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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ggtatgttgttttactggcagctacgtgtgaggtctaaattacttattatattgtgtacaaataatgatatagacacatgccatgctctattaatatgtggtttgcataccaccaGGTAAGCATGCACCTGATGACGTCAAGATCTTACCATTGGATTTATCATCTGGAGAGGATTCTCTTAGGATAGCTGTTGAGAAAGCAGAATCCTTTTTTC

Basic information

species Glycine max
transcript GLYMA18G47960.1
intron # 4
splice site 3'
intron type U2

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|6726744|gb|AW311098.1|AW311098
EST:     TCTCTGCAAGGAATGAAGCTGAGCTAAACCGAGTAAGGACACAGCTGAAA                         GGTAAGCATGCACCTGATGACGTCAAGATCTTACCATTGGATTTATCATCT
genomic: TCTCTGCAAGGAATGAAGCTGAGCTAAACCGAGTAAGGACACAGCTGAAAggtatgttgt ... cataccaccaGGTAAGCATGCACCTGATGACGTCAAGATCTTACCATTGGATTTATCATCT
EST: gi|298188014|gb|HO031971.1|HO031971
EST:     TCTCTGCAAGGAATGAAGCTGAGCTAAACCGAGTAAGGACACAGCTGAAA                         GGTAAGCATGCACCTGATGACGTCAAGATCTTACCATTGGATTTATCATCC
genomic: TCTCTGCAAGGAATGAAGCTGAGCTAAACCGAGTAAGGACACAGCTGAAAggtatgttgt ... cataccaccaGGTAAGCATGCACCTGATGACGTCAAGATCTTACCATTGGATTTATCATCT
EST: gi|192305183|gb|FG993949.1|FG993949
EST:     TCTCTGCAAGGAATGAAGCTGAGCTAAACCGAGTAAGGACACAGCTGAAA                         GGTAAGCATGCACCTGATGACGTCAAGATCTTACCATTGGATTTATCATCT
genomic: TCTCTGCAAGGAATGAAGCTGAGCTAAACCGAGTAAGGACACAGCTGAAAggtatgttgt ... cataccaccaGGTAAGCATGCACCTGATGACGTCAAGATCTTACCATTGGATTTATCATCT
EST: gi|16347967|gb|BI973562.1|BI973562
EST:     TCTCTGCAAGGAATGAAGCTGAGCTAAACCGAGTAAGGACACAGCTGAAA                         GGTAAGCATGCACCTGATGACGTCAAGATCTTACCATTGGATTTATCATCT
genomic: TCTCTGCAAGGAATGAAGCTGAGCTAAACCGAGTAAGGACACAGCTGAAAggtatgttgt ... cataccaccaGGTAAGCATGCACCTGATGACGTCAAGATCTTACCATTGGATTTATCATCT
EST: gi|10845691|gb|BF071167.1|BF071167
EST:     TCTCTGCAAGGAATGAAGCTGAGCTAAACCGAGTAAGGACACAGCTGAAA                         GGTAAGCATGCACCTGATGACGTCAAGATCTTACCATTGGATTTATCATCT
genomic: TCTCTGCAAGGAATGAAGCTGAGCTAAACCGAGTAAGGACACAGCTGAAAggtatgttgt ... cataccaccaGGTAAGCATGCACCTGATGACGTCAAGATCTTACCATTGGATTTATCATCT
EST: gi|18848709|gb|BM567821.1|BM567821
EST:     TCTCTGCAAGGAATGAAGCTGAGCTAAACCGAGTAAGGACACAGCTGAAA                         GGTAAGCATGCACCTGATGACGTCAAGATCTTACCATTGGATTTATCATCT
genomic: TCTCTGCAAGGAATGAAGCTGAGCTAAACCGAGTAAGGACACAGCTGAAAggtatgttgt ... cataccaccaGGTAAGCATGCACCTGATGACGTCAAGATCTTACCATTGGATTTATCATCT
EST: gi|254342710|gb|GR858872.1|GR858872
EST:     TCTCTGCAAGGAATGAAGCTGAGCTAAACCGAGTAAGGACACAGCTGAAA                         GGTAAGCATGCACCTGATGACGTCAAGATCTTACCATTGGATTTATCATCT
genomic: TCTCTGCAAGGAATGAAGCTGAGCTAAACCGAGTAAGGACACAGCTGAAAggtatgttgt ... cataccaccaGGTAAGCATGCACCTGATGACGTCAAGATCTTACCATTGGATTTATCATCT
EST: gi|209725122|gb|BW663062.1|BW663062
EST:     TCTCTGCAAGGAATGAAGCTGAGCTAAACCGAGTAAGGACACAGCTGAAA                         GGTAAGCATGCACCTGATGACGTCAAGATCTTACCATTGGATTTATCATCC
genomic: TCTCTGCAAGGAATGAAGCTGAGCTAAACCGAGTAAGGACACAGCTGAAAggtatgttgt ... cataccaccaGGTAAGCATGCACCTGATGACGTCAAGATCTTACCATTGGATTTATCATCT
EST: gi|6724680|gb|AW309013.1|AW309013
EST:     TCTCTGCAAGGAATGAAGCTGAGCTAAACCGAGTAAGGACACAGCTGAAA                         GGTAAGCATGCACCTGATGACGTCAAGATCTTACCATTGGATTTATCATCT
genomic: TCTCTGCAAGGAATGAAGCTGAGCTAAACCGAGTAAGGACACAGCTGAAAggtatgttgt ... cataccaccaGGTAAGCATGCACCTGATGACGTCAAGATCTTACCATTGGATTTATCATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataatgatatagacacatgccatgctctattaatatgtggtttgcataccaccaGGTAAGCATGCACCTGATGACGTCAAGATCTTACCATTGGATTTATCATCTGGAGAGGATTCTCTTAGGATAGCTGTTGAGAAAGCAGAATCCTTTTTTC
                            tattaat  putative branch site (score: 2)
                          tctattaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtatgttgttttactggcagctacgtgtgaggtctaaattacttattatattgtgtacaaataatgatatagacacatgccatgctctattaatatgtggtttgcataccaccaGGTAAGCATGCACCTGATGACGTCAAGATCTTACCATTGGATTTATCATCTGGAGAGGATTCTCTTAGGATAGCTGTTGAGAAAGCAGAATCCTTTTTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT