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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtcccttatatttagtgtgcatcttttaattgtataatagtgatgctttgcagaatattgatgttgattttatcctgtctttattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATACAAGAACCGGGAACTGCAAACCATGCGTCTTCTGGACC

Basic information

species Glycine max
transcript GLYMA10G01280.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G01280.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 4
-------gttagtcccttatatttagtgtgcatcttttaattgtat-aatagtgatgctttgcagaatattgatgttgattttatcctgt---ctttattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATACAAGAACCGGGAACTGCAAACCATGCGTCTTCTGGACC
        |||| |   |  |||||   ||||  | || | ||| | |||     || | ||  |   |||||||     || ||    |      | |||| ||||| |||||| |||| || || || |||||||||||||||||||||||||||||||||||||| |||||||| || |||||||| |||||  |||| ||||
gtttgtctttagacagatcgatttatgttgcacttgttcagtgtgttaatttgtgtgttctggtggcgattgatgaacccttcatttcttgaatgatcttgtatagGCCAAGTGCCTGGAAACCGGTGAGACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATATAAGAACCGTGAGCTGCAAACAATGCGAGTTCTTGACC

upper sequence: GLYMA10G01280.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g19150.1 (Oryza sativa), 3'ss of exon 4
gttagtcccttatatttagtgtgc-atcttttaattgtataatagtgatgctttgcagaatattgat-gttgattttatcctgtctttattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATACAAGAACCGGGAACTGCAAACCATGCGTCTTCTGGACC
                  ||| || ||   |  ||   ||  |     | | || | |  ||  |||   | |||  ||  | |||||       |||| |||||  | || || || || |  || ||| ||||||| |||||||||||   |||||||||||||||||| |||||||| ||||   |||| || |
------------------gtgggccattggtatatgccattctgtcattacctttctgtttagagattactaattaaat--tatctttg----acagGCTAAGTGTCTAGAAACTGGTGAGAGAGTTGCTGTAAAGAAAGTTCTTCAAGATGCGAGATACAAGAACCGGGAGCTGCAAACGATGCAAGTTCTCGATC

upper sequence: GLYMA10G01280.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G155836_T01 (Zea mays), 3'ss of exon 4
----------------------gttagtcccttatatttagtgtgcatcttttaattgtataatagtgatgctttgcagaatattgatgttgatttt-----atcctgtctttattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATACAAGAACCGGGAACTGCAAACCATGCGTCTTCTGGACC
                       | |  |     ||| | || |  ||  |   |||  |     ||  |   |   ||    ||    |   ||||     |         | ||||  |||| |||||  | || || || || || || |||||||| ||||||||||||||||||||||||||||| || || ||||||||||||||  | || ||||
gtttgttactatacaaatcagtatgaaactgaattatctggtttttattgtagtatttcacttaggtagtaactaatagctccttcccctctttttttataaaaataaatgatcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAAGACAAGAGATACAAGAATCGTGAGCTGCAAACCATGCGAGTGCTTGACC

upper sequence: GLYMA10G01280.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0005g02100.t01 (Vitis vinifera), 3'ss of exon 4
----------------------gttagtcccttatatttagtgtgcatcttttaattgta-taatagtgatgctttgcagaatattgatgttgattttatcctgtctttattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATACAAGAACCGGGAACTGCAAACCATGCGTCTTCTGGACC
                       |  ||  || |      |  ||  | || |   || |  ||   | |||  |||          ||   ||| |     ||  | | || || ||||||||||||| ||||| || ||||| || || || || || ||||||||||||||||||||||||||| | ||  | || || ||||||||||||||||
gtaagagtttggtgagtgggtaatgggtatctgagtaacggcctgtgtgttctggctgaaacaaattttatgtcttgatttggtcaaataaggatata--tatgcttcttttatgcagGCAAAGTGCTTAGAGACTGGTGAAACAGTTGCAATTAAAAAAGTTCTTCAAGACAAGAGATACAAGAACAGAGAGTTACAGACTATGCGTCTTCTGGACC

upper sequence: GLYMA10G01280.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 4
-----gttagtcccttatatttagtgtgcatcttttaattgtataatagtgatgctttgcagaatattgatgttgatt-ttatcctgtctt-tattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATACAAGAACCGGGAACTGCAAACCATGCGTCTTCTGGACC
       ||||   | | |  | |  | ||||| ||  | | | | |  || || |      ||||   ||  | ||   |    || ||  | ||||  |||| || ||| | ||||  ||||| || ||||| ||||||||||| || |||||||||||||||||||| || || || || | |||| | ||  |||| |
tgtactgtagtgg-tgaaacatgggatacatctgtttgtgggacactcatggtgatagaactaatacatattctcatgactgcggtgactcctgttgt-cagGCTAAATGCATTGAGAGCGGGGAGACGGTGGCCATAAAGAAGGTGCTCCAAGACAAGAGATACAAGAATCGAGAGCTCCAGATCATGAGGCTATTGGATC

upper sequence: GLYMA10G01280.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 3
gttagtcccttatatttag---tgtgcatcttttaattgtataatagtgatgctttgcagaatattgatgttgattttatcctgt------ctttattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATACAAGAACCGGGAACTGCAAACCATGCGTCTTCTGGACC
 | | | |  |  |   ||   || |  |  | |     | | |   | | | |  | ||||  | |  | || | | |||  |        ||| ||||  ||||||| ||| | ||||  || |||||||||||||| |||||||| ||||| |||||||||||||||||||| ||||| || | |||||| || ||||| |
-taacttcactggagccagacatggggctgatctgtccatgtgacgttcaaggtg-gtagaac-taggggatgttctgatcgcgagggtaattttgttgt-cagGCAAAATGCATAGAGAGCGGAGAAACTGTGGCTATTAAGAAGGTGCTTCAGGACAAGAGATACAAGAACCGAGAACTTCAGATCATGCGGCTGCTGGAGC

upper sequence: GLYMA10G01280.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 4
gttagtcccttatatttagtgtgcatcttttaattgtataatagtgatgctttgcagaatattgatgttgattttatcctgtctttattg-tgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATACAAGAACCGGGAACTGCAAACCATGCGTCTTCTGGACC
                           | ||  | ||  |  |    |||     |         | | | || |    | |||||     || |||| ||||||||||| || || ||||| |||||||| || ||||| || ||||||||| | ||||||||||| || || || |  ||||| || || ||||
--------------------------gtattgctagtcca--aacagtgcaacaaaagcaggctttatcgtttcttctttctctttgggaatgcagGCCAAGTGCTTGGAAACCGGAGAAACCGTGGCTATCAAAAAGGTCCTCCAAGACAAGCGGTACAAGAACCGAGAGCTCCAGATAATGCGCCTCCTCGACC

upper sequence: GLYMA10G01280.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ10962 (Selaginella moellendorffii), 3'ss of exon 3
gttagtcccttatatttagtgtgcatcttttaattgtataatagtgatgctttgcagaatattgatgttgattttatcctgtctttattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATACAAGAACCGGGAACTGCAAACCATGCGTCTTCTGGACC
                  |||||||      || |      || | || ||       |   | | |||  ||       | ||| | |    |||| |||||| | || ||||| || || ||||| || ||||||||  | || |||||||||||||| |||||||| |||||||  ||||| ||||| ||||
------------------gtgtgca------aact-cgctttaatcattct-------aggctaacgtttcttcctgttgggcttcacttc--agGCCAAGTGCCTCGAAACAGGAGAGACGGTGGCCATCAAGAAGGTGTTACAGGACAAGAGATACAAAAACCGGGAGCTGCAAATAATGCGCCTTCTTGACC

upper sequence: GLYMA10G01280.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 3
gttagtcccttatatttagtgtgcatcttttaattgtataatagtgatgctttgcagaatattgatgttgattttatcctgtctttattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATACAAGAACCGGGAACTGCAAACCATGCGTCTTCTGGACC
                  |||||||      || |      || | || ||       |   | | |||  ||       | ||| | | |  |||| |||||| | || ||||| || || |||||||| ||||||||  | || |||||||||||||| |||||||| |||||||  ||||| ||||| ||||
------------------gtgtgca------aact-cgctttaatcattct-------aggctaacgtttcttcctgttgggcttcacttt--agGCCAAGTGCCTCGAAACAGGAGAGACGGTGGCTATCAAGAAGGTGTTACAGGACAAGAGATACAAAAACCGGGAGCTGCAAATAATGCGCCTTCTTGACC

upper sequence: GLYMA10G01280.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 4
gttagtcccttatatttagtgtgcatcttttaattgtataatagtgatgctttgcagaatattgatgttgattttatcctgtctttattg-tgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATACAAGAACCGGGAACTGCAAACCATGCGTCTTCTGGACC
                         | ||   | |  | || ||||   |     || |   |  | | | || |    | |||||     || |||| ||||||||||| || || ||||| |||||||| || ||||| || ||||||||| | ||||||||||| || || || |  ||||| || || ||||
------------------------gtattgctagtcca-aacagtgcaaca--aaagcaggcttttatcgtttcttctttctctttgggaatgcagGCCAAGTGCTTGGAAACCGGAGAAACCGTGGCTATCAAAAAGGTCCTCCAAGACAAGCGCTACAAGAACCGAGAGCTCCAGATAATGCGCCTCCTCGACC

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|208253805|gb|GE055559.1|GE055559
EST:     ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAG                         GCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAGgttagtccct ... tattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|193625414|gb|FK577458.1|FK577458
EST:     ACATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAG                         GCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAGgttagtccct ... tattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|193457767|gb|FK424023.1|FK424023
EST:     ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAG                         GCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAGgttagtccct ... tattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|207692289|gb|GD674430.1|GD674430
EST:     ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGCGTAGTTTTCCAG                         GCAAAGTGCTTGGAGAC
genomic: ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAGgttagtccct ... tattgtgtagGCAAAGTGCTTGGAGAC
EST: gi|208195307|gb|GD992202.1|GD992202
EST:     ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAG                         GCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAGgttagtccct ... tattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|208191378|gb|GD987840.1|GD987840
EST:     ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAG                         GCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAGgttagtccct ... tattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|193446950|gb|FK416211.1|FK416211
EST:     ACATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAG                         GCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAA
genomic: ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAGgttagtccct ... tattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAA
EST: gi|193400664|gb|FK368319.1|FK368319
EST:     ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAG                         GCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAGgttagtccct ... tattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|24205503|gb|BU964756.1|BU964756
EST:     ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAG                         GCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAGgttagtccct ... tattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|193441743|gb|FK409164.1|FK409164
EST:     ACATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAG                         GCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTT
genomic: ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAGgttagtccct ... tattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTT
EST: gi|193356522|gb|FK320953.1|FK320953
EST:     ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAG                         GCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAGgttagtccct ... tattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|207780088|gb|GD753017.1|GD753017
EST:     ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTCCCAG                         GCAAAGTGCTTGGAGACAGGGGAAACTGTGGCT
genomic: ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAGgttagtccct ... tattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCT
EST: gi|207727122|gb|GD701100.1|GD701100
EST:     ACATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAG                         GCAAAGTGCTT
genomic: ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAGgttagtccct ... tattgtgtagGCAAAGTGCTT
EST: gi|19453652|gb|BM955062.1|BM955062
EST:     ACATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAG                         GCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAGgttagtccct ... tattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|208056463|gb|GD850292.1|GD850292
EST:     ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAG                         GCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAGgttagtccct ... tattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|193716979|gb|FK654677.1|FK654677
EST:     ACATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAG                         GCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAGgttagtccct ... tattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
EST: gi|193388281|gb|FK357030.1|FK357030
EST:     ACATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAG                         GCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA
genomic: ATATGGCTGAGCGAGTTGTTGGAAATGGATCATTTGGTGTAGTTTTCCAGgttagtccct ... tattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagtgatgctttgcagaatattgatgttgattttatcctgtctttattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATACAAGAACCGGGAACTGCAAACCATGCGTCTTCTGGACC
                               ttttatcctgtcttt  CT-rich tract
                           ttgattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtcccttatatttagtgtgcatcttttaattgtataatagtgatgctttgcagaatattgatgttgattttatcctgtctttattgtgtagGCAAAGTGCTTGGAGACAGGGGAAACTGTGGCTATAAAGAAGGTTCTTCAAGACAAGAGATACAAGAACCGGGAACTGCAAACCATGCGTCTTCTGGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC