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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAGCAACTATTCCTCAATGGAAGGTGTTCTTTATTGTAAGCCTCACTTTGAGCAGCTCTTCAAGGAGAGTGGGTCCTTCAGCAAGAACTTCCAGTCACgtatgtgttcttccttttcttctttgagaatgaagctgtgtttgtgtggtttttgaatcatatgcctcattaattggccatatattcattttgaacag

Basic information

species Glycine max
transcript GLYMA11G34830.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G34830.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G55770.6 (Arabidopsis thaliana), 5'ss of exon 4
CTGAGCAACTATTCCTCAATGGAAGGTGTTCTTTATTGTAAGCCTCACTTTGAGCAGCTCTTCAAGGAGAGTGGGTCCTTCAGCAAGAACTTCCAGTCACgtatgtgttcttccttttcttct--ttgagaatgaagctgtgtttgtgtggtttttgaatcatatgcctcattaattggccatatattcattttgaacag
||||| |  || || ||||||||||||||| | || ||||||||||| |||||||||||||| |||||||||||    |||| ||||||||| |||||||||||||  | ||  || |  |    || |   |     |  | |||      |||||  | ||     | || | |    || |  ||  ||    ||||
CTGAGTAGTTACTCATCAATGGAAGGTGTTTTGTACTGTAAGCCTCATTTTGAGCAGCTCTTTAAGGAGAGTGGTAGTTTCAACAAGAACTTTCAGTCACgtatgtagttttgtttctgcttcgattcatgttttttttccgcttgcccttcttttgg-ttattgatttaatcagtcttgca-actttgtttcctcacag

upper sequence: GLYMA11G34830.1 (Glycine max), 5'ss of exon 4
lower sequence: AT2G39900.1 (Arabidopsis thaliana), 5'ss of exon 3
CTGAGCAACTATTCCTCAATGGAAGGTGTTCTTTATTGTAAGCCTCACTTTGAGCAGCTCTTCAAGGAGAGTGGGTCCTTCAGCAAGAACTTCCAGTCACgtatgtgttcttccttttcttctttgagaatgaagctgtgtttgtgtggtt-tttgaatcatatgcctcattaattggccatatattcattttgaacag
|||||||| ||||| ||||||||||| ||  | ||||||| |||||| ||||||||||| |||||||||  |||    |||||||||||||| |||||||||||||     || |||  |    |     |  |||| | |   ||||||   || |||  ||  | |||  || |     | | ||    ||  ||||
CTGAGCAATTATTCATCAATGGAAGGAGTGGTGTATTGTAGGCCTCATTTTGAGCAGCTTTTCAAGGAGTCTGGTAGTTTCAGCAAGAACTTTCAGTCACgtatgtaaaactcttttcttcaccttctggtccagct-tttacatgtggtcactttaattttaatcttca--aact-----ttttttttcctttcacag

upper sequence: GLYMA11G34830.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv13s0019g03280.t01 (Vitis vinifera), 5'ss of exon 3
CTGAGCAACTATTCCTCAATGGAAGGTGTTCTTTATTGTAAGCCTCACTTTGAGCAGCTCTTCAAGGAGAGTGGGTCCTTCAGCAAGAACTTCCAGTCACgtatgtgttcttccttttcttctttgagaatgaagctgtgtttgtgtggtttttgaatcatatgcc--tcattaattggccatatatt-cattttgaacag
|||||||| |||||||||||||| ||||||||||| |||||||||||||||||||||||||| ||||||  |||    |||| |||||| || |||||||||  || |||||       |||       | ||  || ||||||  |  |   ||  |  ||| ||  |  |||||  || ||||||| |||||| |||||
CTGAGCAATTATTCCTCAATGGAGGGTGTTCTTTACTGTAAGCCTCACTTTGAGCAGCTCTTTAAGGAGTCTGGAAATTTCAACAAGAATTTTCAGTCACgtgagtcttctt-----gtttcaccagataagattctttgtttgatttctcaatggtttctattccattgtttaatgtgcaatatatttcattttcaacag

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|192326164|gb|FK016971.1|FK016971
EST:     TGGGCAGCTCTTCAAGGAGAGTGGGTCCTTCAGCAAGAACTTCCAGTCAC                         CTGCAAAGCTAGCAGATAAGACAACACATGAGCTG
genomic: TGAGCAGCTCTTCAAGGAGAGTGGGTCCTTCAGCAAGAACTTCCAGTCACgtatgtgttc ... ttttgaacagCTGCAAAGCTAGCAGATAAGACAACACATGAGCTG
EST: gi|193635326|gb|FK584751.1|FK584751
EST:     GAGCTAGCTCTTCAAGGAGAGTGGGTCCTTCAGCAAGAACTTCCAGTCAC                         CTGCAAAGCTAGCAGATAAGACAACACATGAGCTG
genomic: GAGC-AGCTCTTCAAGGAGAGTGGGTCCTTCAGCAAGAACTTCCAGTCACgtatgtgttc ... ttttgaacagCTGCAAAGCTAGCAGATAAGACAACACATGAGCTG
EST: gi|298174389|gb|HO017725.1|HO017725
EST:     TGAGCAGCTCTTCAAGGAGAGTGGGTCCTTCAGCAAGAACTTCCAGTCAC                         CTGCAAAGCTAGCAGATAAGACAACACATGAGCT
genomic: TGAGCAGCTCTTCAAGGAGAGTGGGTCCTTCAGCAAGAACTTCCAGTCACgtatgtgttc ... ttttgaacagCTGCAAAGCTAGCAGATAAGACAACACATGAGCT
EST: gi|7924672|gb|AW830698.1|AW830698
EST:     TGAGCAGCTCTTCAAGGAGAGTGGGTCCTTCAGCAAGAACTTCCAGTCAC                         CTGCAAAGCTAGCAGATAAGACAACACATGAGCTG
genomic: TGAGCAGCTCTTCAAGGAGAGTGGGTCCTTCAGCAAGAACTTCCAGTCACgtatgtgttc ... ttttgaacagCTGCAAAGCTAGCAGATAAGACAACACATGAGCTG
EST: gi|17963599|gb|BM270346.1|BM270346
EST:     TGAGCAGCTCTTCAAGGAGAGTGGGTCCTTCAGCAAGAACTTCCAGTCAC                         CTGCAAAGCTAGCAGATAAGACAACACATGAGCTG
genomic: TGAGCAGCTCTTCAAGGAGAGTGGGTCCTTCAGCAAGAACTTCCAGTCACgtatgtgttc ... ttttgaacagCTGCAAAGCTAGCAGATAAGACAACACATGAGCTG
EST: gi|193669571|gb|FK607733.1|FK607733
EST:     TGAGCAGCTCTTCAAGGAGAGTGGGTCCTTCAGCAAGAACTTCCAGTCAC                         CTGCAAAGCTAGCAGATAAGACAACACATGAGCTG
genomic: TGAGCAGCTCTTCAAGGAGAGTGGGTCCTTCAGCAAGAACTTCCAGTCACgtatgtgttc ... ttttgaacagCTGCAAAGCTAGCAGATAAGACAACACATGAGCTG
EST: gi|193687249|gb|FK630896.1|FK630896
EST:     TGAGCAGCTCTTCAAGGAGAGTGGGTCCTTCAGCAAGAACTTCCAGTCAC                         CTGCAAAGCTAGCAGATAAGACAACACATGAGCTG
genomic: TGAGCAGCTCTTCAAGGAGAGTGGGTCCTTCAGCAAGAACTTCCAGTCACgtatgtgttc ... ttttgaacagCTGCAAAGCTAGCAGATAAGACAACACATGAGCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGAGCAACTATTCCTCAATGGAAGGTGTTCTTTATTGTAAGCCTCACTTTGAGCAGCTCTTCAAGGAGAGTGGGTCCTTCAGCAAGAACTTCCAGTCACgtatgtgttcttccttttcttctttgagaatgaagctgtgtttgtgtggtttttgaatcatatgcctcattaattggccatatattcattttgaacag

- - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC