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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTCTTGAAGATCTTCAGCGGATCCATGCAGCTGAAGAGCTTGCTGTTGAGGAAGGAGGTGGAGTTGAAATGCATGTCCTTGAAGATGCTGGCCACTGGgtatgtactataatgtcatacagttattattttagagcatgatctcctccaatacgtgtgtttcagcttaggacgtctatgctcatgatatctaaaatac...

Basic information

species Glycine max
transcript GLYMA11G01670.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G01670.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os01g66240.1 (Oryza sativa), 5'ss of exon 12
GGCTCTTGAAGATCTTCAGCGGATCCATGCAGCTGAAGAGCTTGCTGTTGAGGAAGGAGGTGGAGTTGAAATGCATGTCCTTGAAGATGCTGGCCACTGGgtatgtactataatgtcatacagttatt-----attttagagcatgatctcctccaatacgtgtgtttcagcttaggacgtctatgctc-atgatatctaaaatac
||||||||| ||||| ||| | || ||| | ||||| || || ||||  || || || || |||||||||||||| || |||||||||||||| || ||||||||     ||    | |  | ||| |     || ||   |||  ||   |   || |   ||  |       |  |    ||| ||  |  | | || |     
GGCTCTTGATGATCTCCAGAGAATTCATACTGCTGAGGAACTGGCTGCAGATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGATGCTGGACATTGGgtatgcttactatatccttgtaattactcctagatcttctggcagcattctccataagata-gtactgtgatgaaaaagtagtattctttactacagctta-----

upper sequence: GLYMA11G01670.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G007160_T02 (Zea mays), 5'ss of exon 12
GGCTCTTGAAGATCTTCAGCGGATCCATGCAGCTGAAGAGCTTGCTGTTGAGGAAGGAGGTGGAGTTGAAATGCATGTCCTTGAAGATGCTGGCCACTGGgtatgtactataatgtcatacagttattattttagagcatgatctcctccaatacgtgtgtttcagc-ttaggacgtctatgctcatgatatctaaaatac
|||||| ||||| || ||  | ||  || | || || ||  | ||||  || || || || |||||||||||||| || |||||||| ||||| |||||||||| |        | | |    || || ||||  |  || |   |  | ||      | ||| |   || | | || |     ||               
GGCTCTCGAAGACCTCCAAAGAATTTATACTGCGGAGGAATTAGCTGCAGATGAGGGTGGAGGAGTTGAAATGCACGTGCTTGAAGACGCTGGACACTGGgtattttggcacccgccttttttttctttttttttacaataaag-ctgcaaaccaaaatatttgattatttgcatgtttccttccag--------------

upper sequence: GLYMA11G01670.1 (Glycine max), 5'ss of exon 12
lower sequence: AT4G10030.1 (Arabidopsis thaliana), 5'ss of exon 12
GGCTCTTGAAGATCTTCAGCGGATCCATGCAGCTGAAGAGCTTGCTGTTGAGGAAGGAGGTGGAGTTGAAATGCATGTCCTTGAAGATGCTGGCCACTGGgtatgtactataatgtcatacagttattattttagagcatgatctcctccaatacgtgtgtttcagcttaggacgtctatgctcatgatatctaaaatac
||| || ||||| |||||||| ||||| || ||||||||||| ||   ||| ||||| ||||| || |||||||||||| | |||||||| || || ||||||  |   |  |    |  ||  |  |  |  |  || | ||||     | |   | |  |  | |     ||   ||| |   |  | ||        
GGCCCTAGAAGACCTTCAGCGAATCCACGCCGCTGAAGAGCTAGCCTCTGAAGAAGGCGGTGGTGTAGAAATGCATGTCTTGGAAGATGCCGGTCATTGGgtaaattaaacta-actacgcatctgcttctacattgcttcatctttgttattctat-tactgaacccgtaaaccagtattccggttgtgtccgttcag-

upper sequence: GLYMA11G01670.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv18s0001g06010.t01 (Vitis vinifera), 5'ss of exon 12
GGCTCTTGAAGATCTTCAGCGGATCCATGCAGCTGAAGAGCTTGCTGTTGAGGAAGGAGGTGGAGTTGAAATGCATGTCCTTGAAGATGCTGGCCACTGGgtatgta-ctataatgtcatacagttattatt-ttagagcatgatctcctccaatacgtgtgtttcagcttagg--acgtctatgctcatgatatctaaaatac
||| ||||| ||||||||| |||| ||||| ||||| || || |||| ||| ||||| |||||||| ||||||||||| |||||||||||||| || |||||||||  || | |  |  | || || |||   |||     ||| | |  | | ||      || ||| |  |   | |  |    |  |  || | ||||   
GGCCCTTGAGGATCTTCAGAGGATTCATGCTGCTGAGGATCTGGCTGCTGATGAAGGTGGTGGAGTGGAAATGCATGTTCTTGAAGATGCTGGTCATTGGgtatgtggctctcacctgcttcaattcttacaattatcttctgaac-cacctagtatacactttacaggtgtgcttatgcttgcatttcttttaacaaaaa---

upper sequence: GLYMA11G01670.1 (Glycine max), 5'ss of exon 12
lower sequence: PP1S90_13V6.1 (Physcomitrella patens), 5'ss of exon 12
GGCTCTTGAAGATCTTCAGCGGATCCATGCAGCTGAAGAGCTTGCTGTTGAGGAAGGAGGTGGAGTTGAAATGCATGTCCTTGAAGATGCTGGCCACTGGgtatgtactataatgtcatacagttattattttagagca-tgatctcctcc-----aatacgtgtgtttcagcttaggacgtctatgctcatgatatctaaaatac
||| |  |||||| | ||  |||| |||   |||||  || ||||       ||||| |  |||||  |||||||||| ||||| |||||||| ||||||||||||    | |  |  | |   | || |||| |  |  | ||||  ||      |  || |  |||| |  ||   |     |   |  |||||  |   |   
GGCCCACGAAGATGTGCAAAGGATTCATATGGCTGAGCAGATTGCATCCACAGAAGGTGCAGGAGTGCAAATGCATGTGCTTGAGGATGCTGGTCACTGGgtatgtttcctca--ttgtgcttgttttgttttggttcgcttatcttttcttaaagagcacctacgtttaaagttta-attcagaccttggtgatagttttga---

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|7028222|gb|AW458005.1|AW458005
EST:     GGAAGGAGGTGGAGTTGAAATGCATGTCCTTGAAGATGCTGGCCCACTGG                         GTGCATACTGATAACCCGGATGGACTCTTCAGGATACTGTCATCATCTTT
genomic: GGAAGGAGGTGGAGTTGAAATGCATGTCCTTGAAGATGCTGG-CCACTGGgtatgtacta ... cgatcaacagGTGCATACTGATAACCCGGATGGACTCTTCAGGATACTGTCATCATCTTT
EST: gi|209722602|gb|BW682691.1|BW682691
EST:     AGGAAGGAGGTGGAGTTGAAATGCATGTCCTTGAAGATGCTGGCCACTGG                         GTGCATACTGATAACCCGGATGGACTCTTCAGGATACTGTCATCATCTTTC
genomic: AGGAAGGAGGTGGAGTTGAAATGCATGTCCTTGAAGATGCTGGCCACTGGgtatgtacta ... cgatcaacagGTGCATACTGATAACCCGGATGGACTCTTCAGGATACTGTCATCATCTTTC
EST: gi|16346287|gb|BI971882.1|BI971882
EST:     AGGAAGGAGGTGGAGTTGAAATGCATGTCCTTGAAGATGCTGGCCACTGG                         GTGCATACTGATAACCCGGATGGACTCTTCAGGATACTGTCATCATCTTTC
genomic: AGGAAGGAGGTGGAGTTGAAATGCATGTCCTTGAAGATGCTGGCCACTGGgtatgtacta ... cgatcaacagGTGCATACTGATAACCCGGATGGACTCTTCAGGATACTGTCATCATCTTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTCTTGAAGATCTTCAGCGGATCCATGCAGCTGAAGAGCTTGCTGTTGAGGAAGGAGGTGGAGTTGAAATGCATGTCCTTGAAGATGCTGGCCACTGGgtatgtactataatgtcatacagttattattttagagcatgatctcctccaatacgtgtgtttcagcttaggacgtctatgctcatgatatctaaaatac

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcctcc