Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagtgagttattcatctctatactattacatatggccgtatattccattatttagcattgggttgttaaccgcatatattaaattcctttttatttgcagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCAAATAAATCAGGATTTCTGGGTTCTAGGATAAAGTGGAATTTCACCAAGT

Basic information

species Glycine max
transcript GLYMA03G30800.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G30800.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0104g00320.t01 (Vitis vinifera), 3'ss of exon 4
aagtgagtt-attcatctctatactattacatatggccgtatattccattatttagcattgggttgt-taaccgcatatattaaattcctttttatttgcagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCAAATAAATCAGGATTTCTGGGTTCTAGGATAAAGTGGAATTTCACCAAGT
| |||  || |||       | | |  ||||| | ||     ||   |  ||||| ||| |     | |||    | || || |||||  |||| | |  |||| ||||| ||||| |||||| | ||||| |||||||||||||| |||||| | |||   |||||||| || |||||||| || ||||||||||||||||
atgtgtctttattgggtctcaaatttctacattttgctccg-atcataggattta-catagttaaatataatgttaaatgttcaattctcttttgtgtatagGTTCGTGTAAATGGCCCTGATGCTGCACCAGTCTACAAATTCCTCAAAGCACACAAAAGTGGATTTCTTGGATCTAGGATCAAATGGAATTTCACCAAGT
















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|298192383|gb|HO036465.1|HO036465
EST:     AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAGgttgttggtt ... ttatttgcagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|213611742|gb|DB958864.1|DB958864
EST:     AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAGgttgttggtt ... ttatttgcagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|298165676|gb|HO008647.1|HO008647
EST:     AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAGgttgttggtt ... ttatttgcagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|298175980|gb|HO015385.1|HO015385
EST:     AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAGgttgttggtt ... ttatttgcagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|16345172|gb|BI970767.1|BI970767
EST:     AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAGgttgttggtt ... ttatttgcagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|193679145|gb|FK620639.1|FK620639
EST:     CTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: CTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAGgttgttggtt ... ttatttgcagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|298194623|gb|HO043095.1|HO043095
EST:     AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAGgttgttggtt ... ttatttgcagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|58023037|gb|CX709778.1|CX709778
EST:     AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAGgttgttggtt ... ttatttgcagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|8282815|gb|BE020376.1|BE020376
EST:     AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAGgttgttggtt ... ttatttgcagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|298178511|gb|HO024246.1|HO024246
EST:     AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAGgttgttggtt ... ttatttgcagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|298181386|gb|HO022825.1|HO022825
EST:     AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGCCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAGgttgttggtt ... ttatttgcagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|23734566|gb|BU765519.1|BU765519
EST:     AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAGgttgttggtt ... ttatttgcagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|18039234|gb|BM307528.1|BM307528
EST:     AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAGgttgttggtt ... ttatttgcagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|57574515|gb|CX547490.1|CX547490
EST:     AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAGgttgttggtt ... ttatttgcagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
EST: gi|17400959|gb|BM177741.1|BM177741
EST:     AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAG                         GTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA
genomic: AGGAATTTGCCTGCACAAGATACAAGGCCGCGTATCCCATTTTTGGAAAGgttgttggtt ... ttatttgcagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattatttagcattgggttgttaaccgcatatattaaattcctttttatttgcagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCAAATAAATCAGGATTTCTGGGTTCTAGGATAAAGTGGAATTTCACCAAGT
                  tgttaac  putative branch site (score: 2)
                                      ttcctttttatttgc  putative PPT
                            atatattaaattcctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagtgagttattcatctctatactattacatatggccgtatattccattatttagcattgggttgttaaccgcatatattaaattcctttttatttgcagGTACGTGTCAATGGACCTGATACAGCACCTGTCTACAAATTCCTTAAAGCAAATAAATCAGGATTTCTGGGTTCTAGGATAAAGTGGAATTTCACCAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatata