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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatagtttttgaataagctgttctgtttatttaactttgctctactagtttattagttctggctgatgttcttgctgcctgtgtaccagAATTGAAGGGAGTCCCAGTTGAGATTTTGCTGAAATTGATTCCAGAACATGCAAGGAAGCAGTGCCCGTTTCTTGGCTTGTGATATTGTGAAAAATGTAA

Basic information

species Glycine max
transcript GLYMA19G41420.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G41420.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv14s0060g00600.t01 (Vitis vinifera), 3'ss of exon 12
--gtatgatagtttttgaataagctgttctgtt----tatttaactttgctctactagtttattagttctggctgatgttcttgctgcctgtgt--accagAATTGAAGGGAGTCCCAGTTGAGATTTTGCTGAAATTGATTCCAGAACATGCAAGGAAGCAGTGCCCGTTTCTTGGCTTGTGATATTGTGAAAAATGTAA
| || | | || || | || | | | | ||| | | | | || ||| ||| || | || |||||| | ||| | |||||||||||||||| ||||||||||||||| |||||||||| || ||||||||||| ||||| ||||| || ||||| | |||| | |||||| |
gtatgcaatcatcctgaaacaattttatcagcaccagtgtcttgttttcccatgcaaagttgtta---ctgattgttattgctgctgcttctgtcaatcagAATTGAAGGGAGTACCAGTTGAGATTTTGGTGAAATTGATCCCGGAACATGCAAGAAAGCAATGCCCCTTCCTTGGGCTATGATTCCATCTGAAATGTGA
















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|58018658|gb|CX705400.1|CX705400
EST:     CTTGCCAAATGGTCGTTTCCTTCCACCATTGTTCAATTTTAAATCTCATG                         AATTGAAGGGAGTCCCAGTTGAGATTTTGCTGAAATTGATTCCAGAACATG
genomic: CTTGCCAAATGGTCGTTTCCTTCCACCATTGTTCAATTTTAAATCTCATGgtatgatagt ... tgtgtaccagAATTGAAGGGAGTCCCAGTTGAGATTTTGCTGAAATTGATTCCAGAACATG
EST: gi|26047711|gb|CA784420.1|CA784420
EST:     CTTGCCAAATGGTCGTTTCCTTCCACCATTGTTCAATTTTAAATCTCATG                         AATTGAAGGGAGTCCCAGTTGAGATTTTGCTGAAATTGATTCC
genomic: CTTGCCAAATGGTCGTTTCCTTCCACCATTGTTCAATTTTAAATCTCATGgtatgatagt ... tgtgtaccagAATTGAAGGGAGTCCCAGTTGAGATTTTGCTGAAATTGATTCC
EST: gi|9985319|gb|BE659427.1|BE659427
EST:     CTTGCCAAATGGTCGTTTCCTTCCACCATTGTTCAATTTTAAATCTCATG                         AATTGAAGGGAGTCCCAGTTGAGATTTTGCTGAAATTGATTCCAGAACATG
genomic: CTTGCCAAATGGTCGTTTCCTTCCACCATTGTTCAATTTTAAATCTCATGgtatgatagt ... tgtgtaccagAATTGAAGGGAGTCCCAGTTGAGATTTTGCTGAAATTGATTCCAGAACATG
EST: gi|12688301|gb|BG154637.1|BG154637
EST:     CTTGCCAAATGGTCGTTTCCTTCCACCATTGTTCAATTTTAAATCTCATG                         AATTGAAGGGAGTCCCAGTTGAGATTTTGCTGAAATTGATTCCAGAACATG
genomic: CTTGCCAAATGGTCGTTTCCTTCCACCATTGTTCAATTTTAAATCTCATGgtatgatagt ... tgtgtaccagAATTGAAGGGAGTCCCAGTTGAGATTTTGCTGAAATTGATTCCAGAACATG
EST: gi|214009209|gb|DB990583.1|DB990583
EST:     CTTGCCAAATGGTCGTTTCCTTCCACCATTGTTCAATTTTAAATCTCATG                         AATTGAAGGGAGTCCCAGTTGAGATTTTGCTGAAATTGATTCCAGAACATG
genomic: CTTGCCAAATGGTCGTTTCCTTCCACCATTGTTCAATTTTAAATCTCATGgtatgatagt ... tgtgtaccagAATTGAAGGGAGTCCCAGTTGAGATTTTGCTGAAATTGATTCCAGAACATG
EST: gi|58024722|gb|CX711463.1|CX711463
EST:     CTTGCCAAATGGTCGTTTCCTTCCACCATTGTTCAATTTTAAATCTCATG                         AATTGAAGGGAGTCCCAGTTGAGATTTTGCTGAAATTGATTCCAGAACATG
genomic: CTTGCCAAATGGTCGTTTCCTTCCACCATTGTTCAATTTTAAATCTCATGgtatgatagt ... tgtgtaccagAATTGAAGGGAGTCCCAGTTGAGATTTTGCTGAAATTGATTCCAGAACATG
EST: gi|254328747|gb|GR833119.1|GR833119
EST:     CTTGCCAAATGGTCGTTTCCTTCCACCATTGTTCAATTTTAAATCTCATG                         AATTGAAGGGAGTCCCAGTTGAGATTTTGCTGAAATTGATTCCAGAACATG
genomic: CTTGCCAAATGGTCGTTTCCTTCCACCATTGTTCAATTTTAAATCTCATGgtatgatagt ... tgtgtaccagAATTGAAGGGAGTCCCAGTTGAGATTTTGCTGAAATTGATTCCAGAACATG
EST: gi|208088244|gb|GD889412.1|GD889412
EST:     AATGGTCGTTTCCTTCCACCATTGTTCAATTTTAAATCTCATG                         AATTGAAGGGAGTCCCAGTTGAGATTTTGCTGAAATTGATTCCAGAACATG
genomic: AATGGTCGTTTCCTTCCACCATTGTTCAATTTTAAATCTCATGgtatgatagt ... tgtgtaccagAATTGAAGGGAGTCCCAGTTGAGATTTTGCTGAAATTGATTCCAGAACATG
EST: gi|209725617|gb|BW663106.1|BW663106
EST:     CTTGCCAAATGGTCGTTTCCTTCCACCATTGTTCAATTTTAAATCTCATG                         AATTGAAGGGAGTCCCAGTTGAGATTTTGCTGAAATTGATTCCAGAACATG
genomic: CTTGCCAAATGGTCGTTTCCTTCCACCATTGTTCAATTTTAAATCTCATGgtatgatagt ... tgtgtaccagAATTGAAGGGAGTCCCAGTTGAGATTTTGCTGAAATTGATTCCAGAACATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgctctactagtttattagttctggctgatgttcttgctgcctgtgtaccagAATTGAAGGGAGTCCCAGTTGAGATTTTGCTGAAATTGATTCCAGAACATGCAAGGAAGCAGTGCCCGTTTCTTGGCTTGTGATATTGTGAAAAATGTAA
                          ggctgat  putative branch site (score: 4)
 tagtttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatagtttttgaataagctgttctgtttatttaactttgctctactagtttattagttctggctgatgttcttgctgcctgtgtaccagAATTGAAGGGAGTCCCAGTTGAGATTTTGCTGAAATTGATTCCAGAACATGCAAGGAAGCAGTGCCCGTTTCTTGGCTTGTGATATTGTGAAAAATGTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA