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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGAAGATTCGCCTCGAGCAGGAGGACGAAGGCGTTCCCAGCACCGCCATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatccatttcccttctcctttcatttgaatgcaatgtgttgttgtcgatgatgaaattaatgttttatccgtgcgctatttgtcgtgaatttgt...

Basic information

species Glycine max
transcript GLYMA09G03470.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G03470.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os02g03060.1 (Oryza sativa), 5'ss of exon 1
TGAAGAAGATTCGCCTCGAGCAGGAGGACGAAGGCGTTCCCAGCACCGCCATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgt---ttatcatccatttcccttctcctttcatttgaatgcaatg-tgttgtt---gtcgatgatgaaattaatgttttatccg-tgcgctatttgtcgtgaatttgt----------------------
| |||||||| ||||| |||||||||||||| ||||| |||  ||||||||| |||||||| || || ||||| |||||||||||| | ||||| || ||||     | |  |    ||||| ||   | ||| |   |     | ||||| |   || | ||     ||| |||  ||    | |  || ||||||      ||||                       
TCAAGAAGATCCGCCTGGAGCAGGAGGACGAGGGCGTCCCCTCCACCGCCATCCGCGAGATCTCGCTGCTCAAGGAGATGCAGCATCGCAACATCGTCAGgtgacccacctcctccctccctgctagctccatctctctctgcggctgttggttgggtgggtgggtggattgatggattgcgtgatttgcgatttgtgaatgctttgggaatttggattgtgccgtgcag

upper sequence: GLYMA09G03470.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G174596_T02 (Zea mays), 5'ss of exon 2
TGAAGAAGATTCGCCTCGAGCAGGAGGACGAAGGCGTTCCCAGCACCGCCATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatccatttcccttctcctttcatttgaatgcaatgtgttgttgtcgatgatgaaattaatgttttatccgtgcgctatt-tgtcgtgaatttgt
| |||||||| |||||||||||||||||||| ||||| |||  ||||||||| |||||||| || || ||||| |||||||||||  | ||||| || ||||    | | | || ||  ||   ||   || | |    | |       | | ||| ||           | |  |  |||||    || |||| |     
TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCCTCCACCGCCATCCGCGAGATCTCCCTCCTCAAGGAGATGCAGCACCGCAACATCGTCAGgta---cgtacgttgccagtcaggttgtgttcggagtgcaggcccccccggctatgctg----------ctcactcacgcgctcccgtgccgtgcag----

upper sequence: GLYMA09G03470.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G008327_T01 (Zea mays), 5'ss of exon 2
TGAAGAAGATTCGCCTCGAGCAGGAGGACGAAGGCGTTCCCAGCACCGCCATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatccatttcccttctcctttcatttgaatgcaatgtgttgttgtcgatgatgaaattaatgttttatccgtgcgctatttgtcg-tgaatttgt-
| |||||||| |||||||||||||||||||| ||||| ||   ||||||||| |||||||| ||||| ||||| |||||| | ||  | ||||| || ||||        | |   |   |  | | ||||   || |    | |||   | | || |   |  |  | ||||     |  | ||  | ||  | ||  |  
TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctgcgcctgctctgccctcctccatt-atattcccccttttgc-attgctgttattacgacggatttagggtcgatcgatcggccgacgcatccgcg

upper sequence: GLYMA09G03470.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G143213_T02 (Zea mays), 5'ss of exon 2
TGAAGAAGATTCGCCTCGAGCAGGAGGACGAAGGCGTTCCCAGCACCGCCATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgttta--------tcatccatttcccttctcctttcatttgaatgcaatgtgttgttgtcgatgatgaaattaatgttttatccgtgcgctatttgtcgtgaatttgt---------------------------------------------------------------------
| |||||||| |||||||||||||||||||| ||||| ||   ||||||||| |||||||| ||||| ||||| |||||| | ||  | ||||| || ||||           | || ||    |       | || ||| |        |    |||     |||| || | ||| |   |  ||  || ||        | |  |                                                                      
TCAAGAAGATCCGCCTCGAGCAGGAGGACGAGGGCGTCCCGTCCACCGCCATCCGCGAGATCTCTCTCCTCAAGGAGATGAACCACGGCAACATCGTCAGgtccgctttggttttatgcaacagcgggtaggtgtcgttttaggatgggattcgtttgct--cgatggaaatgatggtgcgtatgtatgcaatcaagtaaaagtcagacgcaattttgatgctgcgatgccctgtagtgttggtacgctgacaagctttatactctcctaagtgcag

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|120532704|gb|EH260837.1|EH260837
EST:     ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGG-TTTTGAGTA
genomic: ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatc ... tggatgacagGTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|192312501|gb|FK004987.1|FK004987
EST:     ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatc ... tggatgacagGTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|298169145|gb|HO020505.1|HO020505
EST:     ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatc ... tggatgacagGTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|151396909|gb|EV266782.1|EV266782
EST:     ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGGACATTGTTAG                         GTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatc ... tggatgacagGTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|298190796|gb|HO032917.1|HO032917
EST:     ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatc ... tggatgacagGTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|192295604|gb|FG988178.1|FG988178
EST:     ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatc ... tggatgacagGTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|6073117|gb|AW102504.1|AW102504
EST:     ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatc ... tggatgacagGTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|298178270|gb|HO024005.1|HO024005
EST:     ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatc ... tggatgacagGTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|298182098|gb|HO026273.1|HO026273
EST:     ATTCGCGGGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GT-GCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatc ... tggatgacagGTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|192330928|gb|FK023101.1|FK023101
EST:     ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatc ... tggatgacagGTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|9204181|gb|BE330405.1|BE330405
EST:     ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatc ... tggatgacagGTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|213591734|gb|DB973355.1|DB973355
EST:     ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatc ... tggatgacagGTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|24136151|gb|BU926661.1|BU926661
EST:     ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatc ... tggatgacagGTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|151394972|gb|EV264843.1|EV264843
EST:     ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatc ... tggatgacagGTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|13562876|gb|BG551096.1|BG551096
EST:     ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatc ... tggatgacagGTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|151409597|gb|EV279405.1|EV279405
EST:     ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatc ... tggatgacagGTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|192309058|gb|FK001834.1|FK001834
EST:     ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTGCGCAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatc ... tggatgacagGTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|192312486|gb|FK004986.1|FK004986
EST:     ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatc ... tggatgacagGTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|15813934|gb|BI786209.1|BI786209
EST:     ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatc ... tggatgacagGTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
EST: gi|192300023|gb|FG991841.1|FG991841
EST:     ATTCACGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAG                         GTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA
genomic: ATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatc ... tggatgacagGTTGCAGGATGTAGTGCACAGTGAGAAGCGATTGTATCTGGTTTTTGAGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGAAGATTCGCCTCGAGCAGGAGGACGAAGGCGTTCCCAGCACCGCCATTCGCGAGATTTCTCTTCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtttatcatccatttcccttctcctttcatttgaatgcaatgtgttgttgtcgatgatgaaattaatgttttatccgtgcgctatttgtcgtgaatttgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttctc