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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACCCAAGAACCCATATATTGGTAGGTGTCTTCTCAACACAAAGATCACTGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGGgtaggtgcttaaatatttttctctcaattttacctttttttcccgtcactaatcataacatggatcgcttttaaaaagtcagggtttttgggtaaattaaaaaaaatatgtatatttgtattatttcag

Basic information

species Glycine max
transcript GLYMA11G08230.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G08230.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G168143_T01 (Zea mays), 5'ss of exon 1
AAACCCAAGAACCCATATATTGGTAGGTGTCTTCTCAACACAAAGATCACTGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGGgtaggtgcttaaatatttttctctcaattttacctttttttcccgtcactaatcataacatggatcgcttttaaaaagtcagggtttttgggtaaattaaaaaaaatatgtatatttgtattatttcag
|| |||||| | || ||  | || ||||| || |||||||| |||||||| || || || || || || || || |||||||||||||||||||| || ||||||| || |  |       ||  ||    | ||  ||||  |  |     || |    |  |  ||| |     | ||      | ||  ||||     |   |      |||       |   |||
AAGCCCAAGGAGCCGTACGTCGGCAGGTGCCTCCTCAACACCAAGATCACCGGCGACGACGCGCCGGGGGAGACGTGGCACATGGTCTTCAGCACCGAAGgtaggtactgaggt-------tcaaaaaaaaatctgatttttgctgcctcgttcgttcgttcaactgctgt-----attcgtatcgtatgtataaacgctgatggacgcacgtatgcaccgcacg-cag

upper sequence: GLYMA11G08230.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv18s0001g14450.t01 (Vitis vinifera), 5'ss of exon 2
AAACCCAAGAACCCATATATTGGTAGGTGTCTTCTCAACACAAAGATCACTGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGGgt-aggtgcttaa--atatttttctctc-----aatt------ttacctttttttcccgtcactaatcataacatggatcgcttttaaaaagtca-gggtttttgggtaaattaaaaaa--aatatgtatatttgtattatttcag
| ||||||||| || || || || |  ||||| |||||||| ||||| ||||| || ||||| || ||||| || ||||||||||| |||| |||||||||| || | ||| |  ||   | ||||||     ||||      || | ||||| |    ||  | || ||    | | | | | | || || | | ||| || |   |  |||  |         || ||| |  |  ||   |||
AGACCCAAGAATCCTTACATCGGAAAATGTCTCCTCAACACCAAGATTACTGGAGACGATGCTCCAGGAGAGACCTGGCACATGGTATTCACCACTGAGGgtcagcttctttaccatgcctatctctcttgataattgaaggatttcttttttcttttttcttttataattttttag-tagttgtgaataaattatgggattattcttgcatttgattgttgcgttggataatc-tgataaaacag

upper sequence: GLYMA11G08230.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv04s0023g03510.t01 (Vitis vinifera), 5'ss of exon 2
AAACCCAAGAACCCATATATTGGTAGGTGTCTTCTCAACACAAAGATCACTGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGGgtag-gtgcttaaatatttttctctcaattttacctttttttcccgtcactaatcataacatggatcgcttttaaaaagtcagggtttttgggtaaattaaaaaaaatatgtat--atttgtattatttcag-----------------
|| || ||||| || || ||||| || |||||||||||||| |||||||| ||||||||||| ||||||||||| |||||||||||||||||||| |||||||  |  |||  | ||  | |    |  | ||  ||       |  ||  || |||  | |  ||    | |  ||  |  | ||||||  |   ||        || | | |  |  || |||   |  |                 
AAGCCTAAGAATCCTTACATTGGCAGATGTCTTCTCAACACTAAGATCACCGGGGATGATGCTCCTGGAGAAACATGGCACATGGTCTTCAGCACCGAGGgtaacgaccttttacatgctccatgta--tatatattggaaattcaacag-aaccat--ctttaattttatgtggaacttttgagttttttagctgatcgctcctgatttcttttgagctgaatttgattggtcaattgggttgctcag

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|213619649|gb|DB965595.1|DB965595
EST:     TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGG                         GAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
genomic: TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGGgtaggtgctt ... attatttcagGAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
EST: gi|120534406|gb|EH262539.1|EH262539
EST:     TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGG                         GAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
genomic: TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGGgtaggtgctt ... attatttcagGAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
EST: gi|120531288|gb|EH259421.1|EH259421
EST:     TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGG                         GAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
genomic: TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGGgtaggtgctt ... attatttcagGAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
EST: gi|213591411|gb|DB955731.1|DB955731
EST:     TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGG                         GAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
genomic: TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGGgtaggtgctt ... attatttcagGAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
EST: gi|192306166|gb|FG995030.1|FG995030
EST:     TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGG                         GAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
genomic: TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGGgtaggtgctt ... attatttcagGAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
EST: gi|12773001|gb|BG237928.1|BG237928
EST:     TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGG                         GAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
genomic: TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGGgtaggtgctt ... attatttcagGAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
EST: gi|16105591|gb|BI893331.1|BI893331
EST:     TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGG                         GAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
genomic: TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGGgtaggtgctt ... attatttcagGAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
EST: gi|19452306|gb|BM953716.1|BM953716
EST:     TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGG                         GAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
genomic: TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGGgtaggtgctt ... attatttcagGAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
EST: gi|298172788|gb|HO020342.1|HO020342
EST:     TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGG                         GAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
genomic: TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGGgtaggtgctt ... attatttcagGAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
EST: gi|120531728|gb|EH259861.1|EH259861
EST:     TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGG                         GAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
genomic: TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGGgtaggtgctt ... attatttcagGAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
EST: gi|209725524|gb|BW677823.1|BW677823
EST:     TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGG                         GAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
genomic: TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGGgtaggtgctt ... attatttcagGAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
EST: gi|120531421|gb|EH259554.1|EH259554
EST:     TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGG                         GAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
genomic: TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGGgtaggtgctt ... attatttcagGAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
EST: gi|18693009|gb|BM521857.1|BM521857
EST:     TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGG                         GAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG
genomic: TGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGGgtaggtgctt ... attatttcagGAGAAGTTCCTTACAGAGAAGGACAATCAATCGGGGTAATTCCTGATGGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACCCAAGAACCCATATATTGGTAGGTGTCTTCTCAACACAAAGATCACTGGGGATGATGCACCTGGAGAAACTTGGCACATGGTCTTCAGCACTGAGGgtaggtgcttaaatatttttctctcaattttacctttttttcccgtcactaatcataacatggatcgcttttaaaaagtcagggtttttgggtaaattaaaaaaaatatgtatatttgtattatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA