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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcatcaggtacagagatgttaaatttatatatgcacgtttacgattctggtgccattaatcattcattaaaaaatgcacacaacacagttaacaccataatggcttatacattaatccctattatacattagcaccgtagtggtttatacatgagatgaagaccctgtaccttctaattgttttccaaatgcagATCATTAACGTATATAATCAGGAGTATGAGAGTGGTGCAGCATTCTGGCCTGATGTCCATTTCCGTATCGTGATGGCACTGATTGTCTCACAGATAGTTT

Basic information

species Glycine max
transcript GLYMA20G16230.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G16230.3 (Glycine max), 3'ss of exon 5
lower sequence: AT4G22120.1 (Arabidopsis thaliana), 3'ss of exon 8
gtcatcaggtacagagatgttaaatttatatatgcacgtttacgattctggtgccattaatcattcattaaaaaatgcacacaacacagttaacaccataatggcttatacattaatccctattatacattagcaccgtagtggtttatacatgagatgaagaccctgtaccttctaattgttttccaaatgcagATCATTAACGTATATAATCAGGAGTATGAGAGTGGTGCAGCATTCTGGCCTGATGTCCATTTCCGTATCGTGATGGCACTGATTGTCTCACAGATAGTTT
                                                                                                            ||  ||  ||    |  | | |||  |  || |   ||| |   |   | | ||   ||  | |   |  ||||||        ||||||||||||||||| ||||| || || ||||||| |||||| || ||||| || || |||   ||  || |    ||| || |  | |||||| |  || 
-----------------------------------------------------------------------------------------------------------gtaagtt--tcttcttctttccttaatagggtcg-aatttgt---tttaaagcagtttcttaaacaaatttttgtttctgt----cagATCATTAACGTATACAATCAAGAATACGAGAGTGCTGCAGCGTTTTGGCCAGACGTTCATGGACGAGTCATAGCAGCATTGGTAATATCACAGTTGCTTC

upper sequence: GLYMA20G16230.3 (Glycine max), 3'ss of exon 5
lower sequence: Vv10s0116g00940.t01 (Vitis vinifera), 3'ss of exon 9
gtcatcaggtacagagatgttaaatttatatatgcacgtttacgattctggtgccattaatcattcattaaaaaatgcacacaacacagttaacaccataatggcttatacattaatccctattatacattagcaccgtagtggtttatacatgagatgaagaccctgtaccttctaattgttttccaaatgcagATCATTAACGTATATAATCAGGAGTATGAGAGTGGTGCAGCATTCTGGCCTGATGTCCATTTCCGTATCGTGATGGCACTGATTGTCTCACAGATAGTTT
                                                                  || | ||||  | || ||     ||||     || | |||      |||  || | ||||   | ||     ||||   || ||| |    ||| |      ||  || | ||         ||||||||||||||| || || ||||| ||||||||||||||||||||||||||||| ||||| |||   |||||  |    ||||| ||  |||||||| |  || 
------------------------------------------------------------------atcagaaaacccccataatcagattaat----tatttgct-----gttatgcctttttat-tttcagttgtctagtaaattttacct----tgagg------tattttttgat---------aatgcagATCATTAATGTTTACAATCAAGAGTATGAGAGTGGTGCAGCATTCTGGCCGGATGTTCATGGGCGTATTATTGGTGCACTAATCATCTCACAGCTGCTTC
















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|192306870|gb|FK003040.1|FK003040
EST:     TGTTCTTCCTTTCATAACAGTTTTCTTTGGCCTGGCCTATCTTGTGTTCC                         G
genomic: TGTTCTTCCTTTCATAACAGTTTTCTTTGGCCTGGCCTATCTTGTGTTCCgtcatcaggt ... ccaaatgcag-
EST: gi|192306870|gb|FK003040.1|FK003040
EST:     TGTTCTTCCTTTCATAACAGTTTTCTTTGGCCTGGCCTATCTTGTGTTCC                         G
genomic: TGTTCTTCCTTTCATAACAGTTTTCTTTGGCCTGGCCTATCTTGTGTTCCgtcatcaggt ... ccaaatgcag-
EST: gi|192306870|gb|FK003040.1|FK003040
EST:     TGTTCTTCCTTTCATAACAGTTTTCTTTGGCCTGGCCTATCTTGTGTTCC                         G
genomic: TGTTCTTCCTTTCATAACAGTTTTCTTTGGCCTGGCCTATCTTGTGTTCCgtcatcaggt ... ccaaatgcag-
EST: gi|192306870|gb|FK003040.1|FK003040
EST:     TGTTCTTCCTTTCATAACAGTTTTCTTTGGCCTGGCCTATCTTGTGTTCC                         G
genomic: TGTTCTTCCTTTCATAACAGTTTTCTTTGGCCTGGCCTATCTTGTGTTCCgtcatcaggt ... ccaaatgcag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggtttatacatgagatgaagaccctgtaccttctaattgttttccaaatgcagATCATTAACGTATATAATCAGGAGTATGAGAGTGGTGCAGCATTCTGGCCTGATGTCCATTTCCGTATCGTGATGGCACTGATTGTCTCACAGATAGTTT
                                ttctaat  putative branch site (score: 2)
                                      ttgttttcc  CT-rich tract
                                   taattgtttt  TA-rich tract