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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaatgcgatttgtttgattagattagttgagaggagggtggataattttacttttaggaactctttttttttctgtcttcttacatttttattttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCATGCCGCAGTGT

Basic information

species Glycine max
transcript GLYMA17G05530.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G05530.4 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g42380.1 (Oryza sativa), 3'ss of exon 1
gaaatgcgatttgtttg-attagattagttgagaggagggtggataattttacttttagga----actctttttttttctgtcttcttacatttttatttt-gcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCATGCCGCAGTGT
         ||||  || |  ||  |  ||      | || |  |  | ||| || |||      | |  || ||| | ||| || ||||||||||||||| |||||||||||| ||| | | |||||||||||| |||||||||||| ||||| |||||||||||||
------tagtttgcatgtaccaggcttctttttgctaaggcgtttcctattatttgtagatttttatttcttctttctttgtttttttacatttttatttttgcagATAGAGCCAATCCTTACTGGAAATCTGCCTCCTGGCTTTGATACGAGTACATGCCGCAGTGT

upper sequence: GLYMA17G05530.4 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G008611_T01 (Zea mays), 3'ss of exon 2
gaaatgcgatttgtttgattagattagttgagaggag-ggtggataattttacttttaggaactcttttttttt---ctgtcttcttacatttttat---tttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCATGCCGCAGTGT
         ||| |||  |||  | |  || ||   | | |    |||  ||  | |     || || ||  |    |  | | |||||| || |||   ||||||||||||||| ||  | |||||||| ||||| ||||| |||||||| ||| |||||||||| ||
-------tttttctttatttaagtcaaatgcgaactgcgatatgaaatcatagatgttatctctgttcttcatagaaccttttgcttacacttgtatgtctttgcagATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT

upper sequence: GLYMA17G05530.4 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 1
gaaatgcgatttgtttgattagattagttgagaggagggtggataattttacttttaggaactcttttttttt-----ctgtcttcttacatttttat---tttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCATGCCGCAGTGT
       | ||| ||   |||    |  || ||   | ||  || |  | |    |   | |||| || ||       |  | | |||||| || |||   ||||||||||||||| ||  | |||||||| ||||| ||||| |||||||| ||| |||||||||| ||
-------gttttcttcatttaagacaaatgcgaactgcgtt-atgaaatcatagatgttatctctgttcttcatagaaccttttgcttacacttgtatgtctttgcagATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT

upper sequence: GLYMA17G05530.4 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 1
gaaatgcgatttgtttgattagattagttgagaggagggtggataattttacttttaggaactctttttttt---tctgtcttcttacatttttattttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCATGCCGCAGTGT
|       || | | |   |  | |  |      ||| || |||| ||||| || |||||  | ||||| ||   ||| | || | |||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||| ||| |||||||||||||
gtgtctttatatatcta--tgaaatgctctcagtgagtgttgata-ttttatttctaggatttttttttcttctttctattttttcacatttttattttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGTGT

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|207772747|gb|GD746055.1|GD746055
EST:     TGATGCAACCATCTCTCTACCACCACCCTGCTCTACTTACTCCTCCTCAG                         ATAGAGCCTATCTTGAGTGGAAA
genomic: TGATGCAACCATCTCTCTACCACCACCCTGCTCTACTTACTCCTCCTCAGgttcctcttt ... tattttgcagATAGAGCCTATCTTGAGTGGAAA
EST: gi|193560287|gb|FK516738.1|FK516738
EST:     TGATGCAACCATCTCTCTACCACCACCCTGCTCTACTTACTCCTCCTCAG                         ATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCA
genomic: TGATGCAACCATCTCTCTACCACCACCCTGCTCTACTTACTCCTCCTCAGgttcctcttt ... tattttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCA
EST: gi|193711906|gb|FK647893.1|FK647893
EST:     TGATGCAACCATCTCTCTACCACCACCCTGCTCTACTTACTCTTCCTCAG                         ATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCA
genomic: TGATGCAACCATCTCTCTACCACCACCCTGCTCTACTTACTCCTCCTCAGgttcctcttt ... tattttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCA
EST: gi|14126550|gb|BG790988.1|BG790988
EST:     TGATGCAACCATCTCTCTACCACCACCCTGCTCTACTTACTCCTCCTCAG                         ATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCA
genomic: TGATGCAACCATCTCTCTACCACCACCCTGCTCTACTTACTCCTCCTCAGgttcctcttt ... tattttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCA
EST: gi|7639266|gb|AW733592.1|AW733592
EST:     TGATGCAACCATCTCTCTACCACCACCCTGCTCTACTTACTCCTCCTCAG                         ATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCA
genomic: TGATGCAACCATCTCTCTACCACCACCCTGCTCTACTTACTCCTCCTCAGgttcctcttt ... tattttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCA
EST: gi|193496918|gb|FK462014.1|FK462014
EST:     TGATGCAACCATCTCTCTACCACCACCCTGCTCTACTTACTCCTCCTCAG                         ATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCG
genomic: TGATGCAACCATCTCTCTACCACCACCCTGCTCTACTTACTCCTCCTCAGgttcctcttt ... tattttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCG
EST: gi|11274392|gb|BF324745.1|BF324745
EST:     TGATGCAACCATCTCTCTACCACCACCCTGCTCTACTTACTCCTCCTCAG                         ATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCA
genomic: TGATGCAACCATCTCTCTACCACCACCCTGCTCTACTTACTCCTCCTCAGgttcctcttt ... tattttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCA
EST: gi|193563085|gb|FK520288.1|FK520288
EST:     TGATGCAACCATCTCTCTACCACCACCCTGCTCTACTTACTCCTCCTCAG                         ATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCA
genomic: TGATGCAACCATCTCTCTACCACCACCCTGCTCTACTTACTCCTCCTCAGgttcctcttt ... tattttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttacttttaggaactctttttttttctgtcttcttacatttttattttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCATGCCGCAGTGT
                                 ttcttac  putative branch site (score: 2)
                ctctttttttttctgt  CT-rich tract
                                 ttcttacatttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaatgcgatttgtttgattagattagttgagaggagggtggataattttacttttaggaactctttttttttctgtcttcttacatttttattttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCATGCCGCAGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
gaaatgc
- - - - - ttgtttg
- - - - - - - - - - - - - - - - - - gggtgga