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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcttgttttgagcttgatgcacccttaatttcaaacatatccctttatctgctcaagagatttactttatgtcacaattaataatactttgaacatattttccagTCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGATCGACTAAGACATCTTGCCTCACCTGCTGGAAAG

Basic information

species Glycine max
transcript GLYMA13G00990.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G00990.1 (Glycine max), 3'ss of exon 10
lower sequence: AT4G30210.2 (Arabidopsis thaliana), 3'ss of exon 10
-gtgcttgttttgagcttgatgcacccttaatttcaaacatatccctttatctgctcaagagatttactttatgtcacaattaataatactttgaacatattttccagTCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGATCGACTAAGACATCTTGCCTCACCTGCTGGAAAG
  || |||  || |  ||          |  ||  || ||  |   ||| ||| |  | |||||| |   |      |||||| |   |  || |   | | || |||||||| ||  |||| || ||||||||||||||||||||  | ||||| || ||| ||| ||| ||||| |||||||||||||||
gttggttggattca-tttaccattagactggttataatcagttttgtttctcttcata-gagattcaaact------caattattttcatgtttat--tttcttgcagTCTGCTTTAGTTGCGTTGGCTGCTCATGCATCTGATCCTACCGAAGCAGAACGATTAAAACACCTTGCTTCACCTGCTGGAAAG

upper sequence: GLYMA13G00990.1 (Glycine max), 3'ss of exon 10
lower sequence: AT4G30210.1 (Arabidopsis thaliana), 3'ss of exon 10
-gtgcttgttttgagcttgatgcacccttaatttcaaacatatccctttatctgctcaagagatttactttatgtcacaattaataatactttgaacatattttccagTCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGATCGACTAAGACATCTTGCCTCACCTGCTGGAAAG---
  || |||  || |  ||          |  ||  || ||  |   ||| ||| |  | |||||| |   |      |||||| |   |  || |   | | || |||||||| ||  |||| || ||||||||||||||||||||  | ||||| || ||| ||| ||| ||||| |||||||||||||||   
gttggttggattca-tttaccattagactggttataatcagttttgtttctcttcata-gagattcaaact------caattattttcatgtttat--tttcttgcagTCTGCTTTAGTTGCGTTGGCTGCTCATGCATCTGATCCTACCGAAGCAGAACGATTAAAACACCTTGCTTCACCTGCTGGAAAGGTT
















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|13312892|gb|BG406543.1|BG406543
EST:     TAAGAAAAGCACTTGCACAATATGCGGATGTTTTGAGTTCACCCAAAAAG                         TCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGAT
genomic: TAAGAAAAGCACTTGCACAATATGCGGATGTTTTGAGTTCACCCAAAAAGgtgcttgttt ... tattttccagTCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGAT
EST: gi|105637293|gb|DY577108.1|DY577108
EST:     TAAGAAAAGCACTTGCACAATATGCGGATGTTTTGAGTTCACCCAAAAAG                         TCTGCCTTGCTTGCCTTAGCTGCACATGCATCTGATCCATCTGAAGCTGAT
genomic: TAAGAAAAGCACTTGCACAATATGCGGATGTTTTGAGTTCACCCAAAAAGgtgcttgttt ... tattttccagTCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGAT
EST: gi|7691075|gb|AW759209.1|AW759209
EST:     TAAGAAAAGCACTTGCACAATATGCGGATGTTTTGAGTTCACCCAAAAAG                         TCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGAT
genomic: TAAGAAAAGCACTTGCACAATATGCGGATGTTTTGAGTTCACCCAAAAAGgtgcttgttt ... tattttccagTCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcaagagatttactttatgtcacaattaataatactttgaacatattttccagTCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGATCGACTAAGACATCTTGCCTCACCTGCTGGAAAG
                         aattaat  putative branch site (score: 3)
                                             tattttcc  putative PPT
                       acaattaataatactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcttgttttgagcttgatgcacccttaatttcaaacatatccctttatctgctcaagagatttactttatgtcacaattaataatactttgaacatattttccagTCTGCCTTGCTTGCCTTAGCTGCTCATGCATCTGATCCATCTGAAGCTGATCGACTAAGACATCTTGCCTCACCTGCTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA