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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatttctacttttccctgatgagatatttccagcttttaattataatgttcttgttgtcttctagcaactgctaaccaggatatttaaccatttatctaatacttaaatggaattcccttttcgtttttcagTGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGTTGATA

Basic information

species Glycine max
transcript GLYMA13G34370.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G34370.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g17840.1 (Oryza sativa), 3'ss of exon 2
gtaaatttctacttttccctgatgagatatttccagcttttaattataatgttcttgttgtcttctagcaactgctaaccaggatatttaaccatttatctaatacttaaatggaattcccttttcgtttttcagTGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGTTGATA
                                              |||   || |     |||||  |   |||| |    || ||||   |    || ||     | | |||  |   |||   |||   |||||| || || || |||||||| ||||| || || ||||| |||||||||||||| ||||||||||||||                               
---------------------------------------------gtaagcatccta--aacttctttctcttgctgat-gtgacattttgtcgca-atttagCTTATTATTGG--TGAACTTGCTGTTGCACAGTGAGAATATCATCTGGAAGGCGTTTAGCCCCACAACCATCAACAGTGGGCGTGGTGCTGAATTTGAAGGA------------------------------

upper sequence: GLYMA13G34370.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g17830.1 (Oryza sativa), 3'ss of exon 2
gtaaatttctacttttccctgatgagatatttccagcttttaattataatgttcttgttgtcttctagcaactgctaaccaggatatttaaccatttatctaatacttaaatggaattcccttttcgtttttcagTGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGTTGATA
                                        |||  ||  |    || ||    |        | || |    || ||||    |   || ||     | | |||  |   |||   |||   |||||| || || || |||||||| ||||| || || ||||| |||||||||||||| ||||||||||||||                               
---------------------------------------gtaagcatcttaaatttctttatcttacattcttactgat-gtgacattttgttaca-atttagCTTATTATTGG--TGAACTTGCTGTTGCACAGTGAGAATATCATCTGGAAGGCGTTTAGCCCCACAACCATCAACAGTGGGCGTGGTGCTGAATTTGAAGGA------------------------------

upper sequence: GLYMA13G34370.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 3
gtaaatttctacttttccctgatgagatatttccagcttttaattataatgttcttgttgtcttctagcaactgctaaccaggatatttaaccatttatctaatacttaaatggaattcccttttcgtttttcagTGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGTTGATA
                                                 ||  |   |||   | |        |||     || ||||  | ||| | ||   |||||  ||||| ||  | |  ||     ||||| || || || |||||||||||||| || || || || |||||||| ||||| ||||| || || || ||||| |||||  |||||||| ||||||| 
------------------------------------------------gtgagcacattgaactttgttcttctctattgttgacatttt-ctattcaacttg-actta--tggaaatctttctctgt-----agTGAGAATATCATCTGGAAGGCATTTAGCCCCACAACTATCAACAGTGGCCGTGGTGCTGAGTTCGAGGGGGCTGTCATTGCATTGTTCCATCTGTTGATT

upper sequence: GLYMA13G34370.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G130987_T02 (Zea mays), 3'ss of exon 3
gtaaatttctacttttccctgatgagatatttccagc-ttttaattataatgttcttgttgtcttctagcaactgctaaccaggatatttaaccatttatctaatacttaaatggaattcccttttcgtttttcagTGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGTTGATA
                                  ||| | ||   | ||||  | || |||   | |   |   | |       || ||      |  |  || |  |  |||   | | | ||   ||     ||||| || || || |||||||||||||| || || ||||| |||||||| ||||| |||||||| ||||| ||||| ||||| ||||||||| ||||||| 
-------------------------------gtaagcatgttggatttaatccttttattgatgt-tgatattagattgatgtaatgttctgt--tccacttagtcttataataagactgctttcatgt-----agTGAGAATATCATCTGGAAGGCATTTAGCCCCACAACCATCAACAGTGGTCGTGGCGCTGAATTCGAAGGGGCTGTCATTGCACTGTTCCATCTGTTGATT

upper sequence: GLYMA13G34370.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 2
gtaaatttctacttttccctgatgagatatttccagcttttaattataatgttcttgttgtcttctagcaactgctaaccaggatatttaaccatttatctaatactta-aatggaattcccttttcgtttttcagTGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGTTGATA
                                              |||   |||||  | |||    |   |  | |    | | ||         |  |||  |||| |||   | | | ||   ||     || || || || || |||||||||||||| || || ||||| |||||||| ||||| |||||||||||||| ||||| ||||| ||||| ||| ||||||| 
---------------------------------------------gtaagcatcttg--gacttaatccttttattgat-gtgctgttctgttgc--acttaaagcttataataagaattctttcatgt-----agCGAGAATATCATCTGGAAGGCATTTAGCCCCACAACCATCAACAGTGGTCGTGGTGCTGAATTTGAAGGGGCTGTCATTGCACTGTTTCATCTGTTGATT

upper sequence: GLYMA13G34370.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G307252_T02 (Zea mays), 3'ss of exon 2
gtaaatttctacttttccctgatgagatatttccagcttttaattata-atgttcttgttgtcttctagcaactgctaaccaggatatttaaccatttatctaatacttaaatggaattcccttttcgtttttcagTGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGTTGATA
                      || |  |  |  |||    ||  | | | |  ||   || |   |  ||     || |     ||||      | ||| |    ||||     || ||  | | | | |   ||||| || || || |||||||| ||||| ||||| ||||| |||||||||||||| |||||||||||||| || || |||||  |||||||| | ||||| 
----------------------tgtggcacatttagccacaaaccaaacaggccctaaatgccacatctcattgattagc-----tattc-----tgtatgtgcggcttacggtaaactca-tgtccatgt---agTGAGAATATCATCTGGAAGGCGTTTAGCCCAACAACCATCAACAGTGGGCGTGGTGCTGAATTTGAAGGGGCAGTCATTGCATTGTTCCATCTATTGATT

upper sequence: GLYMA13G34370.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G073498_T03 (Zea mays), 3'ss of exon 3
gtaaatttctacttttccctgatgagatatttccagcttttaatt--ataatgttcttgttgtcttctagcaactgctaaccaggatatttaaccatttatctaatacttaaatggaattcccttttcgtttttcagTGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCGTGGAGCTGAATTTG-AAGGTGCTGTTATTGCTCTGTTCCATTTGTTGATA--
                              |    |   | ||||  |    | | |  |||   | |  || ||| | |  | || |    |  |  |   |  |  |     ||  |||      |          |||      | |||  |   ||||  |     ||   ||     |   | | |   |  ||||  ||||      | |||  || | |  |  | | | |  
------------------------------tcgtggtgctgaatttgaaggggctgtcattgcactgtttcatctgttgattacgagaaccgataaagtccgtgctcttcgtgaggctttctaccgcca---------gAACCTTCCAAATGTGACCAATTTGCTTGCCACAGTCTTGGTCTTCCTCATAGTTATCTATTTCCAAGGCTTCCGTGTTGTCCT-TCCAGTGAGATCAAAGA

upper sequence: GLYMA13G34370.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S323_56V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaaatttctacttttccctgatgagatatttccagcttttaattataatgttcttgttgtcttctagcaactgctaaccaggatatttaaccatttatctaatacttaaatggaattcccttttcgtttttcagTGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGTTGATA
                                 || | |     | |||   |||     |    |    | |     |  |  |||||      |    ||| |  |   |     |||  ||| ||  | |||||| ||||| || ||||| | ||| ||||| |||||||| |||||||| |||||||| || ||||| || |||||||||||||| |||||  |  || | 
------------------------------gcacaacctc---ctgtaactgtctgaagatgcattgttgattttcttctggagtatttcttacgtcggttaacaagttcctt--tctccggttttgtcctgcagTGAGAACATCATTTGGAAAGGATTCAGTCCGACCACCATCAACAGTGGTCGTGGAGCAGAGTTTGAGGGAGCTGTTATTGCTCTCTTCCACCTTCTGTTC

upper sequence: GLYMA13G34370.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S114_48V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaaatttctacttttccctgatgagatatttccagcttttaattataatgttcttgttgtcttctagcaactgctaaccaggatatttaacc-atttatctaatacttaaatggaattccct--tttcgttttt---cagTGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGTTGATA
                                          |    |    |    || | ||   | |   |    || ||   | | |   | |||   ||    | || |||||   ||  | | | |||    |||||||||||| || |||||||||||||| ||||| || || |||||||| ||||||||||| || || || |||||||||||||| |||||  |  |  | 
-----------------------------------------cagcgcagcaattacattttatttaggtacacgtagtcctggtcctctgatttacttagtgaactgatcaagggaatctgctaatgttgatttctcgcagTGAAAACATCATCTGGAAGGCATTTAGCCCAACTACTATCAACAGTGGTCGTGGAGCTGAGTTCGAGGGCGCTGTTATTGCTCTCTTCCACCTTCTTTTC

upper sequence: GLYMA13G34370.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ11193 (Selaginella moellendorffii), 3'ss of exon 2
gtaaatttctacttttccctgatgagatatttccagcttttaattataatgttcttgttgtcttctagcaactgctaaccaggatatttaaccatttatctaatacttaaatggaattcccttttcgtttttcagTGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGTTGATA
                                                                           | |     |  |||     ||  | | |  ||   ||    |    | |   | |  |||||| ||||| || |||||||| |||||||| || ||||| |||||||| ||||||||||| || || || ||| | ||||||||||||||  | ||||| 
--------------------------------------------------------------------------gtgagagaaaccttt-----ttcttttcaagctctgattttttctattgtatctgtgacagTGAGAACATCATCTGGAAGGCGTTTAGTCCGACTACCATCAACAGTGGCCGTGGAGCTGAGTTCGAGGGAGCTATCATTGCTCTGTTCCACCTCTTGATC

upper sequence: GLYMA13G34370.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ15673 (Selaginella moellendorffii), 3'ss of exon 2
gtaaatttctacttttccctgatgagatatttccagcttttaattataatgttcttgttgtcttctagcaactgctaaccaggatatttaaccatttatctaatacttaaatggaattcccttttcgtttttcagTGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGTTGATA
                                                                                ||   |         || || |   ||   ||    |    | |   | |  |||||| | ||| || |||||||| |||||||| || ||||| |||||||| ||||||||||| ||||| || ||| | |||||||| |||||  | ||||| 
-----------------------------------------------------------------------------gtgagagaaaccttttccttttccag--ctctgattatttctattgtgactgtgacagTGAGACCATCATCTGGAAGGCGTTTAGTCCGACTACCATCAACAGTGGCCGTGGAGCTGAGTTTGAGGGAGCTATCATTGCTCTCTTCCACCTCTTGATC

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|192302459|gb|FG994795.1|FG994795
EST:     GGATATGGTCTGGGGTCTGGAATATCCCTATTCATTGCAACCAATATCTG                         TGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCG
genomic: GGATATGGTCTGGGGTCTGGAATATCCCTATTCATTGCAACCAATATCTGgtaaatttct ... cgtttttcagTGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCG
EST: gi|16349322|gb|BI974917.1|BI974917
EST:     GGATATGGTCTGGGGTCTGGAATATCCCTATTCATTGCAACCAATATCTG                         TGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCG
genomic: GGATATGGTCTGGGGTCTGGAATATCCCTATTCATTGCAACCAATATCTGgtaaatttct ... cgtttttcagTGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCG
EST: gi|209721281|gb|BW665775.1|BW665775
EST:     GGATATGGTCTGGGGTCTGGAATATCCCTATTCATTGCAACCAATATCTG                         TGAAAACATTATATG
genomic: GGATATGGTCTGGGGTCTGGAATATCCCTATTCATTGCAACCAATATCTGgtaaatttct ... cgtttttcagTGAAAACATTATATG
EST: gi|16348617|gb|BI974212.1|BI974212
EST:     GGATATGGTCTGGGGTCTGGAATATCCCTATTCATTGCAACCAATATCTG                         TGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCG
genomic: GGATATGGTCTGGGGTCTGGAATATCCCTATTCATTGCAACCAATATCTGgtaaatttct ... cgtttttcagTGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCG
EST: gi|7640034|gb|AW734344.1|AW734344
EST:     TGATATGGTCTGGGGTCTGGAATATCCCTATTCATTGCAACCAATATCTG                         TGAAAACATTATATGGAAGGCATATAGTGCATCCACCATTTACAGTGAGCG
genomic: GGATATGGTCTGGGGTCTGGAATATCCCTATTCATTGCAACCAATATCTGgtaaatttct ... cgtttttcagTGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCG
EST: gi|298168692|gb|HO009622.1|HO009622
EST:     GGATATGGTCTGGGGTCTGGAATATCCCTATTCATTGCAACCAATATCTG                         TGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCG
genomic: GGATATGGTCTGGGGTCTGGAATATCCCTATTCATTGCAACCAATATCTGgtaaatttct ... cgtttttcagTGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCG
EST: gi|151396883|gb|EV266756.1|EV266756
EST:     GGATATGGTCTGGGGTCTGGAATATCCCTATTCATTGCAACCAATATCTG                         TGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATCAACAGTGGACG
genomic: GGATATGGTCTGGGGTCTGGAATATCCCTATTCATTGCAACCAATATCTGgtaaatttct ... cgtttttcagTGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCG
EST: gi|209699069|gb|BW652862.1|BW652862
EST:     GGATATGGTCTGGGGTCTGGAATATCCCTATTCATTGCAACCAATATCTG                         TGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCG
genomic: GGATATGGTCTGGGGTCTGGAATATCCCTATTCATTGCAACCAATATCTGgtaaatttct ... cgtttttcagTGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggatatttaaccatttatctaatacttaaatggaattcccttttcgtttttcagTGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGTTGATA
                 atctaat  putative branch site (score: 3)
                                    ttcccttttcgttttt  putative PPT
     atttaaccatttatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatttctacttttccctgatgagatatttccagcttttaattataatgttcttgttgtcttctagcaactgctaaccaggatatttaaccatttatctaatacttaaatggaattcccttttcgtttttcagTGAAAACATTATATGGAAGGCATTTAGTCCAACCACCATTAACAGTGGGCGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGTTGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT