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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggagctaagatgttcattattttttagaggataaattttcattgtagtttttgcaattaatagtgtttagtgcttacctaatttcaattatgtcaatacattgacaattttagtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCAGAA

Basic information

species Glycine max
transcript GLYMA11G37770.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G37770.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G13000.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaaggagctaagatgttcattattttttagaggataaattttcattgtagtttttgcaattaatagtgtttagtgcttacctaatttcaattatgtcaatacattgacaattttagtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCAGAA
                              |   | | |  || | | | | | | || | |   |   |   | |  || ||  ||| ||  ||       |  ||   ||| ||  | |    | | ||||||||||| ||  |||||||||||||||||||||||||||| ||||||||| ||||||| |||||||||||||| ||  ||||  | ||  ||| ||||
------------------------------gtaaacataactttacttt-gctctagctactccaatcttcctgaggctagcttgttt-aaccattaactctctctggttattgta--tatatattttaagGTGGTATGCTAAAAGGTTTCTGCATCCTGACATTGTGGCACCTTATGACTATGTATTCATCTGGGATGAAGACCTCGGCCTTGAAAACTTCGATGTAGAA

upper sequence: GLYMA11G37770.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G24570.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaaggagctaagatgttcattattttttagaggataaattttcattgtagtttttgcaattaatagtgtttagtgcttacctaatttcaattatgtcaatacattgacaattttagtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCAGAA
                                                             ||  | | | |     ||| | | |||   ||||     |   |||||  | | |  || |     | ||||||||||| ||| | ||  |||| || |||||||| |||| ||| || |||||||||||||||||||| || || || ||||| || ||||||||||||
------------------------------------------------------------gtatcaatatctttgctttaaccacttttttttat-ctggtttcttgactctctcatattgtgaacataagGTGGTATGCAAAGAGATTCTTGCACCCGGACATTGTAGCACGATACGATTATATATTCATATGGGATGAGGATCTTGGAGTTGATCACTTTAATGCAGAA

upper sequence: GLYMA11G37770.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 7
gtaaggagctaagatgttcattattttttagaggataaattttcattgtagtttttgcaattaatagt-gtttagtgcttacctaatttcaattatgtcaatacattgacaattttagtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCAGAA
                                    |||   || || |  | |||    |  | | | |||| |||  |   | | | |       | | | | ||| ||  |  |  | |      ||||||||||||| ||| ||||| |||| ||||| ||||| |||  |||||| ||||| ||| | |||||||||||||||||||| ||||||||||| ||||||
-------------------------------gtaccaaacgctctttat--tctttatggtagaaaatagtttggtgtgtttatgactac-------tgactcccttggcacctggaaatata-----ttagGTGGTATGCAAAGAGGTTTTTGCACCCTGATATTGTAGCAAGATATGATTATATCTTCGTCTGGGATGAAGACCTGGGTGTCGAGCATTTTAACGCAGAA

upper sequence: GLYMA11G37770.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G26440.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaaggagctaagatgttcattattttttagaggataaattttcattgtagtttttgcaattaatagtgtttagtgcttacctaatttcaattatgtcaatacattgacaattttagtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCAGAA
                           | | |  | |||   |        |||||  |  |   ||| |  | || |       ||| |||      || || ||   |||     | ||||  |   ||||||||||| ||  |||||||||||||||| ||  | ||||||||||| ||||||||||| ||||||||||| || || |||||  | ||  | ||||||
--------------------------gtaacaaaacaaacactt-------tttttttatctctcagtttccattgatctaaagctttaaat------aaaacgttttgaat----atgtttctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA

upper sequence: GLYMA11G37770.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 3
gtaaggagctaagatgttcattattttttagaggataaattttcattgtagtttttgcaattaatagtgtttagtgcttacctaatttcaattatgtcaatacattgacaattttagtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCAGAA
||||||||||              | |  | ||||| | |||| |    |  |||  |  ||  | ||   |     | | |||   ||  || | |   |  |    || | || |   ||   || |||||||||||||||  | ||||||||||||||||||||||| ||||||||||||||||| || ||||||||||| || || |||||||||||||||||||||
gtaaggagct--------------tctgcaaaggattatttttgaacagaagtttcactttttctggtaggtttcaataagctatggtctgttttattcttttaacttcattctttgcaattttgtcctagGTGGTATGCCAAAAGATTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA

upper sequence: GLYMA11G37770.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 7
gtaaggagctaagatgttcattattttttagaggataaattttcattgtagtttttgcaattaatagtgtttagtgcttacctaatttcaattatgtcaatacattgacaattttagtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCAGAA
||||||||||              | |  | ||||| | |||| |    |  |||  |  ||  | ||   |     | | |||   ||  || | |   |  |    || | || |   ||   || |||||||||||||||  ||||||||||||||||||||||||| ||||||||||||||||| || ||||||||||| || || |||||||||||||||||||||
gtaaggagct--------------tctgcaaaggattatttttgaacagaagtttcactttttctggtaggtttcaataagctatggtctgttttattcttttaacttcattctttgcaattttgtcctagGTGGTATGCCAAAAGGTTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA

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|58024808|gb|CX711549.1|CX711549
EST:     AAT-GTCAAAAGCAGGCTATTCATGTGAGTGTTCACAAACAGACCAAATG                         GTGGTATGCCAAGCGGTTTCTGCATCTTGACATTGTGGCACCATATGACTA
genomic: AATGGTC-AAAGCAGGCTATTCATGTGAGTGTTCACAAACAGACCAAATGgtaaggagct ... tccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA
EST: gi|51337681|gb|CO981547.1|CO981547
EST:     GAATGGTCAAAGCAGGCTATTCATGTGAGTGTTCACAAACAGACCAAATG                         GTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA
genomic: GAATGGTCAAAGCAGGCTATTCATGTGAGTGTTCACAAACAGACCAAATGgtaaggagct ... tccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA
EST: gi|57574426|gb|CX547401.1|CX547401
EST:     AATNGGTCAAAGCAGGCTATTCATGTGAGTGTTCACAAACAGACCAAATG                         GTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA
genomic: AAT-GGTCAAAGCAGGCTATTCATGTGAGTGTTCACAAACAGACCAAATGgtaaggagct ... tccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA
EST: gi|57574192|gb|CX547167.1|CX547167
EST:     GAATGGTCAAAGCAGGCTATTCATGTGAGTGTTCACAAACAGACCAAATG                         GTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA
genomic: GAATGGTCAAAGCAGGCTATTCATGTGAGTGTTCACAAACAGACCAAATGgtaaggagct ... tccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttacctaatttcaattatgtcaatacattgacaattttagtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCAGAA
                                   ttttagtttttccctc  CT-rich tract
      taatttcaattatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggagctaagatgttcattattttttagaggataaattttcattgtagtttttgcaattaatagtgtttagtgcttacctaatttcaattatgtcaatacattgacaattttagtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCAGAA

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