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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatatttctctttctcactcctcttaattgcacaagcacatgtgaaaaagactcttgactcttgaataaagttctggtgcttggatctccatcttatggttgacattaacaatgcttattgttggccatacagCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCAAATATGAGCATTGTTGTTAAAGCACTCCAACCACTTCTGAAGTCTCCCG

Basic information

species Glycine max
transcript GLYMA10G44210.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G44210.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g67340.3 (Oryza sativa), 3'ss of exon 7
gtatatatttctctttctcactcctcttaattgcacaagcacatgtgaaaaagactcttgactcttgaataaagttctggtgcttggatctccatcttatggttgacattaacaatgcttattgttggccatacagCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCAAATATGAGCATTGTTGTTAAAGCACTCCAACCACTTCTGA--AGTCTCCCG
                     ||    |   |  ||| |||||    |   | || | ||| || ||| ||    ||   | |||   | | |  |  |   ||  || || |    |||  |     | || ||||||||||| ||||| ||  ||||||| || || |||||||||||| | ||||| ||||||||||| || || ||  |    ||||| || |  |||   |  
--------------------gtctcgatctctatacatgcacacaatatttatacacatgagtcatga-tagtcatcctttccttctcttttc-ccccacatttctcacta-ctgcactttct-----cgatgcagCTTGCAGCGGTTGCAGCATTGTGCGTACAATACGAAGCTGAGTTTCGCCCAAACATGAGCATTGTGGTGAAGGCTTTATCTCCACTGCTCACAAGTAAGC--

upper sequence: GLYMA10G44210.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G59350.3 (Arabidopsis thaliana), 3'ss of exon 5
gtatatatttctctttctcactcctcttaattgcacaagcacatgtgaaaaagactcttgactcttgaataaagttctggtgcttggatctccatcttatggttgacattaa--caatgcttattgttggccatac-----agCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCAAATATGAGCATTGTTGTTAAAGCACTCCAACCACTTCTGAAGTCTCCCG
                                          ||  |    |   | |||||  || |||  |   |   |||    | | |  ||  |  | | ||  |||   | || ||    |||  | | |     |||| || || || || ||  |||| ||||| |||||| | |||||||||||||| ||||||||||| || ||||| || |||||| |  ||| |||  |  
----------------------------------------gtataagcttcatctttttgacagtttaatctataacccctgcg-aaaccactttcaaaacgctaaccataaaatactgtttcgccttgttcttgcgcttcagCTCGCTGCAGTAGCAGCATTGTGTGTGCAATATGAATCAGAGTTTAGGCCAAACATGAGCATTGTGGTAAAAGCTCTTCAACCATTGTTGAGGTCATCAA

upper sequence: GLYMA10G44210.1 (Glycine max), 3'ss of exon 8
lower sequence: AT2G43230.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatatatttctctttctcactcctcttaattgcacaagcacatgtgaaaaagactcttgactcttgaataaagttctggtgcttggatctccatcttatggttgacattaacaatgcttattgttggcca-tacagCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCAAATATGAGCATTGTTGTTAAAGCACTCCAACCACTTCTGAAGTCTCCCG
                                      | | |||   | ||   || |     || || | |  ||| |||       | |||  |    | | | ||      ||  | ||| |||  | ||||||||||||| ||||| ||| |||| ||||| || ||||| |||||||||||||| ||||||||||| || ||||| || ||||| ||  ||| |||  |  
--------------------------------------gta-atgaacagaaacttcctagtcatttaa-ataactctagtg-----gaccccacttacaagctaaaat-----gtgtgttttgatggtaaatacagCTTGCAGCGGTTGCAGCGTTGTGTGTGCAATACGAAGCAGAGTTTAGGCCAAACATGAGCATTGTAGTAAAAGCTCTTCAACCGCTCTTGAGGTCAGCAA

upper sequence: GLYMA10G44210.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv05s0124g00360.t01 (Vitis vinifera), 3'ss of exon 7
gtatatatttctctttctcactcctcttaattgcacaagcacatgtgaaaaagactcttgactcttgaataaagttctggtgcttggatctccatcttatggttgacattaacaatgcttattgttggccatacagCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCAAATATGAGCATTGTTGTTAAAGCACTCCAACCACTTCTGAAGTCTCCCG
|| | | |  |||| |||| ||| |||   |  |||   ||||                 ||||    | |||                    | ||  | | | ||  |   |||     | || ||  || ||||| |||||||| || ||  | || || ||||| |||||||||||  |||||||||||||||| ||||| || || |||||||| ||| | ||| || | |
gtctctttgcctctctctctctc-tctctctctcacccacacacac--------------actcacagaaaaa-------------------taactagtagctaactctgtgaat-----tggtgggtgatgcagCTGGCAGCTGTGGCAGCATTATGTGTTCAGTACGAAGCTGAGTTCCGGCCAAATATGAGCATCGTTGTGAAGGCTCTCCAACCGCTTTTAAAGGCTGCTG

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|7692618|gb|AW760720.1|AW760720
EST:     GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAG                         CTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
genomic: GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAGgtatatattt ... ggccatacagCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
EST: gi|11273675|gb|BF324133.1|BF324133
EST:     CGTTGACCCATAACTTGAAGG-AGAATACCCCCCTAATGGGGTTGCTAAA                         CTTGCAGCTGATGCTGCGCTGTGCGTGCAGTATGAAGCTGAGTTGAGGCCA
genomic: CGTTGACCCAAAACT-GAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAGgtatatattt ... ggccatacagCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
EST: gi|14258438|gb|BG881346.1|BG881346
EST:     GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAG                         CTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
genomic: GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAGgtatatattt ... ggccatacagCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
EST: gi|27424278|gb|CA935798.1|CA935798
EST:     GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAG                         CTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
genomic: GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAGgtatatattt ... ggccatacagCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
EST: gi|6725485|gb|AW309884.1|AW309884
EST:     GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAG                         CTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
genomic: GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAGgtatatattt ... ggccatacagCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
EST: gi|7691682|gb|AW759805.1|AW759805
EST:     GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAG                         CTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
genomic: GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAGgtatatattt ... ggccatacagCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
EST: gi|33389378|gb|CA852585.1|CA852585
EST:     GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAG                         CTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
genomic: GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAGgtatatattt ... ggccatacagCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
EST: gi|298178999|gb|HO024734.1|HO024734
EST:     GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAG                         CTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
genomic: GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAGgtatatattt ... ggccatacagCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
EST: gi|6566081|gb|AW233841.1|AW233841
EST:     GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAA-GGGGTTGCTAAG                         CTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
genomic: GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAGgtatatattt ... ggccatacagCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
EST: gi|31456715|gb|CD398743.1|CD398743
EST:     GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAG                         CTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
genomic: GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAGgtatatattt ... ggccatacagCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
EST: gi|192303785|gb|FG996023.1|FG996023
EST:     GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAG                         CTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
genomic: GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAGgtatatattt ... ggccatacagCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
EST: gi|17022632|gb|BM093666.1|BM093666
EST:     GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAG                         CTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
genomic: GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAGgtatatattt ... ggccatacagCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
EST: gi|11688386|gb|BF596062.1|BF596062
EST:     GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAG                         CTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTATGCCA
genomic: GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAGgtatatattt ... ggccatacagCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
EST: gi|23727138|gb|BU761587.1|BU761587
EST:     GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAG                         CTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
genomic: GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAGgtatatattt ... ggccatacagCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
EST: gi|4298543|gb|AI442776.1|AI442776
EST:     CCCCCTAAAGGGGTTGCTAAG                         CTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
genomic: CCCCCTAAAGGGGTTGCTAAGgtatatattt ... ggccatacagCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
EST: gi|192327312|gb|FK019559.1|FK019559
EST:     GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAG                         CTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA
genomic: GCGTTGACCCAAAACTGAAGGGAGAATACCCCCCTAAAGGGGTTGCTAAGgtatatattt ... ggccatacagCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttggatctccatcttatggttgacattaacaatgcttattgttggccatacagCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCAAATATGAGCATTGTTGTTAAAGCACTCCAACCACTTCTGAAGTCTCCCG
                         cattaac  putative branch site (score: 2)
                          attaacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatatttctctttctcactcctcttaattgcacaagcacatgtgaaaaagactcttgactcttgaataaagttctggtgcttggatctccatcttatggttgacattaacaatgcttattgttggccatacagCTTGCAGCTGTTGCGGCGCTGTGCGTGCAGTATGAAGCTGAGTTTAGGCCAAATATGAGCATTGTTGTTAAAGCACTCCAACCACTTCTGAAGTCTCCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG