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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATTCTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTGgtgagttaccgagaatatactgcatagattcacggtagagttatataatgcagaatctagatgaatctcctctatttctttttgtgcttagtaaatctcc...

Basic information

species Glycine max
transcript GLYMA13G44960.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G44960.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os03g27960.1 (Oryza sativa), 5'ss of exon 10
GAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATTCTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAA---AAGTG-
|||||||| || || |||||||||||  | ||||||||  |||||||||| ||||||||||| || || ||||||||||| || ||  |   ||||  ||   ||     | ||  |      | |   |    | |  ||| | |     | |     ||  |||    | |     |   |   |  |  ||||  
GAAGGAACATCGAACTATTTTAAAGGCCTTATGCTTATCTTATGCTATCTCATAGTTGCTGCGAGCTTCTTCGTACATGTTGATCCCGATTCAAgtaagtattttgtttggcattcaacctcgacaactatcccaaaactatttcacc---agttctactggttcttaggtgtaatggtaaattagttatctatctg-

upper sequence: GLYMA13G44960.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G040017_T01 (Zea mays), 5'ss of exon 11
GAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATTCTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTGgtgagttaccgagaatatactgcatagattcacg---gtagagttatataatgcag--aatctagatgaatctcctct----atttctttttgtgcttagtaaatctcc
|| || ||  | || || || |||||  | ||||| || ||||| ||||||||||||||||||||||| || || ||||| || ||  ||    ||||||      || | |  | | ||||  |      |     ||   || | |||  | | ||| | | |  | | |    | |  |  |||| ||  ||   |    
GATGGGACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCATGTTGATCCACAATCAAgtgagt----aggattttcatacttagacccgtttatgctattttccttattccagttagtttagttaatttgcttgtcaagaatcttccttgtact--gttcgtt---

upper sequence: GLYMA13G44960.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G143356_T02 (Zea mays), 5'ss of exon 12
GAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATTCTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTGgtgagttaccgagaatatactgcatagattcacggtagagttatataatgcagaatctagatgaatctcctctatttctttttgtg------cttagtaaatctcc-
|| || ||  | || || || |||||  | ||||| || ||||| ||||||||||||||||||||||| || || || || || ||  ||    ||||||     || || | |    |   | | |  |   | ||| |  | |  | || || |   |    |   || ||| |   |      | | |||  | | | 
GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAAgtgagt-----aggatcttcatagttagtccccctttatgctattt--tccttactccagttagtttagttaatttacttgtcaagaacctcccttgtacttgttct

upper sequence: GLYMA13G44960.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv09s0018g01840.t01 (Vitis vinifera), 5'ss of exon 11
GAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATTCTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTGgtgagtt-accgagaatatactgcatagattcacggtagagttatataatgcagaatctaga-tgaatctc--ctctatttctttttgtgcttagtaaatctcc
||||| || ||||| ||||||||||| ||||||||||||||||||||||| |||||||| ||||| ||||| |||||||| ||||||| ||  ||| ||||   |   | | || | ||   |   |    |   ||| ||  |  |  || | |  | ||| ||   ||||    |  |  ||  | | ||      
GAAGGGACATCAAACTATTTTAAAGGTTTGATGCTTATTCTATGCTATCTCATAGTTGCAGCCAGCTTTTTTGTACATGTTGACCCTACAAAGGgtaagtttgactgaactttatttcaattaaaaaacagacctttacatcgttaatgatattgtctaaatttcatttctacaattgctcctgtcttgaaagg----

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|192319188|gb|FK010668.1|FK010668
EST:     CTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTG                         GTGATGACTAAATATTTAGTGTAGGTATGGCAATTGTCAATGCTGCATTTC
genomic: CTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTGgtgagttacc ... tctggtacagGTGATGACTAAATATTTAGTGTAGGTATGGCAATTGTCAATGCTGCATTTC
EST: gi|213587143|gb|DB982734.1|DB982734
EST:     CTATCTATTAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTG                         GTGATGACTAAATATTTAGTGTAGGTATGGCAATTGTCAATGCTGCATTTC
genomic: CTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTGgtgagttacc ... tctggtacagGTGATGACTAAATATTTAGTGTAGGTATGGCAATTGTCAATGCTGCATTTC
EST: gi|192315878|gb|FK005709.1|FK005709
EST:     CTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTG                         GTGATGACTAAATATTTAGTGTAGGTATGGCAATTGTCAATGCTGCATTTC
genomic: CTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTGgtgagttacc ... tctggtacagGTGATGACTAAATATTTAGTGTAGGTATGGCAATTGTCAATGCTGCATTTC
EST: gi|151402628|gb|EV272441.1|EV272441
EST:     CTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTG                         GTGATGACTAAATATTTAGTGTAGGTATGGCAATTGTCAATGCTGCATTTC
genomic: CTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTGgtgagttacc ... tctggtacagGTGATGACTAAATATTTAGTGTAGGTATGGCAATTGTCAATGCTGCATTTC
EST: gi|192319189|gb|FK010669.1|FK010669
EST:     CTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTG                         GTGATGACTAAATATTTAGTGTAGGTATGGCAATTGTCAATGCTGCATTTC
genomic: CTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTGgtgagttacc ... tctggtacagGTGATGACTAAATATTTAGTGTAGGTATGGCAATTGTCAATGCTGCATTTC
EST: gi|192328537|gb|FK020769.1|FK020769
EST:     CTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTA                         GTGATGACTAAATATTTAGTGTAGGTATGGCAATTGTCAATGCTGCATTTC
genomic: CTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTGgtgagttacc ... tctggtacagGTGATGACTAAATATTTAGTGTAGGTATGGCAATTGTCAATGCTGCATTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATTCTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTGgtgagttaccgagaatatactgcatagattcacggtagagttatataatgcagaatctagatgaatctcctctatttctttttgtgcttagtaaatctcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC