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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATCAGGCAGCCTTCATACTGAGCATACCAAAACGCAAATTACTTGATGAAACTCAGGAGACACTGCGTACATCTGCTTTCCCTAGCACCCATGTTAAGgtatttccatgtcttttgtcctgttaatctactattgttatgttgggaagtatgcagttttatcatgcatgttggtgtttgcaaacccatattttggttg...

Basic information

species Glycine max
transcript GLYMA16G04580.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G04580.1 (Glycine max), 5'ss of exon 16
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 5'ss of exon 16
TGATCAGGCAGCCTTCATACTGAGCATACCAAAACGCAAATTACTTGATGAAACTCAGGAGACACTGCGTACATCTGCTTTCCCTAGCACCCATGTTAAGgtatttccatgtcttttgtcctgttaatctactattgttatgttgggaagtatgcagttttatcatgcatgttggtgtttgcaaacccat--attttggttg
||| |||||||| ||||||||||||||||||||||| ||| |  | || |||||||| || || || ||||| ||||| ||||| ||||||||||| |||||||   ||    |||    || || | | |  |      ||||       ||| || |||||    |    |       | || |      ||||  ||| 
TGACCAGGCAGCTTTCATACTGAGCATACCAAAACGTAAAATGATGGACGAAACTCAAGAAACCCTTCGTACCTCTGCCTTCCCAAGCACCCATGTAAAGgtatgaacacacatttgtcactttttaacca--agcaaattgttcaatcccatgaagatttatttcacggccttagagaagaaatcaagatgatttaagttt

upper sequence: GLYMA16G04580.1 (Glycine max), 5'ss of exon 16
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 5'ss of exon 15
TGATCAGGCAGCCTTCATACTGAGCATACCAAAACGCAAATTACTTGATGAAACTCAGGAGACACTGCGTACATCTGCTTTCCCTAGCACCCATGTTAAGgtatttccatgtcttttgtcctgtt-aatctactattgttatgttgggaagtatgcagttttatcatgcatgttggtgtttgcaaacccatatt---ttggttg-------------
 ||||| ||||||||  | |||||  | ||   | | |||  |   ||||||||||| || ||| |||||||||||||||| || ||||| ||||| |||||||      |||  ||  |  ||  |||  |  | | || |     |  ||||  | |    | |    | |||||      ||  |  || |   ||||||              
GGATCAAGCAGCCTTTGTCCTGAGTGTGCCTCGAAGGAAACCAGCCGATGAAACTCAAGAAACATTGCGTACATCTGCTTTTCCAAGCACTCATGTGAAGgtatgctatggtcgatttgcgcgtcgaatgcaaaaatattgtaggttgtcgtatcgattcccgtta-attttttggtcacgataattctgtactgaattggttcgcattatttacag

upper sequence: GLYMA16G04580.1 (Glycine max), 5'ss of exon 16
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 5'ss of exon 15
TGATCAGGCAGCCTTCATACTGAGCATACCAAAACGCAAATTACTTGATGAAACTCAGGAGACACTGCGTACATCTGCTTTCCCTAGCACCCATGTTAAGgtatttccatgtcttttgtcctgttaatctactattgttat--gttgggaagtatgcagttttatcatgca---------tgttggtgtttgcaaacccatattttggttg-------------
 ||||||||||||||  |  ||||  ||||     | ||   |  ||||||||||||||||||  |||| ||||||||||| || ||||| ||||| ||||| | ||  ||| |||  |       |   |    |  |||  ||   |        | | |||| | | |         ||| | | || |   ||  || |  | ||               
GGATCAGGCAGCCTTTGTTTTGAGTGTACCTCGGAGGAAGCCAGCTGATGAAACTCAGGAGACGTTGCGGACATCTGCTTTTCCAAGCACACATGTGAAGgtttgtctttgtttttcttgaaagagaaagagggcttgtattcgtcatgggagtcaaattattatgaagtaactagcttctgtcgtttttagtggactgatttcctcgtgctcgacttctgcag

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|58016025|gb|CX702767.1|CX702767
EST:     AAACTCAGGAGACACTGCGTACATCTGCTTTCCCTAGCACCCATGTTAAG                         GAAAAATGGGCCAAGAATCTCTACATTGCCTCTATATGTTATGGGCGAACT
genomic: AAACTCAGGAGACACTGCGTACATCTGCTTTCCCTAGCACCCATGTTAAGgtatttccat ... gcctttgcagGAAAAATGGGCCAAGAATCTCTACATTGCCTCTATATGTTATGGGCGAACT
EST: gi|208211886|gb|GE013577.1|GE013577
EST:     AAACTCAGGAGACACTGCGTACATCTGCTTTCCCTAGTACTCATGTCAAG                         GAAAAATGGGCAAAGAA
genomic: AAACTCAGGAGACACTGCGTACATCTGCTTTCCCTAGCACCCATGTTAAGgtatttccat ... gcctttgcagGAAAAATGGGCCAAGAA
EST: gi|208290296|gb|GE082724.1|GE082724
EST:     CTAGCACCCATGTTAAG                         G-AAAATGGGCCAAGAATCTCTACATTGCCTCTATATGTTATGGGCGAACT
genomic: CTAGCACCCATGTTAAGgtatttccat ... gcctttgcagGAAAAATGGGCCAAGAATCTCTACATTGCCTCTATATGTTATGGGCGAACT
EST: gi|15203972|gb|BI426749.1|BI426749
EST:     AAACTCAGGAGACACTGCGTACATCTGCTTTCCCTAGCACCCATGTTAAG                         GAAAAATGGGCCAAGAATCTCTACATTGCCTCTATATGTTATGGGCGAACT
genomic: AAACTCAGGAGACACTGCGTACATCTGCTTTCCCTAGCACCCATGTTAAGgtatttccat ... gcctttgcagGAAAAATGGGCCAAGAATCTCTACATTGCCTCTATATGTTATGGGCGAACT
EST: gi|254328402|gb|GR835367.1|GR835367
EST:     AAACTCAGGAGACACTGCGTACATCTGCTTTCCCTAGCACCCATGTTAAG                         GAAAAATGGGCCAAGAATCTCTACATTGCCTCTATATGTTATGGGCGAACT
genomic: AAACTCAGGAGACACTGCGTACATCTGCTTTCCCTAGCACCCATGTTAAGgtatttccat ... gcctttgcagGAAAAATGGGCCAAGAATCTCTACATTGCCTCTATATGTTATGGGCGAACT
EST: gi|208335893|gb|GE138472.1|GE138472
EST:     AAACTCAGGAGACACTGCGTACATCTGCTTTCCCTAGCACCCATGTTAAG                         GAAAAATGGGCCAAGAATCTCTACATTGCCTCTATATGTTATGGGCGAACT
genomic: AAACTCAGGAGACACTGCGTACATCTGCTTTCCCTAGCACCCATGTTAAGgtatttccat ... gcctttgcagGAAAAATGGGCCAAGAATCTCTACATTGCCTCTATATGTTATGGGCGAACT
EST: gi|58019124|gb|CX705866.1|CX705866
EST:     AAACTCAGGAGACACTGCGTACATCTGCTTTCCCTAGCACCCATGTTAAG                         GAAAAATGGGCCAAGAATCTCTACATTGCCTCTATATGTTATGGGCGAACT
genomic: AAACTCAGGAGACACTGCGTACATCTGCTTTCCCTAGCACCCATGTTAAGgtatttccat ... gcctttgcagGAAAAATGGGCCAAGAATCTCTACATTGCCTCTATATGTTATGGGCGAACT
EST: gi|24135575|gb|BU926085.1|BU926085
EST:     AAACTCAGGAGACACTGCGTACATCTGCTTTCCCTAGCACCCATGTTAAG                         GAAAAATGGGCCAAGAATCTCTACATTGCCTCTATATGTTATGGGCGAACT
genomic: AAACTCAGGAGACACTGCGTACATCTGCTTTCCCTAGCACCCATGTTAAGgtatttccat ... gcctttgcagGAAAAATGGGCCAAGAATCTCTACATTGCCTCTATATGTTATGGGCGAACT
EST: gi|57574923|gb|CX547898.1|CX547898
EST:     AAACTCAGGAGACACTGCGTACATCTGCTTTCCCTAGCACCCATGTTAAG                         GAAAAATGGGCCAAGAATCTCTACATTGCCTCTATATGTTATGGGCGAACT
genomic: AAACTCAGGAGACACTGCGTACATCTGCTTTCCCTAGCACCCATGTTAAGgtatttccat ... gcctttgcagGAAAAATGGGCCAAGAATCTCTACATTGCCTCTATATGTTATGGGCGAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATCAGGCAGCCTTCATACTGAGCATACCAAAACGCAAATTACTTGATGAAACTCAGGAGACACTGCGTACATCTGCTTTCCCTAGCACCCATGTTAAGgtatttccatgtcttttgtcctgttaatctactattgttatgttgggaagtatgcagttttatcatgcatgttggtgtttgcaaacccatattttggttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA