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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCATGATATCACAAGGAGCTTACATTTATGTGTGTGGTGATGCCAAGGGCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAGgtatatgtttttaaataataaaatcttgaattgccttaaattgatggcatgggtgattgcgaatttggtgccttatattagtggctgcttctacctgcag...

Basic information

species Glycine max
transcript GLYMA17G07050.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G07050.1 (Glycine max), 5'ss of exon 17
lower sequence: LOC_Os08g14570.1 (Oryza sativa), 5'ss of exon 16
GAGCATGATATCACAAGGAGCTTACATTTATGTGTGTGGTGATGCCAAGGGCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAGgtatatgtttt-taaataataaaatcttg--aattgccttaaattgatggcatgggtgattgcgaatttggtgccttatattagtggctgcttctacc--tgcag
|  |||||| || || || | ||||||||| || |||||||||||||| ||||||||||| ||||||||  | |  || ||||| ||| | || || ||||||| | | |   |   | || |  ||||   ||    ||   || ||    |  || | |     | |||     || |||  || | | || |  |  | |||
GGACATGATCTCCCAGGGTGGTTACATTTACGTCTGTGGTGATGCCAAAGGCATGGCCAGAGATGTACATAGAGTTCTCCACACCATTGTACAGGAACAGgtatttttctcacagccattacacacttgctgataaaatttgtttcattctgtccgtcagtatatttctggca---taaattgatgacggttttttgcgttacag

upper sequence: GLYMA17G07050.1 (Glycine max), 5'ss of exon 17
lower sequence: GRMZM2G144407_T01 (Zea mays), 5'ss of exon 17
GAGCATGATATCACAAGGAGCTTACATTTATGTGTGTGGTGATGCCAAGGGCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAGgtatatgtttttaaa--taataaaatcttgaattgccttaaattgatggcatgggtgattgcgaatttggtgccttatattagtggctgcttctacctgcag----------------------------
|  |||||| || ||||| |||||||| ||||| |||||||||||||| ||||||||||| ||||||||  | |  || ||||| ||| | || |||||||||  || | |||    || |  || ||| ||      ||  |  |    ||   |   |||   |||    |  |  ||  || | || |||| | ||||                             
GGACATGATCTCCCAAGGTGCTTACATCTATGTCTGTGGTGATGCCAAAGGCATGGCCAGAGATGTACATAGAGTTCTCCACACCATTGTTCAGGAGCAGgtac-tgatcttaggcctagttgaaactttaaaaaaaatacttgcacactataaata--tgcttcttt----ctctgcatctgttgttgtttct-catgcaattgtcgacaatttttttttggcgaacag

upper sequence: GLYMA17G07050.1 (Glycine max), 5'ss of exon 17
lower sequence: AC217947.4_FGT002 (Zea mays), 5'ss of exon 16
GAGCATGATATCACAAGGAGCTTACATTTATGTGTGTGGTGATGCCAAGGGCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAGgtatatgtttttaaa--taataaaatcttgaat----tgccttaa----attgatg-gcatgggtgattgcgaatttggtgccttat--attagtggctgcttctacctg-cag
|  |||||| || ||||| |||||||| ||||| |||||||| ||||| ||||||||||| || |||||  | |  || || || ||| | || |||||||||  || |  ||    || |  || ||| ||     | | |  |    || |||| || |   |   |||   |   ||  || ||  ||| || | |  || |  |   |||
GGACATGATCTCCCAAGGTGCTTACATCTATGTCTGTGGTGACGCCAAAGGCATGGCCAGAGACGTACATAGAGTTCTCCATACCATTGTTCAGGAGCAGgtac-tgatcctaggcctagttcaaacttaaaaaaaatacttagatactatagatgtgcttctatctctgcctctgctgtttctcatgcatttgtcgatatttttggcaatcag

upper sequence: GLYMA17G07050.1 (Glycine max), 5'ss of exon 17
lower sequence: Vv11s0052g00880.t01 (Vitis vinifera), 5'ss of exon 17
GAGCATGATATCACAAGGAGCTTACATTTATGTGTGTGGTGATGCCAAGGGCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAGgtatatgtttttaaataa---taaaatct-tgaattgccttaaattgatggcatgggtgattgcgaatttggtgccttatattagtggctgcttctacctgcag
||   | || || || ||||  ||||||||||| |||||||||||||| |||||||| |||||||| ||| |  | || || || || |||||||||||||||  |   |  ||||||    || |||  ||||| | |  |||| | || |       |    ||         | ||   || ||  | |  | |||     
GAATGTAATTTCTCAGGGAGGCTACATTTATGTCTGTGGTGATGCCAAAGGCATGGCAAGGGATGTCCACAGAACTCTTCATACCATCTTGCAAGAGCAGgtacgttcatacaaataaaatcaacatccctgaatcgac--aaatggctgcctctacctaccttgatgaaatcatcatac-ctaatgtttaccaccacccatt-

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|4313742|gb|AI460861.1|AI460861
EST:     GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAGgtatatgttt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|15203188|gb|BI425956.1|BI425956
EST:     GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAGgtatatgttt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|15202467|gb|BI425417.1|BI425417
EST:     GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAGgtatatgttt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|21594304|gb|BQ610119.1|BQ610119
EST:     GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAGgtatatgttt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|214006112|gb|DB990465.1|DB990465
EST:     GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAGgtatatgttt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|193515096|gb|FK467506.1|FK467506
EST:     GATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAGgtatatgttt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|8402113|gb|BE057747.1|BE057747
EST:     GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAGgtatatgttt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|16346078|gb|BI971673.1|BI971673
EST:     GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATATTTTCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAGgtatatgttt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|58024838|gb|CX711579.1|CX711579
EST:     GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAGgtatatgttt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|7147143|gb|AW509065.1|AW509065
EST:     GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAGgtatatgttt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|254341893|gb|GR853030.1|GR853030
EST:     GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAGgtatatgttt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|254346951|gb|GR856673.1|GR856673
EST:     GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAGgtatatgttt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|58020989|gb|CX707731.1|CX707731
EST:     GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAGgtatatgttt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|14258698|gb|BG881606.1|BG881606
EST:     GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAGgtatatgttt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|9258034|gb|BE346181.1|BE346181
EST:     GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAGgtatatgttt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCATGATATCACAAGGAGCTTACATTTATGTGTGTGGTGATGCCAAGGGCATGGCCAGGGATGTACACCGCGCCCTGCACACAATTTTGCAAGAGCAGgtatatgtttttaaataataaaatcttgaattgccttaaattgatggcatgggtgattgcgaatttggtgccttatattagtggctgcttctacctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG