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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGGTCCTGGAAGCTGATATTGTTGTCGTTGGTGTTGGAGGAAGGCCTCAAACAGCCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgataccatatccgattatccggaggcttgttaacaggctataaaatgttgttatcccaagtcgggaatagtgattcttgtcatcaatgtcaatgatgccatttgttttggttgcag

Basic information

species Glycine max
transcript GLYMA0169S00210.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA0169S00210.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os08g44340.1 (Oryza sativa), 5'ss of exon 8
CAGGGTCCTGGAAGCTGATATTGTTGTCGTTGGTGTTGGAGGAAGGCCTCAAACAGCCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgataccatatccgattatccggaggcttgttaacaggctataaa----atgttgttatcccaagtcggg--aatagtgattcttgtcatcaatgtcaatgatgccatttgttttggttgcag--------------------------------------------------------
 |  || ||||||||||| |||||| | || ||||| || || ||||| |  ||     |  |||| || || |||| ||||||||||||||||||||||||  ||             ||  | | ||  ||  |  |   |||| |        ||  | ||   |  || ||  | |    |||   |||| |    | |   |    |  |  ||| |     |                                                        
AAACGTGCTGGAAGCTGACATTGTTATTGTCGGTGTCGGTGGCAGGCCACTGACTCATCTCTTCAAGGGTCAAGTTGCAGAGGAGAAGGGTGGAATCAAGgtttgtccggtttctgttcatctttcagattctgctctatctgctacatttgttgcgtgatgattgtatttcaggctattgtccatttgagtcaccctaattagcaactgaaccttctttcgagcttgttcttgcttataccttcgaattagctgaacatttcaaatctgcatgtgtcttccag

upper sequence: GLYMA0169S00210.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os09g39380.1 (Oryza sativa), 5'ss of exon 9
CAGGGTCCTGGAAGCTGATATTGTTGTCGTTGGTGTTGGAGGAAGGCCTCAAACAGCCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgataccatatccgattatccggaggcttgttaacag--gctataaaatgttgttatcccaagtcgggaatagtgattcttgtcatcaatgtcaatgatgccatttgttttggttgcag
||| || || ||||||||||||||||| ||||||||||| || || || |  ||  |  |  | ||||| || ||||  |||||||| |||||||| ||||| |||       |  |   | | | | |||||||   ||||  | |   |    |  || |  |||    | || ||||     ||| | |||  |  | | | |  ||| |           
CAGTGTGCTTGAAGCTGATATTGTTGTTGTTGGTGTTGGGGGCAGACCGCTGACTACTCTCTTTAAAGGTCAAGTTGCTGAGGAGAAAGGTGGAATTAAGgttagt-------ttgcttttaacctgtaggcttgaccacagaaggtgctagggatgtttctatcaaa---gaaacagtg-----tgtaaacaac-tggacgtttc--tttatcaaaa------

upper sequence: GLYMA0169S00210.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv08s0007g03610.t01 (Vitis vinifera), 5'ss of exon 8
CAGGGTCCTGGAAGCTGATATTGTTGTCGTTGGTGTTGGAGGAAGGCCTCAAACAGCCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgataccatatccgattatccggaggcttgttaacaggctataaaatgttgttatcccaagtcgggaatagt-gattcttgtcatcaatgtcaatgatgccatttgttttggttgcag
 ||||| ||||||||||| |||||||| ||||||||||| ||||| || |  ||| | ||| ||||||| ||||| ||||||||||| |||||||| ||||| |||      |||| | || |    ||| | |  |      ||   || | || ||||     |||     | || || |||     | ||| | | |||| | |                
TAGGGTGCTGGAAGCTGACATTGTTGTTGTTGGTGTTGGTGGAAGACCCCTTACAACATTATTCAAAGGACAGGTGGAAGAGGAGAAAGGTGGAATTAAGgttagtaga--tatatgc-atcagatagag-cctcctgtttttcttctaagtatt-ttattattggtccttctttgtagaatctctattttaatat-attgat-caa----------------

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|8403523|gb|BE059157.1|BE059157
EST:     GAGAAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTTTCCGATGTATATGCTGTTGGTGAT
genomic: GAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTTTCCGATGTATATGCTGTTGGTGAT
EST: gi|308098764|gb|HO760505.1|HO760505
EST:     AAACAGCCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTTTCCGATGTATATGCTGTTGGTGAT
genomic: AAACAGCCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTTTCCGATGTATATGCTGTTGGTGAT
EST: gi|21677606|gb|BQ629957.1|BQ629957
EST:     AAACAGCCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTTTCCGATGTATATGCTGTTGGTGAT
genomic: AAACAGCCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTTTCCGATGTATATGCTGTTGGTGAT
EST: gi|151398497|gb|EV268368.1|EV268368
EST:     AAACAGCCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTTTCCGATGTATATGCTGTTGGTGAT
genomic: AAACAGCCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTTTCCGATGTATATGCTGTTGGTGAT
EST: gi|26057696|gb|CA800610.1|CA800610
EST:     AAACAGCCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTTTCCGATGTATATGCTGTTGGTGAT
genomic: AAACAGCCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTTTCCGATGTATATGCTGTTGGTGAT
EST: gi|151398847|gb|EV268718.1|EV268718
EST:     AAACAGCCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTTTCCGATGTATATGCTGTTGGTGAT
genomic: AAACAGCCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTTTCCGATGTATATGCTGTTGGTGAT
EST: gi|19938647|gb|BQ081820.1|BQ081820
EST:     AAACAGCCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTTTCCGATGTATATGCTGTTGGTGAT
genomic: AAACAGCCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTTTCCGATGTATATGCTGTTGGTGAT
EST: gi|23725657|gb|BU760790.1|BU760790
EST:     AAACAGCCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTTTCCGATGTATATGCTGTTGGTGAT
genomic: AAACAGCCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTTTCCGATGTATATGCTGTTGGTGAT
EST: gi|27424500|gb|CA936020.1|CA936020
EST:     AGAGGAGAAGGGTGGAATCAAG                         ACCGATGCTTTCTTCAAAACTAATCTTTCCGATGTATATGCTGTTGGTGAT
genomic: AGAGGAGAAGGGTGGAATCAAGgtcagtgata ... ttggttgcagACCGATGCTTTCTTCAAAACTAATCTTTCCGATGTATATGCTGTTGGTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGGGTCCTGGAAGCTGATATTGTTGTCGTTGGTGTTGGAGGAAGGCCTCAAACAGCCTTAGTCAAAGGGCAGGTTGAAGAGGAGAAGGGTGGAATCAAGgtcagtgataccatatccgattatccggaggcttgttaacaggctataaaatgttgttatcccaagtcgggaatagtgattcttgtcatcaatgtcaatgatgccatttgttttggttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA