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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttattgattctctcattcttcgtggatccatttaattgtttttgttgctagctcttgtctgaatatcattactgaaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGACACCCTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG

Basic information

species Glycine max
transcript GLYMA02G12930.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G12930.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0011g00620.t01 (Vitis vinifera), 3'ss of exon 4
gtaagttattgattctctcattcttcgtggatccatttaattgtttttgttgctagctcttgtctgaatatcattactgaaactt--acagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGACACCCTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
||||   ||   || ||        | | || |  || ||   ||||    | | | | | | |||| | | |  | ||||||||  ||||||||||||||||||| |||||||||||||||||||||||||| || ||||||||| |||| || ||||||||||||||||||||| |||| |||||||||
gtaatgcatatgtt-tcaagcatagcataga-ctgttcaagccttttaaaagattgttatggcctga-tttgagaaatgaaacttttacagGGCCTGCCATTTGGCTAAGCAAGCTTTTGATGAGGCAATTGCAGAATTGGACACCTTGAGCGAGGAGTCATACAAGGACAGCACTCTGATTATGCAGCTG

upper sequence: GLYMA02G12930.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S201_25V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaagttattgattc------tctcattcttcgtggatccatttaattgtttttgttgctagctcttgtctgaatatcattactgaa-acttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGACACCCTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
||||| | |||| |       |   || | |   |||     ||   | ||   |  | | |    || |||       | ||||     |   ||||| ||||||||||| |||||||| || || ||||||||||| || ||||||||  ||||||| ||||| |||||||||||||| ||||||||||| || 
gtaagattttgagttgaggttttggatgcctgtgggacgtgcttttcttttggcggggttcgtaactgactgtgcgat-tgactgcgtggtggtagGGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGACACATTGAGTGAGGAGTCGTACAAGGACAGCACATTGATCATGCAACTA

upper sequence: GLYMA02G12930.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S67_176V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------gtaagttattgattctctcattcttcgtggatccatttaatt-gtttttgtt---gctagctcttgtctgaat---atcattactgaaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGACACCCTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
                                                                  |  |||||||     | | ||||         | |||| ||  || |    | | || |  ||   |||    |  |       | ||||||||| ||||||||||| |||||||| ||||||||||| || || ||| |||| ||  ||||||||||||| |||||||||||||| |||||||||||| ||
gtaagattgtggtagttgattatgcggtgaagcagatgagagtgattgaaccgtctattggacggggccattgattgatgaagttttcggtagcatgctgaatttgtgcttatctgggtttgcaccggtaataatcaggtagtggtatggaattacagGGCATGCCATTTGGCGAAGCAAGCATTTGATGAGGCTATCGCTGAGCTGGATACGTTGAGTGAAGAGTCGTACAAGGACAGCACATTGATCATGCAGTTG

upper sequence: GLYMA02G12930.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S46_127V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------gtaagttattgattc-tctcattcttcgtggatccattta---attgtttttgttgctagctcttgtctgaatatcattactgaaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGACACCCTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
                        | || | ||| ||  | | |      ||   |   || |   ||||  | | |||  ||||  || ||||||  ||||   ||   |  |||||| ||||||||||| || ||||| ||||| ||||| ||||| |||||||| ||  | ||||| ||||| |||||||||||||| |||||||||||||| 
gtatgaattttggtcagtagagacttagctgttggttggttttacggcgtgttttttttttcagggattgaatatattgg-agcttgtgactgaatgccatt---gactgtggcagGGCATGCCATTTGGCGAAACAAGCATTTGACGAGGCGATTGCTGAGTTGGATACGTTAAGTGAGGAGTCGTACAAGGACAGCACATTGATCATGCAGCTA

upper sequence: GLYMA02G12930.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S348_15V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------------------------------------------------------gtaagttattgattctctcattcttcgtggatccatttaattgtttttgttgctagctcttgt-ctgaatatcattactgaaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGACACCCTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
                                                                                   ||   |      |         | | |||||| |||    ||||  | ||    |   ||    | |  | |  |      |  || ||| || ||||||||||| |||||||| ||||||||||| || |||||| |||| ||  |||| || ||||| |||||||||||||| |||||||||||||| 
gtaagagtggctgtgtggcatgcggcgaagcggttgagggtgattgtggaggcgtggatggaacgtgggcgtgggatggatgggtggatagcatgtgtgtgggggcgtggtggattcat--ggttgtggtggtccgcaatgctgaaacggggtgtggtggtgtgagatttcagAGCATGCCATTTGGCGAAGCAAGCGTTTGATGAGGCGATCGCGGAGCTGGATACGTTGAGCGAGGAGTCGTACAAGGACAGCACGTTGATCATGCAGCTA

upper sequence: GLYMA02G12930.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ36243 (Selaginella moellendorffii), 3'ss of exon 4
gtaagttattgattctctcattcttcgtggatccatttaattgtttttgttgctagctcttgtctgaatatcattactgaaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGACACCCTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
    || |  |   |||    ||||  | | |   |  |     ||    ||  |  |  || ||   | ||  |  || |||    || || |||||  | ||||||||||||||||| || || || |||||| ||||||| || || ||||| || ||||||||||||||||||||||||||||| 
----gtgagagcgcctcgtcctctttttagttttctcca----cttcaactg--actttgtggctttgtttcgctgttgcaac----agCGCTTGCCAGCTAGCCAAGCAAGCTTTTGACGATGCGATCGCGGAGCTGGACACGCTCAGCGAAGAATCCTACAAGGACAGCACTTTGATCATGCAGCTT

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|7795610|gb|AW781007.1|AW781007
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttatt ... aaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|151412856|gb|EV282668.1|EV282668
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttatt ... aaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|37994792|gb|CF806381.1|CF806381
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttatt ... aaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|10843368|gb|BF067173.1|BF067173
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttatt ... aaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|4306793|gb|AI443955.1|AI443955
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttatt ... aaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|192296241|gb|FG991567.1|FG991567
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttatt ... aaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|192318665|gb|FK006211.1|FK006211
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAG-CAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttatt ... aaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|14011701|gb|BG726623.1|BG726623
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttatt ... aaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|12689676|gb|BG156012.1|BG156012
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttatt ... aaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|18690824|gb|BM519672.1|BM519672
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttatt ... aaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|7284525|gb|AW597114.1|AW597114
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttatt ... aaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|31468373|gb|CD410401.1|CD410401
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttatt ... aaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|21887789|gb|BQ741002.1|BQ741002
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttatt ... aaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|7692312|gb|AW760421.1|AW760421
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttatt ... aaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|57574121|gb|CX547096.1|CX547096
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttatt ... aaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|192326726|gb|FK018883.1|FK018883
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttatt ... aaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|7924046|gb|AW830054.1|AW830054
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttatt ... aaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|31308826|gb|CD394029.1|CD394029
EST:     CTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: CTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttatt ... aaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|16347707|gb|BI973302.1|BI973302
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttatt ... aaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|38193306|gb|CF922512.1|CF922512
EST:     GCACTCAATTTCTCTGTCTTTCATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttatt ... aaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGA
EST: gi|192318664|gb|FK006210.1|FK006210
EST:     GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAG                         GGCCTGCCATTTGGCCAAGCAAGCTTTTGA
genomic: GCACTCAATTTCTCTGTCTTTTATTATGAGATAATGAACTCTCCTGAAAGgtaagttatt ... aaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttaattgtttttgttgctagctcttgtctgaatatcattactgaaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGACACCCTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG
 atttaat  putative branch site (score: 4)
                                aatatcatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttattgattctctcattcttcgtggatccatttaattgtttttgttgctagctcttgtctgaatatcattactgaaacttacagGGCCTGCCATTTGGCCAAGCAAGCTTTTGATGAGGCAATTGCGGAGTTGGACACCCTGAGTGAAGAGTCATACAAGGACAGCACTTTGATCATGCAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG