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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCAgtgagtatcttaacatttaagatgtggtccactcatcagcattttattaatttctgacacaaattatgatatatattgaacaaaagtaaatgatgaaata...

Basic information

species Glycine max
transcript GLYMA19G34390.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G34390.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os12g40880.1 (Oryza sativa), 5'ss of exon 8
GGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCAgtgagt-atcttaaca--tttaagatgtggtccactcatcagcattttattaatttctgacacaaattatgatatatattgaacaaaagtaaatgatgaaata---
|| ||||||||||  ||||||||||| ||||||||||| || ||||||||| |||| || ||||| || |  |||||||| ||| |  ||  |  |  || |  ||   |  |    |||  |  |   |   || | | ||      ||| | ||   |||  ||||| ||||  |   
GGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGTGATCCAGTTGAAAATGACATATTTGTAAAGCCGCAgtgagttatcattgcagatccagaatatattctctttgtag--attgcagaatgcttgaactctagtttct---tatttcgatttaaatcaaatg-tgaagcatgc

upper sequence: GLYMA19G34390.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G035338_T01 (Zea mays), 5'ss of exon 8
GGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCAgtgagtatcttaacatttaagatgtggtccactcatcagcattttattaatttctgacacaaattatgatatatattgaacaaaagtaaatgatgaaata----
|| ||||||||||  ||||||||||| ||||||||||| |||||||||||  |||| || ||||| || |  |||| |||    |   ||| || ||||  | |     |||  |  |  ||    ||  ||  || |||  |    ||   |   | | |   || ||   |     
GGTTCAGTTTATGCTCCATCATTTGATCATGGTGTTGGCGACCCAGTTGAGAATGACATATTTGTAAAGCCACAgtaagttagattggattcaa-atgtattgcttgagtcataaaatcttttggatc-aacttaatttagcac-cgtac-aacttagatttcttgttgcctttcttc

upper sequence: GLYMA19G34390.1 (Glycine max), 5'ss of exon 8
lower sequence: AT1G03030.1 (Arabidopsis thaliana), 5'ss of exon 8
GGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCAgtgagtatct--taacatttaagatgtggtccactca---tcagcattttattaa----tttctgacacaaattatgatatatattgaacaaaagtaaatgatgaaata--
|| ||||||||||| ||||||||||| ||||| |||||||| ||||||||||||||||||||||| | ||| |||| ||||     || | |   | || ||    |  |      ||  |  ||| ||    |||      |  |||  |  | | | | | | ||  ||  |  |    |   
GGCTCAGTTTATGTGCCATCATTTGATCATGGAGTTGGGGATCCAGTTGAAGATGATATCTTTGTTAGCCTCCAgtaagtagtcagtagcttcctaaatctgtcaaatccgaatctagtgtaatatgaaatggttttgtttgcctattccgg-agacagtcagctaacttatgtcctcttcttag

upper sequence: GLYMA19G34390.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv07s0141g00310.t01 (Vitis vinifera), 5'ss of exon 8
GGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCAgtgagtatcttaacatttaagatgtggtccactcatcagcattt--tattaatttc----tgacacaaattatgatatatattgaacaaaagtaaatgatgaaata
|| |||||||||| |||||| ||||| ||||||||||| || ||||||||||||||||| ||| | | ||| |||| ||||  |||    ||       | |   || |||| ||  |     | |||||    |||      |  | ||  | ||| | | |    | |||||      
GGGTCAGTTTATGCACCATCGTTTGATCATGGTGTTGGAGATCCAGTTGAAGATGATATATTTATCAGCCTCCAgtaagtaatttacttctttcacatagataatcttatcaacagctgccgctgatttcataatgaactgggtgtttatgaacatttatccagtccatatgat------

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|192331130|gb|FK020350.1|FK020350
EST:     GACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCA                         GCACAAGGTTGTTATTGTAGAAGGTAACTATTTGC
genomic: GACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCAgtgagtatct ... ctttgtgtagGCACAAGGTTGTTATTGTAGAAGGTAACTATTTGC
EST: gi|192326255|gb|FK017617.1|FK017617
EST:     GACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCA                         GCACAAGGTTGT-ATTGTAGA-GGTAACTATTTGCTCTTGGAAGATGGGG
genomic: GACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCAgtgagtatct ... ctttgtgtagGCACAAGGTTGTTATTGTAGAAGGTAACTATTTGCTCTTGGAAGATGGGG
EST: gi|151405354|gb|EV275168.1|EV275168
EST:     GACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCA                         GCACAAGGTTGT-ATTGTAGAAAGTAACTATTAGCTCTTGGAAGATGGGGT
genomic: GACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCAgtgagtatct ... ctttgtgtagGCACAAGGTTGTTATTGTAGAAGGTAACTATTTGCTCTTGGAAGATGGGGT
EST: gi|58020561|gb|CX707303.1|CX707303
EST:     GACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCA                         GCACAAGGTTGTTATTGTAGAAGGTAACTATTTGCTCTTGGAAGATGGGGT
genomic: GACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCAgtgagtatct ... ctttgtgtagGCACAAGGTTGTTATTGTAGAAGGTAACTATTTGCTCTTGGAAGATGGGGT
EST: gi|58020732|gb|CX707474.1|CX707474
EST:     GACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCA                         GCACAAGGTTGTTATTGTAGAAGGTAACTATTTGCTCTTGGAAGATGGGGT
genomic: GACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCAgtgagtatct ... ctttgtgtagGCACAAGGTTGTTATTGTAGAAGGTAACTATTTGCTCTTGGAAGATGGGGT
EST: gi|192325118|gb|FK019064.1|FK019064
EST:     GACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCA                         GCACAAGGTTGTTATTGTAGAAGGTAACTATTTGCTCTTGGAAGATGGGGT
genomic: GACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCAgtgagtatct ... ctttgtgtagGCACAAGGTTGTTATTGTAGAAGGTAACTATTTGCTCTTGGAAGATGGGGT
EST: gi|193411805|gb|FK380340.1|FK380340
EST:     GACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCA                         GCACAAGGTTGTTATTGTAGAAGGTAACTATTTGCTCTTGGAAGATGGGGT
genomic: GACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCAgtgagtatct ... ctttgtgtagGCACAAGGTTGTTATTGTAGAAGGTAACTATTTGCTCTTGGAAGATGGGGT
EST: gi|20815079|gb|BQ299557.1|BQ299557
EST:     GACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCA                         GCACAAGGTTGTTATTGTAGA
genomic: GACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCAgtgagtatct ... ctttgtgtagGCACAAGGTTGTTATTGTAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATCAGTTTATGTACCATCATTTGACCATGGTGTTGGGGACCCAGTTGAAGATGATATCTTTGTGAACCTTCAgtgagtatcttaacatttaagatgtggtccactcatcagcattttattaatttctgacacaaattatgatatatattgaacaaaagtaaatgatgaaata

- - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - -  AAGATG