcatgccct--ttgtactaccgatattattaagctgtaaaaaatatcgattttcta----gttaatg--cgatcta----ttattctttttggg---cagTTCTTATGTTGTTCATGGTACTGAACTCACACCAGATGTCTCCGAACTTTTTG

upper sequence: GLYMA18G04160.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0019g01960.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------------------ggtattaa-tgttctcatattatgcttgttttaaccac-attttgtgaatgtgttttttccttcctttatattgcatcaaggtcccatttacgccttactgcttatatgtttcaGTTCTTCTGTTATTCATGATACTGAACTCTCACCAGATGTCCCCAAACTTTCT-
                                        | ||   | | ||  | ||||  || ||||||     | ||| |  | ||| |||    |||    | | |||||     ||  ||  ||   |||||  |   ||    |||||||| || | ||||||||||| ||||| ||||||||||| || |||||||| 
gtctttttaatatttaatttttaaagttatatcttttttatgttctctctcctttttttatttttattttaatttttaatttttacaagtggtttgagtttctaacaaaatgcat-----tctaatccacattttacttgtctgattcaacagTTCTTTTGCTGTTCATGATACTAAACTCACACCAGATGTCACCTAACTTTCTG
















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|15202365|gb|BI425363.1|BI425363
EST:     TTCATGCAACACGTCCTAGTAATTCCAATTCACTCACTTTTCTCGTGACA                         GTTCTTCTGTTATTCATGATA
genomic: TTCATGCAACACGTCCTAGTAATTCCAATTCACTCACTTTTCTCGTGACAggtattaatg ... atatgtttcaGTTCTTCTGTTATTCATGATA
EST: gi|6481566|gb|AW200837.1|AW200837
EST:     TCATGCAACACGTCCTAGTAATTCCAATTTCACTCACTTTTCTCGTGACA                         GTTCTTCTGTTATTCATGATACTGAACTCTCACCAGATGTCCCCAAACTTT
genomic: TCATGCAACACGTCCTAGTAATTCCAATT-CACTCACTTTTCTCGTGACAggtattaatg ... atatgtttcaGTTCTTCTGTTATTCATGATACTGAACTCTCACCAGATGTCCCCAAACTTT
EST: gi|21255789|gb|BQ452677.1|BQ452677
EST:     TTCATGCAACACGTCCTAGTAATTCCAATTCACTCACTTTTCTCGTGACA                         GTTCTTCTGTTATTCATGATACTGAACTCTCACCAGATGTCCCCAAACTTT
genomic: TTCATGCAACACGTCCTAGTAATTCCAATTCACTCACTTTTCTCGTGACAggtattaatg ... atatgtttcaGTTCTTCTGTTATTCATGATACTGAACTCTCACCAGATGTCCCCAAACTTT
EST: gi|58016501|gb|CX703243.1|CX703243
EST:     TTCATGCAACACGTCCTAGTAATTCCAATTCACTCACTTTTCTCGTGACA                         GTTCTTCTGTTATTCATGATACTG-ACTTCTCACCAGATGTCCCCAAACTT
genomic: TTCATGCAACACGTCCTAGTAATTCCAATTCACTCACTTTTCTCGTGACAggtattaatg ... atatgtttcaGTTCTTCTGTTATTCATGATACTGAAC-TCTCACCAGATGTCCCCAAACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttcctttatattgcatcaaggtcccatttacgccttactgcttatatgtttcaGTTCTTCTGTTATTCATGATACTGAACTCTCACCAGATGTCCCCAAACTTTCT
                                 gccttac  putative branch site (score: 3)
                                           ttatatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtattaatgttctcatattatgcttgttttaaccacattttgtgaatgtgttttttccttcctttatattgcatcaaggtcccatttacgccttactgcttatatgtttcaGTTCTTCTGTTATTCATGATACTGAACTCTCACCAGATGTCCCCAAACTTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG