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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ggtatggttcttatggtttttacatgcttcattgcatttgaatttgcttactgcctcccagaaagttatcacattcaattaatttttttttcttcaaacatttttataggctattgttgttgtattgttataGGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCTTGCAGATTATGTTCACGGCAAGGGTCTTAAGCTTGGAATTTATTCAGAT

Basic information

species Glycine max
transcript GLYMA18G44820.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G44820.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G146463_T01 (Zea mays), 3'ss of exon 5
ggtatggttcttatggtttttacatgcttcattgcatttgaatttgcttactgcctcccagaaagttatcacattcaattaatttttttttcttcaaacatttttataggctattgttgttgtattgttataGGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCTTGCAGATTATGTTCACGGCAAGGGTCTTAAGCTTGGAATTTATTCAGAT-
    | || | || |  |  |    ||| | |  |  |||   |   |||||  |    | |   ||       | ||  |  | ||| ||    |   ||  | || | ||  || ||          | ||||  |  |||| || ||       || || || || |||||||| || || |||||||| |||||| ||||||| ||||||||||| || || ||     
---gtagtacgtacgagtgct----gctacgtgac-cttgtcgtcagttactttcagttaaattcttgcactgctgaagcacgtgtttgtttaagaggaatgctaatcgact--tgctg----------acagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTGGCAGATTACGTTCACAGCAAGGGGCTTAAGCTTGGCATCTACTCTTCCG

upper sequence: GLYMA18G44820.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G146463_T03 (Zea mays), 3'ss of exon 5
ggtatggttcttatggtttttacatgcttcattgcatttgaatttgcttactgcctcccagaaagttatcacattcaattaatttttttttcttcaaacatttttataggctattgttgttgtattgttataGGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCTTGCAGATTATGTTCACGGCAAGGGTCTTAAGCTTGGAATTTATTCAGAT-
      || | || |  |  |    ||| | |  |  |||   |   |||||  |    | |   ||       | ||  |  | ||| ||    |   ||  | || | ||  || ||          | ||||  |  |||| || ||       || || || || |||||||| || || |||||||| |||||| ||||||| ||||||||||| || || ||     
------gtacgtacgagtgct----gctacgtgac-cttgtcgtcagttactttcagttaaattcttgcactgctgaagcacgtgtttgtttaagaggaatgctaatcgact--tgctg----------acagGGATACATGGTCGCTAACCCCAAGACATTCCCATCCGGAATCAAGGCCCTGGCAGATTACGTTCACAGCAAGGGGCTTAAGCTTGGCATCTACTCTTCCG

upper sequence: GLYMA18G44820.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G08380.1 (Arabidopsis thaliana), 3'ss of exon 4
ggtatggttcttatggtttttacatgcttcattgcatttgaatttgcttactgcctcccagaaagttatcacattcaattaatttttttttcttcaaacatttttataggctattgttgttgtattgttataGGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCTTGCAGATTATGTTCACGGCAAGGGTCTTAAGCTTGGAATTTATTCAGAT-
                               |   ||   ||||  |||  ||  |||  |     | |||  |    ||  |    ||||  |  |    ||||||   ||    |   | | || ||  |||| | ||||||  |||| || ||||| || ||||||||||| |||||  |||| |||||||||||| | || || ||||||||||| ||||| |||||| 
------------------------------gtattatcataatt--ctttgtgtttcctgg-----tttcatttcttgtttctgcagttttgctaga----ttttat---cttccttaactctgtt-ttccagGGAAGTCTGGTGCCAAAGAAGTCAACTTTCCCTTCTGGAATTAAAGCGGTTGCGGATTATGTTCACAGTAAAGGCCTTAAGCTTGGGATTTACTCAGATG

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|209711065|gb|BW676421.1|BW676421
EST:     GATGATTGTTGGGCTGAATTAAATCGGGATGCTAA                         GGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCT
genomic: GATGATTGTTGGGCTGAATTAAATCGGGATGCTAAggtatggttc ... tattgttataGGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCT
EST: gi|192312271|gb|FK005275.1|FK005275
EST:     GATGATTGTTGGGCTGAATTAAATCGGGATGCTAA                         GGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCT
genomic: GATGATTGTTGGGCTGAATTAAATCGGGATGCTAAggtatggttc ... tattgttataGGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCT
EST: gi|208153437|gb|GD945698.1|GD945698
EST:     GATGATTGTTGGGCTGAATTAAATCGGGATGCTAA                         GGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCT
genomic: GATGATTGTTGGGCTGAATTAAATCGGGATGCTAAggtatggttc ... tattgttataGGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCT
EST: gi|193384258|gb|FK349746.1|FK349746
EST:     GATGATTGTTGGGCTGAATTAAATCGGGATGCTAA                         GGGTAATCTGGTAGCAAAAA-TTCAAACGTTTCCTTCTGGAATCAAAGCTC
genomic: GATGATTGTTGGGCTGAATTAAATCGGGATGCTAAggtatggttc ... tattgttataGGGTAATCTGGTAGCAAAAAATTCAA-CGTTTCCTTCTGGAATCAAAGCTC
EST: gi|151412992|gb|EV282800.1|EV282800
EST:     GATGATTGTTGGGCTGAATTAAATCGGGATGCTAA                         GGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCT
genomic: GATGATTGTTGGGCTGAATTAAATCGGGATGCTAAggtatggttc ... tattgttataGGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCT
EST: gi|298193345|gb|HO033779.1|HO033779
EST:     GATGATTGTTGGGCTGAATTAAATCGGGATGCTAA                         GGGTAATCTGGTAGCAAAAAGTTCAACGTTTCCTTCTGGAATCAAAGCTCT
genomic: GATGATTGTTGGGCTGAATTAAATCGGGATGCTAAggtatggttc ... tattgttataGGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCT
EST: gi|213596908|gb|DB964115.1|DB964115
EST:     GATGATTGTTGGGCTGAATTAAATCGGGATGCTAA                         GGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCT
genomic: GATGATTGTTGGGCTGAATTAAATCGGGATGCTAAggtatggttc ... tattgttataGGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCT
EST: gi|193530996|gb|FK487097.1|FK487097
EST:     GATGATTGTTGGGCTGAATTAAATCGGGATGCTAA                         GGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCT
genomic: GATGATTGTTGGGCTGAATTAAATCGGGATGCTAAggtatggttc ... tattgttataGGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCT
EST: gi|24206259|gb|BU965512.1|BU965512
EST:     GTTGGGCTGAATTATATCCCGATGCTAA                         GGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCT
genomic: GTTGGGCTGAATTAAATCGGGATGCTAAggtatggttc ... tattgttataGGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCT
EST: gi|6481859|gb|AW201130.1|AW201130
EST:     GATGATTGTTGGGCTGAATTAAATCGGGATGCTAA                         GGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCT
genomic: GATGATTGTTGGGCTGAATTAAATCGGGATGCTAAggtatggttc ... tattgttataGGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaatttttttttcttcaaacatttttataggctattgttgttgtattgttataGGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCTTGCAGATTATGTTCACGGCAAGGGTCTTAAGCTTGGAATTTATTCAGAT
 aattaat  putative branch site (score: 3)
     tttttttttcttcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtatggttcttatggtttttacatgcttcattgcatttgaatttgcttactgcctcccagaaagttatcacattcaattaatttttttttcttcaaacatttttataggctattgttgttgtattgttataGGGTAATCTGGTAGCAAAAAATTCAACGTTTCCTTCTGGAATCAAAGCTCTTGCAGATTATGTTCACGGCAAGGGTCTTAAGCTTGGAATTTATTCAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT