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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatttcataatggagatatgaattgtggaaatactaaaaccagaaatgccaaagtatcatgatgatttatgttaattttgtaatttactgttttgctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGGTATTGTACAGATGTGTTTGACTATTTAACACTTTCTGCAATTA

Basic information

species Glycine max
transcript GLYMA20G23310.4
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G23310.4 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 4
-agatttcataatggagatatgaattgtg--gaaatactaaaaccagaaatgccaaagtatcatgatgatttatgttaattttgtaatttactgttttgctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGGTATTGTACAGATGTGTTTGACTATTTAACACTTTCTGCAATTA
 | | |||||  |   || |    |||||   | |||     || | | |||     |  |  | |||||  |     |  | ||| ||| ||  |||  ||||| ||||| || || ||||| ||||| ||||||||||| ||||| ||||| ||||||||||| || ||||| ||||||||  | || ||||| ||||| |
tacagttcatcctcctgacagactttgtgctcatatatctgcactacacatgtatttg-gtgcttatgatgcagtaacacatagtatttttctaattt--tagGTGTATGGTTTCTACGATGAGTGCCAAAGGAAGTATGGGAATGCGAATGCATGGCGGTATTGCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCA

upper sequence: GLYMA20G23310.4 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G055905_T02 (Zea mays), 3'ss of exon 4
--------agatttcataatggagatatgaattgtggaaatactaaaaccagaaatgccaaag--tatcatgatgattta-tgttaattttgtaatttactgttttgctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGGTATTGTACAGATGTGTTTGACTATTTAACACTTTCTGCAATTA
         |  | |||| || |   |  ||| |  ||||     | ||  || ||| |  ||  || |||| ||   || |  ||||  ||| | |||   ||     |||| ||||| || |||||||| || ||||||||||||||||| |||||||| ||||||||||| || ||||| ||||| ||  | || || || ||||| |
tgcatgtttgtatccatactgtac-cacaaatggctgaaa-----acacttgacatgtcttagcttaccatgctggcatactaataataatgtgacttatcctt-----agGTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCATGGCGGTATTGCACTGATGTTTTTGATTACCTTACGCTATCAGCAATCA

upper sequence: GLYMA20G23310.4 (Glycine max), 3'ss of exon 4
lower sequence: AT3G19980.1 (Arabidopsis thaliana), 3'ss of exon 4
agatttcataatggagatatgaattgtggaaatactaaaaccagaaatg---ccaaagtatcatgatgatttatgtta----attttgtaatttactgttttgctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGGTATTGTACAGATGTGTTTGACTATTTAACACTTTCTGCAATTA
    | |||   |   || ||  |      |  |  ||||  | | |||    |     ||     |  |||||   |    |   | | ||||||| ||||   |||| ||||| || ||||| |||||||||||||||||||| || || ||||| ||||| ||||| |||||||| ||||||||| | || || || || ||||
---atgcatttcgtgaatctgc-tgactagatgatcaaaattatacatggattctcgacattgaactcctttataacacagaaccatttgatttactttttt---agGTGTATGGTTTCTATGACGAATGCCAGAGGAAGTATGGTAACGCTAATGCGTGGCGATATTGCACAGATGTTTTTGACTATCTTACCCTGTCAGCTATTA

upper sequence: GLYMA20G23310.4 (Glycine max), 3'ss of exon 4
lower sequence: AT1G50370.1 (Arabidopsis thaliana), 3'ss of exon 4
agatttcataatggagatatgaattgtggaaatactaaaaccagaaatgccaaagtatcatgatgat-ttatgttaattttgtaatttactgttttgctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGGTATTGTACAGATGTGTTTGACTATTTAACACTTTCTGCAATTA
| ||    |      ||     ||||| |  ||| |     |      |    | | | ||  |  | |||  ||    |   |||||  | ||| ||||||| ||||| || ||||| |||||||| ||||||||||| ||||| ||||||||| | ||||| || ||||| ||||||||| | |||||||| || ||||
acatccactgtcaaggacgaagattgtagtgatattttgtgccctgcaggttcatttttatagttttcttaaattgtcgtaccaattttatattt-gctagGTGTATGGTTTCTATGACGAATGCCAAAGGAAGTATGGTAATGCTAATGCTTGGAGATATTGCACGGATGTTTTTGACTATCTTACACTTTCAGCTATTA

upper sequence: GLYMA20G23310.4 (Glycine max), 3'ss of exon 4
lower sequence: Vv10s0071g00950.t01 (Vitis vinifera), 3'ss of exon 4
---agatttcataatggagatatgaattgtggaaatactaaaaccagaaatgccaaagtatcatgatgatttatgttaattttgtaatttactgttttgctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGGTATTGTACAGATGTGTTTGACTATTTAACACTTTCTGCAATTA
    | || |  |     |||   |    | | |  |||   || ||| ||     | |||  | | ||| | | ||| | |  || ||| ||  ||| | |||||||||| || |||||||| |||||||||||||| || ||||| ||||| |||||||| || |||||||| ||||||||  |||| || ||||| || |
aactgtttccccacataggatgaaacacattgcacaactgtgacaagagatttaccaatat--ttaggatatttattagtgt-atacttttcttcttttccagGTCTATGGTTTCTATGATGAGTGCCAGAGGAAGTACGGAAATGCTAATGCATGGCGGTACTGCACAGATGTTTTTGACTACCTAACCCTCTCTGCGATAA

upper sequence: GLYMA20G23310.4 (Glycine max), 3'ss of exon 4
lower sequence: PP1S31_220V6.1 (Physcomitrella patens), 3'ss of exon 4
-agatttcataatggagatatgaat-tgtggaaatactaaaaccagaaatgccaaagtatcatgatgatttatgttaattttgtaatttactgttttgctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGGTATTGTACAGATGTGTTTGACTATTTAACACTTTCTGCAATTA
  |||||  |    || | |   || ||||    | |    | ||  | |     | || |       ||| || |  | |   || |        ||  ||||||||||||||||||||||||| ||| | |||||||| ||  | ||||||||||||||||| || || || ||||||||  | ||||| || || || |
ctgattttctctaagatacagctatctgtgtgcgtgcatccatca--atttttggaataaccgagacgtttctgattttgtccgaagtggtatgcctgacagGTCTATGGATTTTATGATGAATGTCAGCGTAAGTATGGAAACCCAAATGCTTGGCGGTATTGCACTGACGTTTTTGACTACCTGACACTCTCGGCTATCA

upper sequence: GLYMA20G23310.4 (Glycine max), 3'ss of exon 4
lower sequence: PP1S207_36V6.1 (Physcomitrella patens), 3'ss of exon 4
--agatttcataatggagatatgaattgtggaaatactaaaaccagaaatgccaaagtatcatgatgatttatgttaattttgta---atttactgt-tttgctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGGTATTGTACAGATGTGTTTGACTATTTAACACTTTCTGCAATTA
    || |  | ||| |  |   | || |   ||| | |  ||      ||     | | |||||  | |  ||||  ||||| |   | ||  ||| ||||  |||| |||||||||||||| ||||||||| |||||||||| ||  | |||||||||||||| || || ||||| ||||||||  | ||||| || || || |
tgccatatatttatgcatgtgaaagttatctgaattcaattactttttgtgt----ggaccatga--aatgttgttggttttgaacggaattggtgtgtttgacagGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCTTGGCGGTACTGCACTGATGTTTTTGACTACCTTACACTCTCAGCCATAA

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|213588325|gb|DB967811.1|DB967811
EST:     CTAATATTACTCTTTTACGTGGAAATCATGAAAGTAGACAATTAACCCAG                         GTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCT
genomic: CTAATATTACTCTTTTACGTGGAAATCATGAAAGTAGACAATTAACCCAGgtacgctttg ... gttttgctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCT
EST: gi|254318584|gb|GR832752.1|GR832752
EST:     CTAATATTACTCTTTTACGTGGAAATCATGAAAGTAGACAATTAACCCAG                         GTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCT
genomic: CTAATATTACTCTTTTACGTGGAAATCATGAAAGTAGACAATTAACCCAGgtacgctttg ... gttttgctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCT
EST: gi|298191713|gb|HO035795.1|HO035795
EST:     CTAATATTACTCTTTTACGTGGAAATCATGAAAGTAGACAATTAACCCAG                         GTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCT
genomic: CTAATATTACTCTTTTACGTGGAAATCATGAAAGTAGACAATTAACCCAGgtacgctttg ... gttttgctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCT
EST: gi|37994239|gb|CF805985.1|CF805985
EST:     CTAATATTACTCTTTTACGTGGAAATCATGAAAGTAGACAATTAACCCAG                         GTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCT
genomic: CTAATATTACTCTTTTACGTGGAAATCATGAAAGTAGACAATTAACCCAGgtacgctttg ... gttttgctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCT
EST: gi|18719747|gb|BM523222.1|BM523222
EST:     CTAATATTACTCTTTTACGTGGAAATCATGAAAGTAGACAATTAACCCAG                         GTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCT
genomic: CTAATATTACTCTTTTACGTGGAAATCATGAAAGTAGACAATTAACCCAGgtacgctttg ... gttttgctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCT
EST: gi|192305488|gb|FG998300.1|FG998300
EST:     CTAATATTACTCTTTTACGTGGAAATCATGAAAGTAGACAATTAACCCAG                         GTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCT
genomic: CTAATATTACTCTTTTACGTGGAAATCATGAAAGTAGACAATTAACCCAGgtacgctttg ... gttttgctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCT
EST: gi|6567303|gb|AW234914.1|AW234914
EST:     CTAATATTACTCTTTTACGTGGAAATCATGAAAGTAGACAATTAACCCAG                         GTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCT
genomic: CTAATATTACTCTTTTACGTGGAAATCATGAAAGTAGACAATTAACCCAGgtacgctttg ... gttttgctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgccaaagtatcatgatgatttatgttaattttgtaatttactgttttgctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGGTATTGTACAGATGTGTTTGACTATTTAACACTTTCTGCAATTA
                         tgttaat  putative branch site (score: 3)
                                           ctgtttt  putative PPT
                    atttatgttaattttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agatttcataatggagatatgaattgtggaaatactaaaaccagaaatgccaaagtatcatgatgatttatgttaattttgtaatttactgttttgctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGGTATTGTACAGATGTGTTTGACTATTTAACACTTTCTGCAATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - gaaatac
- - - - - - - - - - - - - - - - - - aaaaccag
- - - - - - - - - - - - - - - - - - - - - - -aatgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgatg