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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatcttttccgaattttttttttgtattttcgatttcagaaagtgttcttttgcataaattgttgtctttttccatttggggtgcgttggattgacatggatcaggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA

Basic information

species Glycine max
transcript GLYMA08G01940.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G01940.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 1
--------------------------------------------------------gtgatcttttccgaatt-----ttttttttgtattttcgatttc-agaaagtgttcttttgcataaattgttgtctttttccatttggggtgcgttgg-attgacatggat-caggtcat--cagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA
||| | || ||| || |||| ||| |||| | | || | | ||| || | | |||| |||| ||||| | | || ||| | ||| | | || | |||||||||||| || ||||||||||||| ||| |||||||| ||||| |||||||| |||||||||| || || | || |
gtgaggatcttgtcctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctttctattggtggtctccatcgtctaatctgatgtgttgttgtttgttgttttgggggtggggggattggggattttcttggtttcttgttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA

upper sequence: GLYMA08G01940.2 (Glycine max), 3'ss of exon 1
lower sequence: AC149818.2_FGT006 (Zea mays), 3'ss of exon 1
gtgatcttttccgaattttttttttgtattttcgatttcagaaagtgttcttttgcataaattgttgtctttttccatttggggtgcgttgg-attgacatggatcaggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA
| |||||| | |||| | | | |||| | | || | | || || | ||| |||||| | || | | | | | | |||||||||||| || ||||||||||||| ||| |||||||| ||||| ||||||||||| ||||| | || || || || |
--------------gtgaggattttgtggcgt--gtttcggtgatttttctatgggatt--tcgatggggattcc---ttgatctgcgtttctactggct--gttgatgcctgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAA

upper sequence: GLYMA08G01940.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G150867_T01 (Zea mays), 3'ss of exon 1
gtgatcttttccgaattttttttttgtattttcgatttcagaaagtgttcttttgcataaattgttgtctttttccatttggggtgcgttggattgacatggatcaggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA
| | | ||| | |||| ||| | | | ||| |||||| |||| | | | | |||||||||||| || ||||||||||| | ||| |||||||| ||||| ||||||||||| ||||| | || || || || |
-------------------------------gtggcgtgattcggtgattttttctataggatttcgatgcggattccttgatctgcgtttctactgcatgt-tgatgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAA

upper sequence: GLYMA08G01940.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G150867_T02 (Zea mays), 3'ss of exon 1
gtgatcttttccgaattttttttttgtatttt--cgatttcagaaagtgttcttttgcataaattgttgtctttttccatttggggtgcgttggattgacatggatcaggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA
| | ||| | | | | ||| | |||| ||| | | | ||| |||||| |||| | | | | |||||||||||| || ||||||||||| | ||| |||||||| ||||| ||||||||||| ||||| | || || || || |
---------------------gtgaggattctggtggcgtgattcggtgattttttctataggatttcgatgcggattccttgatctgcgtttctactgcatgt-tgatgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAA

upper sequence: GLYMA08G01940.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G053764_T01 (Zea mays), 3'ss of exon 1
gtgatcttttccgaattttttttttgtattttcgatttcagaaagtgttcttttgcataaattgttgtctttttccatttggggtgcgttg--gattgacatgg---atcaggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA
|||| | || | | || | | ||||| | ||| | | || ||| | | ||||| || ||| ||| | | | ||| ||| | |||||||||||| || ||||||||||||| ||| |||||||| ||||| || ||||| || |||||| | || || || |
gtgaggatgctggacctctcttggtctgttttccaattctg----cctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA

upper sequence: GLYMA08G01940.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 1
gtgatcttttccgaattttttttttgtattttcgatttcagaaagtgttct-tttgcataaattgttgtctttttccatttggggtgcgttggattgacatggatcaggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA
| | |||| | || | | || ||||||| |||| | || ||| | | ||||| | | | | ||| | ||| | |||||||||||| || ||||||||||||| ||| |||||||| ||||| || ||||| || |||||| | || || || |
----------------gtctgttttccaattctgcct---gaccgtgttctgcttgcttttttttttga-tctggccattcttgccg-gctttcttggttt--atcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA

upper sequence: GLYMA08G01940.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G053764_T06 (Zea mays), 3'ss of exon 1
gtgatcttttccgaattttttttttgtattttcgatttcagaaagtgttcttttgcataaattgttgtctttttccatttggggtgcgttg--gattgacatgg---atcaggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA--------------------
|||| | || | | || | | ||||| | ||| | | || ||| | | ||||| || ||| ||| | | | ||| ||| | |||||||||||| || ||||||||||||| ||| |||||||| ||||| || ||||| || |||||| | || || || |
gtgaggatgctggacctctcttggtctgttttccaattctg----cctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAGTAATAGCCCTCGCGCTGAA

upper sequence: GLYMA08G01940.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G053764_T02 (Zea mays), 3'ss of exon 1
gtgatcttttccgaattttttttttgtattttcgatttcagaaagtgttct-tttgcataaattgttgtctttttccatttggggtgcgttggattgacatggatcaggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA
| || | | |||| | | | | || ||||||| |||| | || ||| | | ||||| | | | | ||| | ||| | |||||||||||| || |||||||| |||| ||| |||||||| ||||| || ||||| || |||||| | || || || |
-------tctcttggtctgttttccaattctgc-----ctgaccgtgttctgcttgcttttttttttga-tctggccattcttgccg-gctttcttggttt--atcggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA

upper sequence: GLYMA08G01940.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G053764_T05 (Zea mays), 3'ss of exon 1
gtgatcttttccgaattttttttttgtattttcgatttcagaaagtgttcttttgcataaattgttgtctttttccatttggggtgcgttg--gattgacatgg---atcaggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA--------------------
|||| | || | | || | | ||||| | ||| | | || ||| | | ||||| || ||| ||| | | | ||| ||| | |||||||||||| || |||||||| |||| ||| |||||||| ||||| || ||||| || |||||| | || || || |
gtgaggatgctggacctctcttggtctgttttccaattctg----cctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAGTAATAGCCCTCGCGCTGAA

upper sequence: GLYMA08G01940.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G053764_T04 (Zea mays), 3'ss of exon 1
gtgatcttttccgaattttttttttgtattttcgatttcagaaagtgttcttttgcataaattgttgtctttttccatttggggtgcgttg--gattgacatgg---atcaggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA
|||| | || | | || | | ||||| | ||| | | || ||| | | ||||| || ||| ||| | | | ||| ||| | |||||||||||| || |||||||| |||| ||| |||||||| ||||| || ||||| || |||||| | || || || |
gtgaggatgctggacctctcttggtctgttttccaattctg----cctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA

upper sequence: GLYMA08G01940.2 (Glycine max), 3'ss of exon 1
lower sequence: AT5G41340.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgatcttttccgaattttttttttgtattttcgatttcagaaagtgttcttttgcataaattgttgtctttttccatttggggtgcgttggattgacatggatcaggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA
|| || || | ||||||||| | | ||| ||||| | |||||| | | | || | ||| | ||| || ||| || | || | |||||||||||| ||||| || ||||| ||| ||||||||||||||||||| |||| ||| |||||| | || ||||||||||
gtaataactttctaatttttttctc----tgtcggtttcatttgtta--cttttgatttgagttttttgtttctatgattgatttgatttgattttatattg----------cagGATGATGAGCGATTATAAAGTGGAAACGATCAACGATGGCATGCAAGAATTCTATGTTGAATTCAATGGTCCCAAAGACA

upper sequence: GLYMA08G01940.2 (Glycine max), 3'ss of exon 1
lower sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgatcttttccgaattttttttttgt------attttcgatttcagaaagtgttcttttgcataa-attgttgtctttttccatttggggtgcgttggattgacatggatcaggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA
|| || |||| || || | || | ||| | ||||| | | |||| ||| || | | | || | | ||| ||| || | | |||||||||||||| ||||||||||||| | |||| ||||||||||||||||||||||| |||||| |||||||||||||
gtaatttttttaatcttattatcttatcagtttattcttgattttgagctccgattttttttctaatgtttgtttggcgatttgattcgatttttttgtgatgatttgatgtgagagtttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA

upper sequence: GLYMA08G01940.2 (Glycine max), 3'ss of exon 1
lower sequence: EFJ23672 (Selaginella moellendorffii), 3'ss of exon 1
-------gtgatcttttccgaattt----tttttttgtattttcgatt---tcagaaagtgttcttttgcataaattgttgtctttttcc--atttggggtgcgttggattgacatg--gatcaggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA
| | ||||||| | || | | || | | | |||| ||| || | | || | || | | | ||| | || || | | || | ||||||||||||||| ||||||||||||| ||| |||||||| ||| | ||||| |||||| ||||| ||||| || |
gtgagtctcgcctcctctcgaatttcaattccttcttcgctctccagtggctatgaaaaacctctctttcttcgctttcttcctctctgctaattcattgcttcttctttttgcttcccattcctctttccagGATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATA

upper sequence: GLYMA08G01940.2 (Glycine max), 3'ss of exon 1
lower sequence: EFJ34378 (Selaginella moellendorffii), 3'ss of exon 1
------gtgatcttttccgaattttttttttgtattttcgatttcagaaagtgttcttttgcataaattgttgtctttttcc--atttggggtgcgttggattgacatg--gatcaggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA
| || || | ||| || | | |||| | || | ||| || | | || | || | | | ||| | || || | | || | ||||||||||||||| ||||||||||||| ||| |||||||| ||| | ||||| |||||| ||||| ||||| || |
gtgagtctcgcctcctctcgaatttcaattcct-tcttcgctctccagtggacctctctttcttcgctttcttcctctctgctaattcattgcttcttctttttgcttcccattcctctttccagGATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATA

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|298182580|gb|HO031315.1|HO031315
EST:     AG                         GATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
genomic: --gtgatctttt ... aggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
EST: gi|298182580|gb|HO031315.1|HO031315
EST:     AG                         GATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
genomic: --gtgatctttt ... aggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
EST: gi|298182580|gb|HO031315.1|HO031315
EST:     AG                         GATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
genomic: --gtgatctttt ... aggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
EST: gi|298182580|gb|HO031315.1|HO031315
EST:     AG                         GATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
genomic: --gtgatctttt ... aggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
EST: gi|18039609|gb|BM307903.1|BM307903
EST:     CAATGTCTTCCCCAAGCAAACGCCGAGACATGGACTTGATGAA---G-CT                         GATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTT
genomic: CAATGTCTTCCCCAAGCAAACGCCGAGACATGGACTTGATGAAGCTGTCTgtgatctttt ... aggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTT
EST: gi|193562259|gb|FK521268.1|FK521268
EST:     AG                         GATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
genomic: --gtgatctttt ... aggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
EST: gi|193562259|gb|FK521268.1|FK521268
EST:     AG                         GATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
genomic: --gtgatctttt ... aggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
EST: gi|193562259|gb|FK521268.1|FK521268
EST:     AG                         GATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
genomic: --gtgatctttt ... aggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
EST: gi|193562259|gb|FK521268.1|FK521268
EST:     AG                         GATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
genomic: --gtgatctttt ... aggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
EST: gi|193681729|gb|FK620903.1|FK620903
EST:     AG                         GATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
genomic: --gtgatctttt ... aggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
EST: gi|193681729|gb|FK620903.1|FK620903
EST:     AG                         GATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
genomic: --gtgatctttt ... aggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
EST: gi|193681729|gb|FK620903.1|FK620903
EST:     AG                         GATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
genomic: --gtgatctttt ... aggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
EST: gi|193681729|gb|FK620903.1|FK620903
EST:     AG                         GATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
genomic: --gtgatctttt ... aggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
EST: gi|192324802|gb|FK016873.1|FK016873
EST:     CAATGTCTTCCCCAAGCAAACGCCGAGACATGGACTTGATGAA---G-CT                         GATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTT
genomic: CAATGTCTTCCCCAAGCAAACGCCGAGACATGGACTTGATGAAGCTGTCTgtgatctttt ... aggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTT
EST: gi|298198506|gb|HO040045.1|HO040045
EST:     AG                         GATGATGAGGGATTACAAGGTGGAGACGGTCAACGATGGCATGCGAGAGT
genomic: --gtgatctttt ... aggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
EST: gi|298198506|gb|HO040045.1|HO040045
EST:     AG                         GATGATGAGGGATTACAAGGTGGAGACGGTCAACGATGGCATGCGAGAGT
genomic: --gtgatctttt ... aggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
EST: gi|298198506|gb|HO040045.1|HO040045
EST:     AG                         GATGATGAGGGATTACAAGGTGGAGACGGTCAACGATGGCATGCGAGAGT
genomic: --gtgatctttt ... aggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT
EST: gi|298198506|gb|HO040045.1|HO040045
EST:     AG                         GATGATGAGGGATTACAAGGTGGAGACGGTCAACGATGGCATGCGAGAGT
genomic: --gtgatctttt ... aggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgttgtctttttccatttggggtgcgttggattgacatggatcaggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA
                               gattgac  putative branch site (score: 3)
 tcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatcttttccgaattttttttttgtattttcgatttcagaaagtgttcttttgcataaattgttgtctttttccatttggggtgcgttggattgacatggatcaggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA