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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaggagctaagcggttaattattttttagataataaattatcgttgtagtttttgcaagtattagtgttcaatgcttacctaatttcaattatgttattatattgacaattttggtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCGGAA

Basic information

species Glycine max
transcript GLYMA18G01710.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G13000.1 (Arabidopsis thaliana), 3'ss of exon 7
gttaggagctaagcggttaattattttttagataataaattatcgttgtagtttttgcaagtattagtgttcaatgcttacctaatttcaattatgttattatattgacaattttggtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCGGAA
                              |  || | |   |   | | | | | || | |   |   | |   |  || ||  ||| ||  ||    |     ||   ||| |   | |    | | ||||||||||| ||  |||||||||||||||||||||||||||| ||||||||| ||||||| |||||||||||||| ||  ||||  | ||  |||  |||
------------------------------gtaaacataactttacttt-gctctagctactccaatcttcctgaggctagcttgttt-aaccattaactctctctggttattgta--tatatattttaagGTGGTATGCTAAAAGGTTTCTGCATCCTGACATTGTGGCACCTTATGACTATGTATTCATCTGGGATGAAGACCTCGGCCTTGAAAACTTCGATGTAGAA

upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G24570.1 (Arabidopsis thaliana), 3'ss of exon 6
gttaggagctaagcggttaattattttttagataataaattatcgttgtagtttttgcaagtattagtgttcaatgcttacctaatttcaattatgttattatattgacaattttggtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCGGAA
                                                            |||| | | |       ||| | | |||   |||| |  || | |||||  | |    || |     | ||||||||||| ||| | ||  |||| || |||||||| |||| ||| || |||||||||||||||||||| || || || ||||| || |||||||| |||
------------------------------------------------------------gtatcaatatctttgctttaaccacttttttttatctggtt-tcttgactctctcatattgtgaacataagGTGGTATGCAAAGAGATTCTTGCACCCGGACATTGTAGCACGATACGATTATATATTCATATGGGATGAGGATCTTGGAGTTGATCACTTTAATGCAGAA

upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 7
gttaggagctaagcggttaattattttttagataataaattatcgttgtagtttttgcaagtattagtgttcaatgcttacctaatttcaattatgttattatattgacaattttggtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCGGAA
                                ||  |||   || || |  ||| ||  || |  |  |||   ||  |   | | | |       | | |   ||| ||  |     | |      ||||||||||||| ||| ||||| |||| ||||| ||||| |||  |||||| ||||| ||| | |||||||||||||||||||| ||||||||||| || |||
-------------------------------gtaccaaacgctctttattctttatggtagaaa-atagtttggtgtgtttatgactac-------tgactcccttggcacctggaaatata-----ttagGTGGTATGCAAAGAGGTTTTTGCACCCTGATATTGTAGCAAGATATGATTATATCTTCGTCTGGGATGAAGACCTGGGTGTCGAGCATTTTAACGCAGAA

upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G26440.1 (Arabidopsis thaliana), 3'ss of exon 7
gttaggagctaagcggttaattattttttagataataaattatcgttgtagtttttgcaagtattagtgttcaatgcttacctaatttcaattatgttattatattgacaattttggtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCGGAA
                                ||| |||  |         |||||  |  | | ||| | || || |     |  || || ||     ||   ||||  || ||      ||  |   ||||||||||| ||  |||||||||||||||| ||  | ||||||||||| ||||||||||| ||||||||||| || || |||||  | ||  | || |||
-------------------------------gtaacaaaaca--aacactttttttttatctctcagtttccattgatc-taaagctttaaataaaacgtt---ttgaatatgtt------tctattgaagGTGGTATGCTAAAAGGTTTCTGCATCCTGATATCATAGCACCATATGAATATATATTCATTTGGGATGAAGATCTTGGCGTTGAAAACTTCGACGCAGAA

upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 3
gttaggagctaa-gcggttaattattttttagataataaattatcgttgtagtttttgcaagtattagtgttcaatgcttacctaatttcaattatgttattatattgacaattttggtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCGGAA
|| |||||||   ||     |||||||||  ||  | || || ||  | |  || | | | ||       ||||||    | |||   ||  || | || || ||    || | || |   ||   || |||||||||||||||  | ||||||||||||||||||||||| ||||||||||||||||| || ||||||||||| || || ||||||||||||||||| |||
gtaaggagcttctgcaaaggattattttt--gaacagaagtt-tcacttt--ttctggtaggt-------ttcaata---agctatggtctgttttattcttttaacttcattctttgcaattttgtcctagGTGGTATGCCAAAAGATTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA

upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 7
gttaggagctaa-gcggttaattattttttagataataaattatcgttgtagtttttgcaagtattagtgttcaatgcttacctaatttcaattatgttattatattgacaattttggtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCGGAA
|| |||||||   ||     |||||||||  ||  | || || ||  | |  || | | | ||       ||||||    | |||   ||  || | || || ||    || | || |   ||   || |||||||||||||||  ||||||||||||||||||||||||| ||||||||||||||||| || ||||||||||| || || ||||||||||||||||| |||
gtaaggagcttctgcaaaggattattttt--gaacagaagtt-tcacttt--ttctggtaggt-------ttcaata---agctatggtctgttttattcttttaacttcattctttgcaattttgtcctagGTGGTATGCCAAAAGGTTTCTGCATCCTGACATTGTGGCGCCATATGACTATATATTTATCTGGGATGAAGATCTAGGAGTTGAGCATTTTAATGCAGAA

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|15661819|gb|BI699190.1|BI699190
EST:     GAATGGTCAAAGCAGGCTATTCATGTCAGTGTTCACAAACAGACCAAATG                         GTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA
genomic: GAATGGTCAAAGCAGGCTATTCATGTCAGTGTTCACAAACAGACCAAATGgttaggagct ... tccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA
EST: gi|192319061|gb|FK010625.1|FK010625
EST:     GAATGGTCAAAGCAGGCTATTCATGTCAGTGTTCACAAACAGACCAAATG                         GTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA
genomic: GAATGGTCAAAGCAGGCTATTCATGTCAGTGTTCACAAACAGACCAAATGgttaggagct ... tccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttacctaatttcaattatgttattatattgacaattttggtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCGGAA
                          tattgac  putative branch site (score: 2)
                                   ttttggtttttccctc  putative PPT
      taatttcaattatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaggagctaagcggttaattattttttagataataaattatcgttgtagtttttgcaagtattagtgttcaatgcttacctaatttcaattatgttattatattgacaattttggtttttccctcttagGTGGTATGCCAAGCGGTTTCTGCATCCTGACATTGTGGCACCATATGACTATATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCGGAA

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