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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatttctaccctaacgatatatttcctgcttgtaatctataatgttcttgttgtcttctagcaactgctaaccagaatgtttaaccatttatcaaatacttaaaaggaattcccttgtcatttttcagTGAAAACATTATATGGAAGGCATTTAGTCCCACCACTATTAACAGTGGACGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGCTGATA

Basic information

species Glycine max
transcript GLYMA12G35990.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G35990.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 3
gtaaatttctaccctaacgatatatttcctgcttgtaatctataatgttcttgttgtcttctagcaactgctaaccagaatgtttaaccatttatcaaatacttaaaaggaattcccttgtcatttttcagTGAAAACATTATATGGAAGGCATTTAGTCCCACCACTATTAACAGTGGACGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGCTGATA
                                  || | | | | ||  |||  | ||||||  | | || | ||    || ||   | ||| | |    |||||   |||| ||  |      | |  ||||| || || || |||||||||||||| ||||| ||||| |||||||| ||||| ||||| || || || ||||| |||||  |||||||| || |||| 
----------------------------------gtgagc-acattgaactttgt-tcttct--ctattgttgac----atttt---ctattcaacttg-acttat--ggaaatctttc-----tctgtagTGAGAATATCATCTGGAAGGCATTTAGCCCCACAACTATCAACAGTGGCCGTGGTGCTGAGTTCGAGGGGGCTGTCATTGCATTGTTCCATCTGTTGATT

upper sequence: GLYMA12G35990.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g17840.1 (Oryza sativa), 3'ss of exon 2
gtaaatttctaccctaacgatatatttcctgcttgtaatctataatgttcttgttgtcttctagcaactgctaaccagaatgtttaaccatttatcaaatacttaaaaggaattcccttgtcatttttcagTGAAAACATTATATGGAAGGCATTTAGTCCCACCACTATTAACAGTGGACGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGCTGATA
                                          |||   || |     |||||  |   |||| |   ||   |||   |     | |  |  |||   |  |    ||||   ||   |||||| || || || |||||||| ||||| ||||| || || |||||||| ||||| ||||||||||||||                               
-----------------------------------------gtaagcatccta--aacttctttctcttgctgatgtga-cattttgtcgcaatttagCTTATTATTGGTGAA---CTTGCTGTTGCACAGTGAGAATATCATCTGGAAGGCGTTTAGCCCCACAACCATCAACAGTGGGCGTGGTGCTGAATTTGAAGGA------------------------------

upper sequence: GLYMA12G35990.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g17830.1 (Oryza sativa), 3'ss of exon 2
gtaaatttctaccctaacgatatatttcctgcttgtaatctataatgttcttgttgtcttctagcaactgctaaccagaatgtttaaccatttatcaaatacttaaaaggaattcccttgtcatttttcagTGAAAACATTATATGGAAGGCATTTAGTCCCACCACTATTAACAGTGGACGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGCTGATA
                                  |||| |        | |  || ||||  |     | || |   ||   |||    |    | |  |  |||   |  |    ||||   ||   |||||| || || || |||||||| ||||| ||||| || || |||||||| ||||| ||||||||||||||                               
----------------------------------gtaagcatcttaaatttctttatcttacattc-ttactgatgtga-cattttgttacaatttagCTTATTATTGGTGAA---CTTGCTGTTGCACAGTGAGAATATCATCTGGAAGGCGTTTAGCCCCACAACCATCAACAGTGGGCGTGGTGCTGAATTTGAAGGA------------------------------

upper sequence: GLYMA12G35990.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G130987_T02 (Zea mays), 3'ss of exon 3
gtaaatttctaccctaacgatatatttcctgcttgtaatctataatgttcttgttgtcttctagcaactgctaaccagaatgtttaaccatttatcaaatacttaaaaggaattcccttgtcatttttcagTGAAAACATTATATGGAAGGCATTTAGTCCCACCACTATTAACAGTGGACGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGCTGATA
                              || |||    | ||||  | || |||   | |   |   | |      ||||||   |  ||   |  |  |||| ||  |     ||| |||| |   ||||| || || || |||||||||||||| ||||| || || |||||||| ||||| |||||||| ||||| ||||| ||||| ||||||||| || |||| 
--------------------------gtaagcatgttggatttaatccttttattgatgt-tgatattagattgatgtaatgtt---ctgttccacttagtcttataataagactgctt-tcatgt---agTGAGAATATCATCTGGAAGGCATTTAGCCCCACAACCATCAACAGTGGTCGTGGCGCTGAATTCGAAGGGGCTGTCATTGCACTGTTCCATCTGTTGATT

upper sequence: GLYMA12G35990.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 2
gtaaatttctaccctaacgatatatttcctgcttgtaatctataatgttcttgttgtcttctagcaactgctaaccagaatgtttaaccatttatcaaatacttaaaaggaattcccttgtcatttttcagTGAAAACATTATATGGAAGGCATTTAGTCCCACCACTATTAACAGTGGACGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGCTGATA
                                          |||   |||||  | |||    |   |  | |   |  ||||          | ||     ||| | ||||||  |  |        || || || || || |||||||||||||| ||||| || || |||||||| ||||| |||||||||||||| ||||| ||||| ||||| ||| || |||| 
-----------------------------------------gtaagcatcttg--gacttaatccttttattgatgtgc-tgttctgttgcacttaaagcttataataagaattctttcatg------tagCGAGAATATCATCTGGAAGGCATTTAGCCCCACAACCATCAACAGTGGTCGTGGTGCTGAATTTGAAGGGGCTGTCATTGCACTGTTTCATCTGTTGATT

upper sequence: GLYMA12G35990.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G307252_T02 (Zea mays), 3'ss of exon 2
gtaaatttctaccctaacgatatatttcctgcttgtaatctataatgttcttgttgtcttctagcaactgctaaccagaatgtttaaccatttatcaaatacttaaaaggaattcccttgtcatttttcagTGAAAACATTATATGGAAGGCATTTAGTCCCACCACTATTAACAGTGGACGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGCTGATA
                  |  | ||||   ||    || | |  | |  ||   || |   |  ||     || | |   ||| |   |   |      |||   |||   ||  || |||        ||||| || || || |||||||| ||||| || || || || |||||||| ||||| |||||||||||||| || || |||||  |||||||| |  |||| 
---------------tgtggcacattta--gccacaaaccaaacaggccctaaatgccacatctcattgattagctattctgtatgtgcggct------tacggtaaactcatgtccatgt--------agTGAGAATATCATCTGGAAGGCGTTTAGCCCAACAACCATCAACAGTGGGCGTGGTGCTGAATTTGAAGGGGCAGTCATTGCATTGTTCCATCTATTGATT

upper sequence: GLYMA12G35990.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S323_56V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaaatttctaccctaacgatatatttcctgcttgtaatctataatgttcttgttgtcttctagcaactgctaaccagaatgtttaaccatttatcaaatacttaaaaggaattcccttgtcatttttcagTGAAAACATTATATGGAAGGCATTTAGTCCCACCACTATTAACAGTGGACGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGCTGATA
                     | |    |   |     |||  |      ||||||  ||       || ||        | ||    |  ||| ||| | | |         |||  | |  |  | |||||| ||||| || ||||| | ||| ||||| ||||| || |||||||| |||||||| || ||||| || |||||||||||||| |||||  | ||| | 
-------------------gcacaacctcctgtaactgtctgaagatgcattgttgatttt------cttctggagtatttcttacgtcggttaacaagttccttt------ctccggttttgtcctgcagTGAGAACATCATTTGGAAAGGATTCAGTCCGACCACCATCAACAGTGGTCGTGGAGCAGAGTTTGAGGGAGCTGTTATTGCTCTCTTCCACCTTCTGTTC

upper sequence: GLYMA12G35990.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S114_48V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaaatttctaccctaacgatatatttcctgcttgtaatctataatgttcttgttgtcttctagcaactgctaaccagaatgtttaacc-atttatcaaatacttaaaaggaattccct--tgtcattttt---cagTGAAAACATTATATGGAAGGCATTTAGTCCCACCACTATTAACAGTGGACGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGCTGATA
                                           |    |    || | ||   | |   |    || |    | | |   | |||   ||    | || |||||   ||  |||   |||    |||||||||||| || |||||||||||||| || || ||||| |||||||| ||||||||||| || || || |||||||||||||| |||||  | ||  | 
-------------------------------------cagcgcagcaattacattttatttaggtacacgtagtcctggtcctctgatttacttagtgaactgatcaagggaatctgctaatgttgatttctcgcagTGAAAACATCATCTGGAAGGCATTTAGCCCAACTACTATCAACAGTGGTCGTGGAGCTGAGTTCGAGGGCGCTGTTATTGCTCTCTTCCACCTTCTTTTC

upper sequence: GLYMA12G35990.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ11193 (Selaginella moellendorffii), 3'ss of exon 2
gtaaatttctaccctaacgatatatttcctgcttgtaatctataatgttcttgttgtcttctagcaactgctaaccagaatgtttaaccatttatcaaatacttaaaaggaattcccttgtcattttt-cagTGAAAACATTATATGGAAGGCATTTAGTCCCACCACTATTAACAGTGGACGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGCTGATA
                                                                            |||            || ||||   ||    |    |||  ||||   | |  |||||| ||||| || |||||||| |||||||| || || || |||||||| ||||||||||| || || || ||| | ||||||||||||||  |  |||| 
-------------------------------------------------------------------------gtgagagaaacctttttcttttcaagctct---gattttttctattgtatctgtgacagTGAGAACATCATCTGGAAGGCGTTTAGTCCGACTACCATCAACAGTGGCCGTGGAGCTGAGTTCGAGGGAGCTATCATTGCTCTGTTCCACCTCTTGATC

upper sequence: GLYMA12G35990.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ15673 (Selaginella moellendorffii), 3'ss of exon 2
gtaaatttctaccctaacgatatatttcctgcttgtaatctataatgttcttgttgtcttctagcaactgctaaccagaatgtttaaccatttatcaaatacttaaaaggaattcccttgtcattttt-cagTGAAAACATTATATGGAAGGCATTTAGTCCCACCACTATTAACAGTGGACGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGCTGATA
                                                                            |||            || || |   ||    |  | |||  |||| | | |  |||||| | ||| || |||||||| |||||||| || || || |||||||| ||||||||||| ||||| || ||| | |||||||| |||||  |  |||| 
-------------------------------------------------------------------------gtgagagaaaccttttccttttccagctct---gattatttctattgtgactgtgacagTGAGACCATCATCTGGAAGGCGTTTAGTCCGACTACCATCAACAGTGGCCGTGGAGCTGAGTTTGAGGGAGCTATCATTGCTCTCTTCCACCTCTTGATC

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|254335629|gb|GR847157.1|GR847157
EST:     GGATATGGTCTGGGGTCTGGAATTTCCCTTTTCATAGCAACTAATATCTG                         TGAAAACATTATATGGAAGGCATTTAGTCCCACCACTATTAACAGTGGACG
genomic: GGATATGGTCTGGGGTCTGGAATTTCCCTTTTCATAGCAACTAATATCTGgtaaatttct ... catttttcagTGAAAACATTATATGGAAGGCATTTAGTCCCACCACTATTAACAGTGGACG
EST: gi|254316195|gb|GR827732.1|GR827732
EST:     GGATATGGTCTGGGGTCTGGAATTTCCCTTTTCATAGCAACTAATATCTG                         TGAAAACATTATATGGAAAGGCATTTAGTCCCACCACTATTAACAGTGGAC
genomic: GGATATGGTCTGGGGTCTGGAATTTCCCTTTTCATAGCAACTAATATCTGgtaaatttct ... catttttcagTGAAAACATTATATGGAA-GGCATTTAGTCCCACCACTATTAACAGTGGAC
EST: gi|254347543|gb|GR853792.1|GR853792
EST:     GGATATGGTCTGGGGTCTGGAATTTCCCTTTTCATAGCAACTAATATCTG                         TGAAAACATTATATGGAAGGCATTTAGTCCCACCACTATTAACAGTGGACG
genomic: GGATATGGTCTGGGGTCTGGAATTTCCCTTTTCATAGCAACTAATATCTGgtaaatttct ... catttttcagTGAAAACATTATATGGAAGGCATTTAGTCCCACCACTATTAACAGTGGACG
EST: gi|13562944|gb|BG551164.1|BG551164
EST:     GGAATTTCCCTTTTCATAGCAACTAATATCTG                         TGAAAACATTATATGGAAGGCATTTAGTCCCACCACTATTAACAGTGGACG
genomic: GGAATTTCCCTTTTCATAGCAACTAATATCTGgtaaatttct ... catttttcagTGAAAACATTATATGGAAGGCATTTAGTCCCACCACTATTAACAGTGGACG
EST: gi|298172300|gb|HO019340.1|HO019340
EST:     GGATATGGTCTGGGGTCTGGAATTTCCCTTTTCATAGCAACTAATATCTG                         TGAAAACATTATATGGAAGGCATTTAGTCCCACCACTATTAACAGTGGACG
genomic: GGATATGGTCTGGGGTCTGGAATTTCCCTTTTCATAGCAACTAATATCTGgtaaatttct ... catttttcagTGAAAACATTATATGGAAGGCATTTAGTCCCACCACTATTAACAGTGGACG
EST: gi|254329727|gb|GR839280.1|GR839280
EST:     GGATATGGTCTGGGGTCTGGAATTTCCCTTTTCATAGCAACTAATATCTG                         TGAAAACATTATATGGAAGGCATTTAGTCCCACCACTATTAACAGTGGACG
genomic: GGATATGGTCTGGGGTCTGGAATTTCCCTTTTCATAGCAACTAATATCTGgtaaatttct ... catttttcagTGAAAACATTATATGGAAGGCATTTAGTCCCACCACTATTAACAGTGGACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaatgtttaaccatttatcaaatacttaaaaggaattcccttgtcatttttcagTGAAAACATTATATGGAAGGCATTTAGTCCCACCACTATTAACAGTGGACGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGCTGATA
     gtttaac  putative branch site (score: 3)
                                    ttcccttgtcattttt  putative PPT
             atttatcaaatactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatttctaccctaacgatatatttcctgcttgtaatctataatgttcttgttgtcttctagcaactgctaaccagaatgtttaaccatttatcaaatacttaaaaggaattcccttgtcatttttcagTGAAAACATTATATGGAAGGCATTTAGTCCCACCACTATTAACAGTGGACGTGGAGCTGAATTTGAAGGTGCTGTTATTGCTCTGTTCCATTTGCTGATA

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