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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattcttttatcattaattagctcttccatgtgttccattttcattgattgctaaaaaatgttgtggttttgcagATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCACAGGAAGTGCTTCTAACTTCTAAGTACAAAATATGCTTCAATGGTGAAAT

Basic information

species Glycine max
transcript GLYMA05G32220.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 4
------------------------------------------------gtgattcttttatcattaattagctct---------tccatgt---gttccattttcattgatt-gctaa--aaaatgttgtggttttgc-----------------agATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCACAGGAAGTGCTTCT-AACTTCTAAGTACAAAATATGCTTCAATGGTGAAAT
                                                 | | |  || || |  |||    | |         ||||      |||  ||||| || | || |||||   | ||||  |   |||||                 |||||||||| || || | ||| |||||||| ||||||||| | ||||| |||||||||||||||| |  |||| |        | ||| ||  |  || | |
gtaagtccttatcattacagcttcttagatgctcaccagaattagttcataactacttcataaccaatccattttgtttatttgtccacaccaagttgtattttaatggttttgctaatgcacatgtgatttgtttgcttggcattgataaaaacagATGTGGATATCGAAGGATGAGTATGATGAATCTGGCCCAGCAATTGTTCACAGGAAGTGCTTCTGAGTTTCTCATGCTGCCCTGTGCGTCGGTT-TGTACT

upper sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g61970.1 (Oryza sativa), 3'ss of exon 4
---------gtgattcttttatcattaattagctcttccat--gtgttccattttcattgattgctaaaaa-----atgttgtggtttt-------gcagATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCACAGGAAGTGCTTCTAACTTCTAAGTACAAAATATGCTTCAATGGTGAAAT-
          ||||| |    | || || ||| |    |||   | ||  ||    | || | | |||| |     ||  |||  ||||       |||||||||||| ||||| || || |||||||| || ||||| || || ||||||||||| ||||||||| | | |         |  |  |    ||||     
atttgctatttgattatgccctaataaactagattacacattaattttgaatgcaaaatgttagataaagacacttatcctgttctttttcctgtcgcagATGTGGATATCTAAGGGAGAGTATGATGAATCCGGCCCTTCAATCGTCCACAGGAAATGCTTCTAA-TCCGAGCCTTGCTCTGAGTATTTTCGGTGTGCCT

upper sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g36650.1 (Oryza sativa), 3'ss of exon 4
gtgattct---tttatcattaattagctcttc-catgtgttccattttcattga-----ttgctaaaaaatgttg---------tggttttgcagATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCACAGGAAGTGCTTCTAACTTCTAAGTACAAAATATGCTTCAATGGTGAAAT--
|| || |    |    ||  | |||  ||||   |    ||| |  ||  | ||     ||  | | | |||||          |  || ||||||||||||| || |  | ||| ||||| || ||||||||| | || ||||||||||||||||||||  |      ||     |||  |||| ||   |     
gtaatgcaaaatcatccaacagttaattcttgatacactttctagattgttcgagaaggttcttgacatatgtttctttccttttttttgtgcagATGTGGATCTCAAGGGCTGAGTATGAAGAATCTGGCCCAGCTATCGTCCACAGGAAGTGCTTCTAGATGTGGCCTA-GCTGTATCTTTCA-TGAGAACCCCT

upper sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g06390.6 (Oryza sativa), 3'ss of exon 4
gtgattctt----ttatcattaattagctcttccatgtgttc-cattttcattgattgctaaaa--aatgttgtgg------ttttgcagATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCACAGGAAGTGCTTCTAACTTCTAAGTACAAAAT-ATGCTTCAATGGTGAAAT
|| |  |||     ||   || || || |        ||     ||||    |   || ||| |  | | || |||      |  | ||||||||||| || || || || ||||||||||| || ||| | ||||| ||| ||||||||||||||  |||   |    |||      || |    | |  
gtaaaccttacgcctacactttatgaggtagcaagaatgcaggtatttctgctttctgttaacatcattcttttggcatctatgctacagATGTGGATCTCAAAGGGAGAGTATGATGAGTCGGGTCCAGCAATTGTTCACCGGAAGTGCTTCTAAGCTCTGGCTTTTTAATCGCTTATCTACAAGGCAG-

upper sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G030169_T02 (Zea mays), 3'ss of exon 4
-------------------------------------------------------------------gtgattcttttatcattaattagctcttccatgt-gttccattttcattgattgctaaaaaatgttgtggttttgcagATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCACAGGAAGTGCTTCTA-ACTTCTAAGTACA-AAATATGCTTCAATGGTGAAAT
                                                                     | |    ||      ||   | |  |   ||  | | |  |  |||| | | |      || || |   | ||||||||||||| || |  | ||| ||||| |||||||| ||| | ||||||||||||||||||||||| || ||      |    | |||| |   |        
gtaacaccaagtcttccgacggctgttctgtatccacaatctatgtttatttgtgaaaatgcacctcacggtagggttgcggagaaaaggtttatttgtgaagctactctgacattaagtcc------atcttttccctgtgcagATGTGGATCTCAAGGGCTGAGTATGAGGAGTCTGGTCCAGCTATTGTCCACAGGAAGTGCTTCTAGACGTCACTCCTCGTGGAAATGCCTTTGTTTCATG--

upper sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G082484_T01 (Zea mays), 3'ss of exon 4
-------gtgattcttttatcattaattagc-tcttccatgtgttccattttcattgattgctaaaaaatgttgtggtttt------gcagATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCACAGGAAGTGCTTCTAACTTCTAAGTACAAAATATGCTTCAATGGTGAAAT
           || |        || |  |  ||| | || ||   |  |||  |  | | || | | | ||| | |||||      |||||||||||| || |  | ||| ||||| |||||||| ||| | |||||||||||||||||||||||      |  ||      || || |  |||  | | 
gtaacaccaagttttccggcggctattctgtatctactatctgagtctattttgtgaagttctgacataagttcttgttttccctgtgcagATGTGGATCTCAAGGGCTGAGTATGAGGAGTCTGGTCCAGCTATTGTCCACAGGAAGTGCTTCTAGACGTCACCTAGCCTTAATTCTCCTCTGGAAATAC

upper sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G067985_T05 (Zea mays), 3'ss of exon 5
----------------------------------gtgattcttttatcattaattagctcttccatgtgtt----ccattttcattgattgctaaaaaatgttgt-ggttttgcagATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCACAGGAAGTGCTTCTAACTTCTAAGTACAAAATATGCTTCAATGGTGAAAT
                                  |   ||  ||| || | || | |   |   |||          | ||        || ||  |  ||   | | |||  ||||||||||| ||||| |  || || ||||||||||||||  | ||||| |||||||||||||||||   |                               
gtatgttgtattgtttatattactttcagctgctgcattttatttctc-tgaactcgtattatgatgaaacgaaataacttctgagttctgttatgacgtgcccttgatttaccagATGTGGATATCTAAGGAGGAGTACGATGAGTCTGGCCCGGCAATTGTTCACAGGAAGTGCTTCTAGGCT-------------------------------

upper sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G067985_T02 (Zea mays), 3'ss of exon 4
----------------------------------gtgattcttttatcattaattagctcttccatgtgtt----ccattttcattgattgctaaaaaatgttgt-ggttttgcagATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCACAGGAAGTGCTTCTAA-CTTC-TAAGTACAAAATATGCTTCAATGGTGAAAT
                                  |   ||  ||| || | || | |   |   |||          | ||        || ||  |  ||   | | |||  ||||||||||| ||||| |  || || ||||||||||||||  | ||||| |||||||||||||||||  ||||  |||| |   ||      | |   | ||  
gtatgttgtattgtttatattactttcagctgctgcattttatttctc-tgaactcgtattatgatgaaacgaaataacttctgagttctgttatgacgtgcccttgatttaccagATGTGGATATCTAAGGAGGAGTACGATGAGTCTGGCCCGGCAATTGTTCACAGGAAGTGCTTCTAGGCTTCGCAAGTTCCTCATCGTTGCCTAGTCTCAA--

upper sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G067985_T07 (Zea mays), 3'ss of exon 4
----------------------------------gtgattcttttatcattaattagctcttccatgtgtt----ccattttcattgattgctaaaaaatgttgtggttttgc-agATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCACAGGAAGTGCTTCTAACTTCTAAGTACAAAATATGCTTCAATGGTGAAAT
                                  |   ||  ||| || | || | |   |   |||          | ||        || ||  |  ||   | | ||| | |||||||||| ||||| |  || || ||||||||||||||  | ||||| |||||||||||||||||                                   
gtatgttgtattgtttatattactttcagctgctgcattttatttctc-tgaactcgtattatgatgaaacgaaataacttctgagttctgttatgacgtgcccttgatttaccagATGTGGATATCTAAGGAGGAGTACGATGAGTCTGGCCCGGCAATTGTTCACAGGAAGTGCTTCTAG----------------------------------

upper sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G104017_T04 (Zea mays), 3'ss of exon 4
---------------------------------gtgattcttttatcattaattagc----tcttccatgtgttc-cattttcattgattgctaaaaaatgttgt-ggttttgcagATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCACAGGAAGTGCTTCTAACTTCT--AAGTACAAAATATGCTTCAATGGTGAAAT
                                 |   ||| ||| |  | | | ||     |  |  |  || |  || || |      || |   |  ||   | | | |  ||||||||||| || || |  || |||||||||||||||||  | || ||||||||||||||||||||  |||   |||| |   ||     || |   | ||  
gtatgcggttgtttatatctactttcagctgctgcacttcatttgttttaactcagtaacatggttgaaatgataacacttccgaattctgttgtgatgtggcattgatgtaccagATGTGGATATCCAAGGAGGAGTATGATGAGTCTGGCCCGGCAATCGTCCACAGGAAGTGCTTCTAGGTTCCGCAAGTTCCTCATTGTTATCTAGTCTCAA--

upper sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G110378_T05 (Zea mays), 3'ss of exon 4
-----------------------------------gtgattcttttatcatt---aat-tagctcttccatgtgttccattttcattgattgctaaaaaatgttgt-ggttttgcagATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCACAGGAAGTGCTTCTAACTTCTAAGTACAAAATATGCTTCAATGGTGAAAT
                                    |||||  ||| | | |   ||| | |||    ||   ||  | | |  |||   || ||    |||   | | |||  ||||||||||| || || |  || || ||||||||||||||  | ||||| |||||||||||||||||  ||                               
gtatgggttgtttatattgctttcagctgctgcacttgatttctttttaactcccaatatggctgaaacaaa-gtcacgtctgaatt--ctgttatgcgatgccattgatttaccagATGTGGATATCAAAGGAGGAGTACGATGAGTCTGGCCCGGCAATTGTTCACAGGAAGTGCTTCTAGGTT-------------------------------

upper sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G110378_T04 (Zea mays), 3'ss of exon 5
-----------------------------------gtgattcttttatcatt---aat-tagctcttccatgtgttccattttcattgattgctaaaaaatgttgt-ggttttgcagATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCACAGGAAGTGCTTCTAACTT----CTAAGTACAAAATATGCTTCAATGGTGAAAT
                                    |||||  ||| | | |   ||| | |||    ||   ||  | | |  |||   || ||    |||   | | |||  ||||||||||| || || |  || || ||||||||||||||  | ||||| |||||||||||||||||  ||    | |||| |   |  |||||  | |||     
gtatgggttgtttatattgctttcagctgctgcacttgatttctttttaactcccaatatggctgaaacaaa-gtcacgtctgaatt--ctgttatgcgatgccattgatttaccagATGTGGATATCAAAGGAGGAGTACGATGAGTCTGGCCCGGCAATTGTTCACAGGAAGTGCTTCTAGGTTTCTGCCAAGTTCGTCAAGTGCTTTTAGGGTT----

upper sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
---------gtgattct-tttatcattaattagctcttccatgtgttccattttcattgat-tgctaaaaaat-gttgtggttttg---------cagATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCACAGGAAGTGCTTCTAACTTCTAAGTACAAAATATGCTTCA--ATGGTGAAAT
            ||||    | |    || |  |   ||||| | |   |  |   |  |  | || |||  | ||| || || ||         |||||||||||||| ||  |||| || |||||||| || ||||| ||||| |||||||| ||||||||| |      |     || || |||    ||||||   
gtaaaaatcccaattccgcctctttaaaactttcagctccatttatgaaacatgagtgaaaatactgaaattttgttttgtttgtgtgtgtgaatcagATGTGGATTTCAAAGAGTGAGTACGATGAGTCAGGTCCATCGATTGTTCACAGGAAATGCTTCTAAGTGTGTCTTGTCTTATCTGGTTCGTGGTGGTGAG--

upper sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0044g00580.t01 (Vitis vinifera), 3'ss of exon 5
gtgattcttttatcat-taattagctcttccatgtgttcca---ttttcattgattg---ctaaaaaatgttgtggttttgcagATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCACAGGAAGTGCTTCTAACTTCTAAGTACAAAATATGCTTCAATGGTGAAAT-------
|||||| |  | |  | |  || | | || ||  || |       ||| ||||  ||   |||| |    || || |  | ||||||||||| || || |||||||||||||| ||||| |||||||||||||||||||||||||||||| |    | |||||    |||||  |||||||  |       
gtgattttcattttttgtttttggtttttacaaatggtttgattcttttattgcatgatactaacatgctttttgttggtacagATGTGGATCTCAAAGGGTGAATATGATGAATCTGGTCCATCCATTGTCCACAGGAAGTGCTTCTAAGT----AATACAA---GTGCTTTGATGGTGAGTTCCTTTTT

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|5606874|gb|AI900972.1|AI900972
EST:     GTGTCTGGATTGGAGGATCAATCCTTGCATCCCTCAGCACCTTCCAGCAG                         ATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCAC
genomic: GTGTCTGGATTGGAGGATCAATCCTTGCATCCCTCAGCACCTTCCAACAGgtgattcttt ... ggttttgcagATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCAC
EST: gi|298188723|gb|HO035416.1|HO035416
EST:     GTGTCTGGATTGGAGGATCAATCCTTGCATCCCTCAGCACCTTCCAACAG                         ATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCAC
genomic: GTGTCTGGATTGGAGGATCAATCCTTGCATCCCTCAGCACCTTCCAACAGgtgattcttt ... ggttttgcagATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCAC
EST: gi|16996973|gb|BM086345.1|BM086345
EST:     GTGTCTGGATTGGAGGATCAATCCTTGCATCCCTCAGCACCTTCCAGCAG                         ATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCAC
genomic: GTGTCTGGATTGGAGGATCAATCCTTGCATCCCTCAGCACCTTCCAACAGgtgattcttt ... ggttttgcagATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCAC
EST: gi|16347204|gb|BI972799.1|BI972799
EST:     GTGTCTGGATTGGAGGATCAATCCTTGCATCCCTCAGCACCTTCCAACAG                         ATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCAC
genomic: GTGTCTGGATTGGAGGATCAATCCTTGCATCCCTCAGCACCTTCCAACAGgtgattcttt ... ggttttgcagATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCAC
EST: gi|13790240|gb|BG652831.1|BG652831
EST:     GTGTCTGGATTGGAGGATCAATCCTTGCATCCCTCAGCACCTTCCAGCAG                         ATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCAC
genomic: GTGTCTGGATTGGAGGATCAATCCTTGCATCCCTCAGCACCTTCCAACAGgtgattcttt ... ggttttgcagATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcttccatgtgttccattttcattgattgctaaaaaatgttgtggttttgcagATGTGGATTTCTAAAGGTGAATATGATGAGTCTGGCCCATCCATTGTCCACAGGAAGTGCTTCTAACTTCTAAGTACAAAATATGCTTCAATGGTGAAAT
                             tgctaaa  putative branch site (score: 2)
                                taaaaaatgtt  TA-rich tract