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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatattgatctaagtgctctgttagttgatggaagctactgttttttgtcctcaagtttcatccatgtgcttctaattcattagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACCGAATATACAACTGCCATAGATATAT

Basic information

species Glycine max
transcript GLYMA12G28730.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 7
lower sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaagatattgatctaagtgctctgttagttgatggaagctactgttttttgtcctcaagtttcatccatgtgcttctaattcattagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACCGAATATACAACTGCCATAGATATAT
              |||||  | | ||     |  |    ||  |  ||   || |  ||| | |  ||||| ||  |   ||  ||||| ||||||||||| |||||||||||||||||||| |||||||| |||||||| ||||| || ||||| ||||  ||||| |||||||| || |||||||
-------------gtaagt--tttattgac--acagcttttaacgaattcattcttggagtatga--catgttctcgtt-ctctgtagGTAAAAGGAGAACCCAATGTTTCTTACATCTGTTCTAGATACTATCGTGCTCCAGAACTCATTTTTGGTGCCAGTGAATACACAACTGCAATTGATATAT

upper sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 7
lower sequence: AT1G57870.3 (Arabidopsis thaliana), 3'ss of exon 8
gtaagatat-tgatctaagtgctctgttagttgatggaagctactgttttttgtcctcaagtttcatccatgtgcttctaattcattagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACCGAATATACAACTGCCATAGATATAT
||||  | | | | |||   |||||  |||| | |   || |    |  |   | || |  ||      | ||| |  |  | ||  |||||||||||||||| ||| |||||||||| |||||||||||||| ||||| || || || || ||||| |||||||| || |||||||| ||||| ||||
gtaaagtttatcagctata-gctct--tagtggttt--agttttcctagtccatgcttagattatg---acgtg-tcatggtccac-agGTGAAAGGAGAACCCAATATTTCTTACATTTGTTCAAGATACTATCGTGCCCCAGAGCTCATTTTTGGAGCCACCGAGTACACAACTGCAATAGACATAT

upper sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 6
gtaagatattgatctaagtgctctgttagttgatgg-------aagctactgttttttgtcctcaagtttcatccatgtgcttctaattcattagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACCGAATATACAACTGCCATAGATATAT
|||| || || ||| |   || ||| |  || ||||       |||  |   | |||  |       | |    ||  |  |||   || || |||| ||||||||||| ||||||||||| ||||| |||||||| |||||||| || ||||| |||||||| ||||| |||||||| ||||| |||||||| |
gtaa-attttcatcca---gcactggttattaatggtgtcatgaagtcatcttgtttcattgcttgatgttggtcagct--ttccgttttatcagGTAAAAGGAGAACCCAATGTTTCTTATATCTGCTCAAGATATTACCGTGCCCCAGAACTCATATTTGGTGCCACTGAATATACGACTGCTATAGATATTT

upper sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 7
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------gtaagatattgatctaagtgctctgttagttgatggaagctactgttttttg-tcctcaagtttcatccatgtgcttctaattcattagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACCGAATATACAACTGCCATAGATATAT
                 ||||  | | |    ||   | | |   | | | ||||   ||  | |   |  | | ||  |    | | |||| |  | ||   ||||||||| || || ||| | || ||||| |||||  | ||||||||||||||||| ||||| ||||| || || || || || ||||||||||||||||
ctgacgagttgttcgagaagacttcgtttctggtatgcggatgtctca-gtaagcgggtgcgtgtgaatagtgatgtaaccgagacgggcttgttgtgca---gGTGAAAGGGGAGCCCAATATCTCGTACATTTGTTCGCGGTACTACCGTGCTCCGGAGCTTATTTTTGGAGCGACGGAGTACACGACTGCCATAGATATAT

upper sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 7
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 6
--------gtaagatattgatc-taagtgctctgttagttgatggaagctactgttttt-tgtcctcaagtttcatcc--atgtgcttctaattcattagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACCGAATATACAACTGCCATAGATATAT
            | |  | ||  || |     |||    ||  | |  |   ||  |   ||    ||   || |||    || | ||  | ||    |||||||||| || |||||| |||| ||||| |||||| |||| ||||||||||| || || |||||||| || || ||||| |||||||| || || ||||
gagtctgcagtggttgctcataatatggaaattgtctcgtgcggtattcagttgaatgcgtgggtgcagcattgatcatagtgagatttgagttgtgcagGTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCTCCCGAGCTGATATTTGGAGCTACAGAATACACAACTGCGATTGACATAT

upper sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 7
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------------------------------------gtaagatattgatctaagtg--ctctgttagt-tgatggaa--gctactgttttttgtcctcaagtttcatccatgtgcttctaattcat---------------tagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACCGAATATACAACTGCCATAGATATAT
                                               || |   ||  |    | ||  || |  | || || ||||   | | |  |  ||  |  | | | | | ||   |||   | |  | |                 |||||||||| || || ||| |||| ||||| |||||| | |||||||||||||| || || || ||||| || || || || || |||||||| |||||||
gtgagtatctgttggatgagagtgagcattgttcaaattgtgaggctgtgaaccatccagtggaatggactttacttgtgtggtggagatgttgcactaattcctgattagggtacttctcggtggagcgacatgacggaggtggtgttgtgcagGTGAAAGGGGAGCCCAATATTTCGTACATTTGTTCACGGTACTACCGTGCTCCTGAGCTGATTTTTGGAGCGACAGAGTACACGACTGCCATCGATATAT

upper sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 7
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 5
--------gtaagatattgatctaagtgctctgttagttg--atggaagctactgttttttgtcctcaagtttcatccatgtgcttctaattcat---tagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACCGAATATACAACTGCCATAGATATAT
        |||| | || |   | | |  | | ||    |  || ||    | | |||         ||||  |  |  || |  |   | |  |    |||||||||| ||||||||  | || || ||||||||| | || ||||||||||| || || |||||||| || || ||||| || ||||| ||||| ||||
agtagtgggtaacacat-ggcatgaataatgtcttctccgctatcgagttgaatatttgagtggagaaagtggcgacactgagaattcgagtactgtgcagGTGAAAGGGGAACCTAACATCTCGTATATCTGTTCACGGTATTACCGTGCTCCTGAGCTGATATTTGGAGCGACGGAATACACCACTGCGATAGACATAT

upper sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 7
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 7
gtaagatattgatctaagtgctctgttagttgatggaagctactgttttttgtcctcaagtttcatccatgtgcttctaattcattagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACCGAATATACAACTGCCATAGATATAT
||  |   ||      ||    ||   | || |     ||  ||| |||  ||   |   |||  |            ||   |  ||||||||||||| || ||  | || || ||||||||  | || |||||||||||||||||||||||||| || || || || ||||| ||||| || || |
gtgggtgcttacaaataggatccttggaattca-----gcagctgatttgcgtttcctgcttttcttggca-------aaacaaacagGTGAAAGGAGAGCCCAACATATCGTATATCTGTTCCCGTTATTACCGTGCTCCGGAACTTATATTTGGTGCAACTGACTACACAACAGCCATCGACATCT

upper sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 7
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 7
gtaagatattgatctaagtgctctgttagttgatggaagctactgttttttgtcctcaagtttcatccatgtgcttctaattcattagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACCGAATATACAACTGCCATAGATATAT
              |  |||||     |   |||    |  | |           |   ||||| | | | | ||   ||  ||  ||||||| ||||| || ||  | || || ||||||||  | ||||||||||||||||||||||||||||| || || || || ||||| ||||| || || |
-------------gtgggtgcttacaaataggatccttggaattcagcagctgatttgcgtttcctgcttttcctggcaaaacaacagGTGAAGGGAGAGCCCAACATATCGTATATCTGTTCCCGTTACTACCGTGCTCCGGAACTTATATTTGGTGCAACTGACTACACAACAGCCATCGACATCT

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|21678169|gb|BQ630520.1|BQ630520
EST:     CGCACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTG                         GTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCT
genomic: CGCACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTGgtaagatatt ... aattcattagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCT
EST: gi|193630915|gb|FK585070.1|FK585070
EST:     CACACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTG                         GTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCT
genomic: CGCACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTGgtaagatatt ... aattcattagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCT
EST: gi|208208274|gb|GE004247.1|GE004247
EST:     CTATGTGATTTTGGGAGTGCAAAAGTGTTG                         GTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCT
genomic: CTATGTGATTTTGGGAGTGCAAAAGTGTTGgtaagatatt ... aattcattagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCT
EST: gi|193548282|gb|FK505275.1|FK505275
EST:     CGCACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTG                         GTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCT
genomic: CGCACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTGgtaagatatt ... aattcattagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCT
EST: gi|37995772|gb|CF807361.1|CF807361
EST:     CGCACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTG                         GTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCT
genomic: CGCACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTGgtaagatatt ... aattcattagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaagctactgttttttgtcctcaagtttcatccatgtgcttctaattcattagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACCGAATATACAACTGCCATAGATATAT
                                         ttctaat  putative branch site (score: 2)
                                            taattcatta  TA-rich tract