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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAGgtgcttgcttttctaaattagataattgtttaatggattttaatgtttctgtgtcatactcatgcttaacatgatattgaaattactgtaaacaatatga...

Basic information

species Glycine max
transcript GLYMA10G24350.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G24350.2 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os02g13990.3 (Oryza sativa), 5'ss of exon 6
GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAGgtgcttgcttttctaaattagataat-tgtttaatggattttaatgtttctgtgtcatactcatgcttaacatgatattgaaattactgtaaacaatatga
||||||||||||||||||||||| ||||| |||||||| || |||||||||||      |  | |   |||| |  |  | ||  |  | |||       ||       |||   |  | ||||    ||   | |||||| |  | ||   
GCTGCCATTGTGAATTCTCAGACACTTGAGGAGGTTGCAAGGCTTGAAAAGgtagcatgtcctttcgtttagctcctgcgctttgtacagtttggaacagcta------actatgggctcacatttctttttcactactgtgatgattag--

upper sequence: GLYMA10G24350.2 (Glycine max), 5'ss of exon 7
lower sequence: Vv01s0150g00590.t01 (Vitis vinifera), 5'ss of exon 6
GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAGgtgcttgctttt-ctaaattagat---aattgtttaatggattttaatgtttctgtgtcatactcatgcttaacatgatattgaaattactgtaaacaatatga
|| || ||||||||||| |||||||||||||||||||| || ||||||||||||||  |||||  | |||||||     |||   |  ||  ||| ||||||| |   | ||  | |     | |||| | |   |   | |||         | 
GCCGCAATTGTGAATTCACAGACTCTTGAAGAGGTTGCAAGGCTTGAAAAGgtgctgtcttttgtttaattagacttggatttcattttgtttttcaatgtttattctttatttttaa---caccatgttttcatatgaattgtgcttgggtag-

upper sequence: GLYMA10G24350.2 (Glycine max), 5'ss of exon 7
lower sequence: PP1S49_103V6.1 (Physcomitrella patens), 5'ss of exon 7
GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAGgtgct--tgcttt-tctaaattagataattg----tttaatggattttaatgtttctgtgtcatactcatgcttaacatgatattgaaat-tactgtaaacaatatga----------------------------------------------
 | || ||||  ||||||||||| ||||||||||| || || ||||||||||| ||  ||||   | ||  ||||  |||||    |    |   |||| |  |   | |     | ||||      ||  | ||| |  | | | ||    ||| |                                                
ACCGCTATTGCAAATTCTCAGACGCTTGAAGAGGTCGCCAGGCTTGAAAAGgtactactgctcggtatattttaggaaattgagtttccttttactttttacttgattttagttcaatcattaagttcacaacattcagttatgccgtggtgaatttttatttggcacattgtgcatgcattgagatcttatttttcttttgcag

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|58016033|gb|CX702775.1|CX702775
EST:     CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG                         GCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
genomic: CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAGgtgcttgctt ... atgattgcagGCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
EST: gi|193670506|gb|FK610376.1|FK610376
EST:     CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG                         GCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAN
genomic: CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAGgtgcttgctt ... atgattgcagGCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
EST: gi|151403344|gb|EV273154.1|EV273154
EST:     CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG                         GCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
genomic: CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAGgtgcttgctt ... atgattgcagGCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
EST: gi|213605917|gb|DB983622.1|DB983622
EST:     TTG-CATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG                         GCATTGAAGTCAGGCCTCCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
genomic: CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAGgtgcttgctt ... atgattgcagGCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
EST: gi|192309061|gb|FG999036.1|FG999036
EST:     CTGCCATTGTGAATTTTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG                         GCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
genomic: CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAGgtgcttgctt ... atgattgcagGCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
EST: gi|26268201|gb|CA819264.1|CA819264
EST:     CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG                         GTATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
genomic: CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAGgtgcttgctt ... atgattgcagGCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
EST: gi|10252487|gb|BE820253.1|BE820253
EST:     CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG                         GCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
genomic: CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAGgtgcttgctt ... atgattgcagGCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
EST: gi|58023144|gb|CX709885.1|CX709885
EST:     CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG                         GCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
genomic: CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAGgtgcttgctt ... atgattgcagGCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
EST: gi|15203108|gb|BI425876.1|BI425876
EST:     CTGCCATTGTGAATTCTCAGACTCTTGATTTTGTTGCTAGACTTGAAAAG                         GCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
genomic: CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAGgtgcttgctt ... atgattgcagGCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
EST: gi|23052917|gb|BU577408.1|BU577408
EST:     CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG                         GCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
genomic: CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAGgtgcttgctt ... atgattgcagGCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
EST: gi|6951211|gb|AW423340.1|AW423340
EST:     CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG                         GCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
genomic: CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAGgtgcttgctt ... atgattgcagGCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
EST: gi|13790409|gb|BG653000.1|BG653000
EST:     CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG                         GCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
genomic: CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAGgtgcttgctt ... atgattgcagGCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
EST: gi|193564897|gb|FK520096.1|FK520096
EST:     CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG                         GCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
genomic: CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAGgtgcttgctt ... atgattgcagGCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
EST: gi|8282401|gb|BE019962.1|BE019962
EST:     CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG                         GCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
genomic: CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAGgtgcttgctt ... atgattgcagGCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
EST: gi|192320514|gb|FK011924.1|FK011924
EST:     CTGCCATTGTGAATTTTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG                         GCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
genomic: CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAGgtgcttgctt ... atgattgcagGCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
EST: gi|214008290|gb|DB989832.1|DB989832
EST:     CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG                         GCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
genomic: CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAGgtgcttgctt ... atgattgcagGCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
EST: gi|16344759|gb|BI970354.1|BI970354
EST:     CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG                         GCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
genomic: CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAGgtgcttgctt ... atgattgcagGCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
EST: gi|193602036|gb|FK558817.1|FK558817
EST:     CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAG                         GCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT
genomic: CTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAGgtgcttgctt ... atgattgcagGCATTGAAGTCAGGCCAGCTTCCTGCAGATTTATTGTTGGATAATGTTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCCATTGTGAATTCTCAGACTCTTGAAGAGGTTGCTAGACTTGAAAAGgtgcttgcttttctaaattagataattgtttaatggattttaatgtttctgtgtcatactcatgcttaacatgatattgaaattactgtaaacaatatga

- - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - AAGAGG