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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcagcttcacttctcatgtttcaatctttaataatgattacacaatcttatatattaatattaatatatcgtgatatttcacagATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATCATAGACATGGATGCTGATGTGATCACCATTGAGAACTCCAGATCAGATG

Basic information

species Glycine max
transcript GLYMA04G30350.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G30350.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G20980.2 (Arabidopsis thaliana), 3'ss of exon 11
----------------------------------------------------------------------------------------------gttcagcttcacttctcatgtttcaatctttaataatgattacacaa---------tcttatatattaatat-------taatata-tcgtgatatttca--cagATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATCATAGACATGGATGCTGATGTGATCACCATTGAGAACTCCAGATCAGATG
                                                                                               |  |   | |  ||          |  |  || ||| | || | ||         ||| || |||| | ||       |||| |  |  |  || ||||  ||||| ||||| |||||||||||||| || ||||| |||||||| |||||||| || || |||||||||||||||||||| |||||||||||  | |||||||
gtatttgtatttcactttattgctccttcccacttaaagaatgttttttacgagtatgttgaccataatgtggtttctgccattttcgtggacaatagaatgtgatatcaagatgaaggacgtgaaacaattactaaataaaggaagagatctaatttattcaaatgacaccttaatgttcttcttgtacttcatgcagATCCACACCCACATGTGCTACTCAAATTTCAACGACATCATCCACTCAATTATTGATATGGATGCTGATGTGATCACTATTGAGAACTCACGGTCAGATG

upper sequence: GLYMA04G30350.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv06s0009g01080.t01 (Vitis vinifera), 3'ss of exon 11
--------gttcagcttcacttctcatgtttcaatctttaataatg---attacacaat--cttatatatt-aatattaatatatcgtgatatttcacagATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATCATAGACATGGATGCTGATGTGATCACCATTGAGAACTCCAGATCAGATG
        ||      ||   ||  ||     ||  | |   || |   || | ||| |  ||   ||  | ||  |   | ||   |  | | | |||||| || |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||
tgttaggagtatgtgatcgtatcatataaggaaacgtatgcaaaaggaaatgaaacagtgactagaattctgaacgtctttttaatattgtttctaacagATCCATACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATCATAGACATGGATGCTGACGTGATCACCATTGAGAACTCCAGATCAGATG

upper sequence: GLYMA04G30350.1 (Glycine max), 3'ss of exon 11
lower sequence: EFJ05611 (Selaginella moellendorffii), 3'ss of exon 11
gttcagcttcacttctcatgtttcaatctttaataatgattacacaatcttatatattaatattaatatatcgtgatatttcacagATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATCATAGACATGGATGCTGATGTGATCACCATTGAGAACTCCAGATCAGATG
                     |  ||      |  | | ||  | |   |  |  ||  | | |    |    ||| ||  ||||||| ||||| || |||||||||||| ||||||| ||||||||     | ||||| |||||||| || ||||||||||| || || |||||  | || ||||
--------------------gtaaaagacgcgacga-gtttctatagcttcgtgaat-gacactggcgttgtttgaaatc-cacagATCCACACCCATATGTGCTACTCCCACTTCAACGACATCATCACAGCCATCATCGACATGGACGCCGATGTGATCACGATCGAAAACTCTCGCTCGGATG

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|192312936|gb|FK003616.1|FK003616
EST:     CTGTTCACTCATTTAGGATTACCAACTGTGGTGTGGAGGACACTACTCAG                         ATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC
genomic: CTGTTCACTCATTTAGGATTACCAACTGTGGTGTGGAGGACACTACTCAGgttcagcttc ... tatttcacagATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC
EST: gi|208235227|gb|GE032045.1|GE032045
EST:     CTGTTCACTCATTTAGGATTACCAACTGTGGTGTGGAGGACACTACTCAG                         ATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC
genomic: CTGTTCACTCATTTAGGATTACCAACTGTGGTGTGGAGGACACTACTCAGgttcagcttc ... tatttcacagATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC
EST: gi|6454593|gb|AW185276.1|AW185276
EST:     CTGTTCACTCATTTAGGATTACCAACTGTGGTGTGGAGGACACTACTCAG                         ATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC
genomic: CTGTTCACTCATTTAGGATTACCAACTGTGGTGTGGAGGACACTACTCAGgttcagcttc ... tatttcacagATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC
EST: gi|209721377|gb|BW654573.1|BW654573
EST:     CTGTTCACTCATTTAGGATTACCAACTGTGGTGTGGAGGACACTACTCAG                         ATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC
genomic: CTGTTCACTCATTTAGGATTACCAACTGTGGTGTGGAGGACACTACTCAGgttcagcttc ... tatttcacagATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC
EST: gi|214006783|gb|DB988332.1|DB988332
EST:     CTGTTCACTCATTTAGGATTACCAACTGTGGTGTGGAGGACACTACTCAG                         ATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC
genomic: CTGTTCACTCATTTAGGATTACCAACTGTGGTGTGGAGGACACTACTCAGgttcagcttc ... tatttcacagATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC
EST: gi|105634473|gb|DW247563.1|DW247563
EST:     CTGTTCACTCATTTAGGATTACCAACTGTGGTGTGGAGGACACTACTCAG                         ATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC
genomic: CTGTTCACTCATTTAGGATTACCAACTGTGGTGTGGAGGACACTACTCAGgttcagcttc ... tatttcacagATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC
EST: gi|208324011|gb|GE121350.1|GE121350
EST:     GTTCACTCTATTTAGGATTAACCAACTGTGGTGTGGAGGACACTACTCAG                         ATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC
genomic: GTTCACTC-ATTTAGGATT-ACCAACTGTGGTGTGGAGGACACTACTCAGgttcagcttc ... tatttcacagATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC
EST: gi|254341544|gb|GR852681.1|GR852681
EST:     CTGTTCACTCATTTAGGATTACCAACTGTGGTGTGGAGGACACTACTCAG                         ATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC
genomic: CTGTTCACTCATTTAGGATTACCAACTGTGGTGTGGAGGACACTACTCAGgttcagcttc ... tatttcacagATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC
EST: gi|254341545|gb|GR852682.1|GR852682
EST:     CTGTTCACTCATTTAGGATTACCAACTGTGGTGTGGAGGACACTACTCAG                         ATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC
genomic: CTGTTCACTCATTTAGGATTACCAACTGTGGTGTGGAGGACACTACTCAGgttcagcttc ... tatttcacagATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC
EST: gi|193686481|gb|FK626868.1|FK626868
EST:     CTGTTCACTCATTTAGGATTACCAACTGTGGTGTGGAGGACACTACTCAG                         ATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC
genomic: CTGTTCACTCATTTAGGATTACCAACTGTGGTGTGGAGGACACTACTCAGgttcagcttc ... tatttcacagATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC
EST: gi|151406914|gb|EV276729.1|EV276729
EST:     AGGATTACCAACTGTGGTGTGGAGGACACTACTCAG                         ATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC
genomic: AGGATTACCAACTGTGGTGTGGAGGACACTACTCAGgttcagcttc ... tatttcacagATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC
EST: gi|22931658|gb|BU548797.1|BU548797
EST:     CTGTTCACTCATTTAGGATTACCAACTGTGGTGTGGAGGACACTACTCAG                         ATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC
genomic: CTGTTCACTCATTTAGGATTACCAACTGTGGTGTGGAGGACACTACTCAGgttcagcttc ... tatttcacagATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC
EST: gi|22927399|gb|BU544538.1|BU544538
EST:     CTGTTCACTCATTTAGGATTACCAACTGTGGTGTGGAGGACACTACNNNG                         ATTCACACTCACATGTGNNACTCCAACTTCAATGACATCATTCACTCAANN
genomic: CTGTTCACTCATTTAGGATTACCAACTGTGGTGTGGAGGACACTACTCAGgttcagcttc ... tatttcacagATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataatgattacacaatcttatatattaatattaatatatcgtgatatttcacagATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATCATAGACATGGATGCTGATGTGATCACCATTGAGAACTCCAGATCAGATG
                             tattaat  putative branch site (score: 2)
            acaatcttatatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcagcttcacttctcatgtttcaatctttaataatgattacacaatcttatatattaatattaatatatcgtgatatttcacagATTCACACTCACATGTGCTACTCCAACTTCAATGACATCATTCACTCAATCATAGACATGGATGCTGATGTGATCACCATTGAGAACTCCAGATCAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG