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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

taatgaaattcattaaattttctgaggaacatttgtggttttgttcaatgttttatattttgacatttttgttttggttcatatgccaaaatctactttgttccagaTCTTGTTAATGTGTTTGAGGTGTTTCTACCTCAACTTCTGCTGTATCCCAATCCATCAGACCCCTTGAATGGAGAAGCTGCAGCTTTAATGATGCGTGAT

Basic information

species Glycine max
transcript GLYMA18G46940.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G46940.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G150867_T02 (Zea mays), 3'ss of exon 4
------------------------------taatgaaattca--ttaaattttctgaggaacatttgtggtttt---gttcaatgttttatattttgacatttttgttttggttcatatgccaaaatctactttgttccagaTCTTGTTAATGTGTTTGAGGTGTTTCTACCTCAACTTCTGCTGTATCCCAATCCATCAGACCCCTTGAATGGAGAAGCTGCAGCTTTAATGATGCGTGAT
                               |  || |  ||  | |   | |||| |    || |||    ||   | |  ||||||| || | ||  ||    |  ||   |   |  ||    | |  | | || ||||||||||||||||||| ||||| || || || ||||||||| | ||||| ||||| || || || || |||||||| || || || || ||||||||||| 
gtaagattgatctttgcatttcattattaggatcgacaaccagttcattctctctgtgccttatctgtacagttaaagcttcatgttttgtactctgttataacagggttaacttgaa--cctgtgtgtgatattttgcagATCTTGTTAATGTGTTCGAGGTCTTCCTTCCACAACTTCTGTTATATCCTAATCCTTCTGATCCATTAAATGGAGATGCAGCTGCGTTGATGATGCGTGA-

upper sequence: GLYMA18G46940.1 (Glycine max), 3'ss of exon 4
lower sequence: AC149818.2_FGT006 (Zea mays), 3'ss of exon 4
----------taatgaaat----tcattaaattttctgaggaacatttgtg-----gttttgttcaatgttttatattttgacatttttgttttggttcatatgccaaaatctactttgttccagaTCTTGTTAATGTGTTTGAGGTGTTTCTACCTCAACTTCTGCTGTATCCCAATCCATCAGACCCCTTGAATGGAGAAGCTGCAGCTTTAATGATGCGTGAT
          |  | | ||    | ||||   | || | |    || |||       |   | || ||||||| || | ||  ||    |  ||   |  |   || |  | |  | | || |||||||||| |||||||| ||||| || || || ||||||||| | ||||| ||||| || || || || |||||||| || || || || ||||||||||| 
gtaagattgatctttacatctcattattaggatctccgcgccttatctgtatacaattagcgctccatgttttgtactctgttataacagggttaactt-tgaacctatgtgtgatattttgcagATCTTGTCAATGTGTTCGAGGTCTTCCTTCCACAACTTCTGTTATATCCTAATCCTTCTGATCCATTAAATGGAGATGCAGCTGCGTTGATGATGCGTGA-

upper sequence: GLYMA18G46940.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ34378 (Selaginella moellendorffii), 3'ss of exon 4
taatgaaattcattaaattttctgaggaacatttgtggttttgttcaatgttttatattttgacatttttgttttggttcatatgc-caaaatctactttgttccagaTCTTGTTAATGTGTTTGAGGTGTTTCTACCTCAACTTCTGCTGTATCCCAATCCATCAGACCCCTTGAATGGAGAAGCTGCAGCTTTAATGATGCGTGAT
                                                         |   ||   |||  |      |   | || |  ||  | | ||| |  |||| |  | || ||||||||||||||||||||||| || || || |||||||| ||  |||| ||  | || || ||||| || || || |||||| | || 
--------------------------------------------------------gtaaagatgatttgctcgaaagtttcaagctctgaaagttcgttggtatagATTTGATCAACGTGTTTGAGGTGTTTCTACCTCAGCTGCTACTCTATCCCAACCCCACAGATCCACTCAACGGTGAAGCGGCCGCGTTGATGATGAGGGA-

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|298191785|gb|HO035867.1|HO035867
EST:     GGATCAGTTTGTCTGGATGTTATCAATCAAACCTGGAGTCCCATGTTTGA                         TCTTGTTAATGTGTTTGTGGTGTTTCTACCTCAACTTCTGCTGTATCCCAA
genomic: GGATCAGTTTGTCTGGATGTTATCAATCAAACCTGGAGTCCCATGTTTGGtaatgaaatt ... ttgttccagaTCTTGTTAATGTGTTTGAGGTGTTTCTACCTCAACTTCTGCTGTATCCCAA
EST: gi|208233444|gb|GE034069.1|GE034069
EST:     GGATCAGTTTGTCTGGATGTTATCAATCAAACCTGGAGTCCCATGTTTGA                         TCTTGTTAATGTGTTTGAGGTGTTTCTACCTCAACTTCTGCTGTATCCCAA
genomic: GGATCAGTTTGTCTGGATGTTATCAATCAAACCTGGAGTCCCATGTTTGGtaatgaaatt ... ttgttccagaTCTTGTTAATGTGTTTGAGGTGTTTCTACCTCAACTTCTGCTGTATCCCAA
EST: gi|18734265|gb|BM528084.1|BM528084
EST:     GGATCAGTTTGTCTGGATGTTATCAATCAAACCTGGAGTCCCATGTTTGA                         TCTTGTTAATGTGTTTGAGGTGTTTCTACCTCAACTTCTGCTGTATCCCAA
genomic: GGATCAGTTTGTCTGGATGTTATCAATCAAACCTGGAGTCCCATGTTTGGtaatgaaatt ... ttgttccagaTCTTGTTAATGTGTTTGAGGTGTTTCTACCTCAACTTCTGCTGTATCCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatattttgacatttttgttttggttcatatgccaaaatctactttgttccagaTCTTGTTAATGTGTTTGAGGTGTTTCTACCTCAACTTCTGCTGTATCCCAATCCATCAGACCCCTTGAATGGAGAAGCTGCAGCTTTAATGATGCGTGAT
     ttttgac  putative branch site (score: 3)
                                           ctttgttcc  putative PPT
            atttttgtttt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatgaaattcattaaattttctgaggaacatttgtggttttgttcaatgttttatattttgacatttttgttttggttcatatgccaaaatctactttgttccagaTCTTGTTAATGTGTTTGAGGTGTTTCTACCTCAACTTCTGCTGTATCCCAATCCATCAGACCCCTTGAATGGAGAAGCTGCAGCTTTAATGATGCGTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT