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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatgctttgtttgtcattcaggagttaaacttgaacctaatttattggaattaggtatttttttttctttatttgttaattttcttatggatgggacagGTTGGGAGACCTGCATTTGATGAGTTTCTGAAGAAATATATTGCTACCTTCAAGTTCAAATCCATTGATACCGAAACATTCCTTGACTTCCTTAAAGCCA

Basic information

species Glycine max
transcript GLYMA20G38780.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38780.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G139662_T01 (Zea mays), 3'ss of exon 1
----------------------gcatgctttgtttgtcattcaggagttaaacttgaacctaatttatt--ggaattaggtatttttttttctttatttgttaattttcttatggatgggacagGTTGGGAGACCTGCATTTGATGAGTTTCTGAAGAAATATATTGCTACCTTCAAGTTCAAATCCATTGATACCGAAACATTCCTTGACTTCCTTAAAGCCA
                      |||  || |  |  || | |  |    |  |||  |   || ||| |   | ||| |     ||| |  | | || | |||    | ||     ||   ||| |||| |||||||| || || |||||| | ||||| || ||||| |||||||||||| |||| || ||||| || ||||| ||||| ||||| ||| |||
gtgggtggaagtatggaacatggca-actcttctactcttccttgcaacattctttcagtaaaattacttcagtattggactaatttctaacgtgatgtcttatgcatgttgct--tgtatcagATTGGCAGACCTGCTTTCGACGAGTTTTTAAAGAAGTACATTGCAACCTTCAAGTTCCAATCAATAGATACAGAGACATTTCTTGAATTCCTCAAAACCA

upper sequence: GLYMA20G38780.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G13520.1 (Arabidopsis thaliana), 3'ss of exon 2
gcatgctttgtttgtcattcaggagttaaacttgaacctaatttattggaattaggtatttttttttctttatttgttaattttcttatggatgggacagGTTGGGAGACCTGCATTTGATGAGTTTCTGAAGAAATATATTGCTACCTTCAAGTTCAAATCCATTGATACCGAAACATTCCTTGACTTCCTTAAAGCCA
             || | |   || ||   ||     || |  | ||    |  |  || |||       |  |  |  |||| ||     |     ||| |||| ||| |||| ||||| || || || |||||||| |||||||| ||||||||||| || || |||||  | ||||| ||||| ||||| ||||| |
-------------gttagtt--gaattgccctcttcgcttaggtgttttgttatgtaatgtttacaataatggtcatctatttactggaaaacttt-cagATTGGAAGAACTGCTTTTGACGAATTCCTCAAGAAATACATTGCTACTTTCAAGTTCAAGTCAATCGATACAAACACATTTCTTGAATTCCTGAAAGCAA

upper sequence: GLYMA20G38780.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0067g03300.t01 (Vitis vinifera), 3'ss of exon 2
gcatgctttgtttgtcattcaggagttaaacttgaacctaatttattggaattaggtatttttttttctttatttgttaattttcttatggatgggacagGTTGGGAGACCTGCATTTGATGAGTTTCTGAAGAAATATATTGCTACCTTCAAGTTCAAATCCATTGATACCGAAACATTCCTTGACTTCCTTAAAGCCA
| ||| || ||||| || | ||  |||    ||||   |  || | || ||  |  |||    ||   | | |||      | | |  || |||   ||| |||| || |||||||||||||| || || |||||||||||||  |||||||||||| |||| ||||| || || |  || ||    ||||| ||| | |
gtatg-ttggtttgacagttagaggtt----ttgaggttg-ttcaatgaaa--aaatatgagattggttgtgttt------tgtttcttgaatgtt-cagATTGGAAGGCCTGCATTTGATGAATTCCTAAAGAAATATATTGGCACCTTCAAGTTCCAATCAATTGACACAGATATGTTTCTAATTTTCCTGAAAACGA

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|298164042|gb|HO013687.1|HO013687
EST:     AGGTTCCCTATGAGAAAGGTTTTCAGTTCTTATGGCGCATTGAGCGACAG                         GTTGGGAGACCTGCATTTGATGAGTTTCTGAAGAAATATATTGCTACCTTC
genomic: AGGTTCCCTATGAGAAAGGTTTTCAGTTCTTATGGCGCATTGAGCGACAGgtatctgaat ... gatgggacagGTTGGGAGACCTGCATTTGATGAGTTTCTGAAGAAATATATTGCTACCTTC
EST: gi|7691304|gb|AW759497.1|AW759497
EST:     AGGTTCCCTATGAGAAAGGTTTTCAGTTCTTATGGCGCATTGAGCGACAG                         GTTGTGAGACCTGCATTTGATGAGTTTCTGAAGAAATATATTGCTACCTTC
genomic: AGGTTCCCTATGAGAAAGGTTTTCAGTTCTTATGGCGCATTGAGCGACAGgtatctgaat ... gatgggacagGTTGGGAGACCTGCATTTGATGAGTTTCTGAAGAAATATATTGCTACCTTC
EST: gi|298175857|gb|HO015262.1|HO015262
EST:     GGTTCCCTATGAGAAAGGTTTTCAGTTCTTATGGCGCATTGAGCGACAG                         GTTGGGAGACCTGCATTTGATGAGTTTCTGAAGAAATATATTGCTACCTTC
genomic: GGTTCCCTATGAGAAAGGTTTTCAGTTCTTATGGCGCATTGAGCGACAGgtatctgaat ... gatgggacagGTTGGGAGACCTGCATTTGATGAGTTTCTGAAGAAATATATTGCTACCTTC
EST: gi|208052060|gb|GD852995.1|GD852995
EST:     TTGAGCGACAG                         GTTGGGAGACCTGCATTTGATGAGTTTCTGAAGAAATATATTGCTACCTTC
genomic: TTGAGCGACAGgtatctgaat ... gatgggacagGTTGGGAGACCTGCATTTGATGAGTTTCTGAAGAAATATATTGCTACCTTC
EST: gi|19270287|gb|BM886543.1|BM886543
EST:     AGGTTCCCTATGAGAAAGGTTTTCAGTTCTTATGGCGCATTGAGCGACAG                         GTTGGGAGACCTGCATTTGATGAGTTTCTGAAGAAATATATTGCTACCTTC
genomic: AGGTTCCCTATGAGAAAGGTTTTCAGTTCTTATGGCGCATTGAGCGACAGgtatctgaat ... gatgggacagGTTGGGAGACCTGCATTTGATGAGTTTCTGAAGAAATATATTGCTACCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggaattaggtatttttttttctttatttgttaattttcttatggatgggacagGTTGGGAGACCTGCATTTGATGAGTTTCTGAAGAAATATATTGCTACCTTCAAGTTCAAATCCATTGATACCGAAACATTCCTTGACTTCCTTAAAGCCA
                             tgttaat  putative branch site (score: 3)
     attaggtatttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgctttgtttgtcattcaggagttaaacttgaacctaatttattggaattaggtatttttttttctttatttgttaattttcttatggatgggacagGTTGGGAGACCTGCATTTGATGAGTTTCTGAAGAAATATATTGCTACCTTCAAGTTCAAATCCATTGATACCGAAACATTCCTTGACTTCCTTAAAGCCA

gcatgct
- - - - tgtttgt
- - - - - - - -cattcag
- - - - - - - - - - - - - - - cttgaac