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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgggaaaaacacctatggaaactaagttttgtacaattgcatattgatttattttattttattgtttgaattgtttgtttatttaaaaaaacaaacagGAGACTGCACTTAATCATGTTAAGACCGCTGGGCTTCTAGGTGATGGATTTGGTTCCACGCCTGAAATGTGTAAGAAGAACCTGATATGGGTGGTGACTA

Basic information

species Glycine max
transcript GLYMA06G23560.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G23560.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G079308_T01 (Zea mays), 3'ss of exon 9
aatgggaaaaacacctatggaaactaagttttgt-acaattgca-tattgatttattttattttattgtttgaattgtttgtttatttaaaaaaacaaacagGAGACTGCACTTAATCATGTTAAGACCGCTGGGCTTCTAGGTGATGGATTTGGTTCCACGCCTGAAATGTGTAAGAAGAACCTGATATGGGTGGTGACTA
                         | | ||||| ||| |||   | |    || || |   | |  | ||| | | |       |||  |     |  ||||| || |||||||||||||| |||||||||||||| |||||||||||||| || ||||| || || ||| ||||   |||| |  | |||||||| |   
----------------------gtaaggatttgttacatttgaggtgtgagattgttgtggctgag-gattggactatgaaaaagtttggatttg-atccagGAAACGGCACTTAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTCGGCTCCACACCAGAGATGAGTAAACGGAACTTATTCTGGGTGGTTAGCC

upper sequence: GLYMA06G23560.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G406603_T02 (Zea mays), 3'ss of exon 2
aatgggaaaaacacctatggaaactaagttttgtacaattgcatattgatttattttatt-ttattgtttgaattgtttgtttatttaaaaaaacaaacagGAGACTGCACTTAATCATGTTAAGACCGCTGGGCTTCTAGGTGATGGATTTGGTTCCACGCCTGAAATGTGTAAGAAGAACCTGATATGGGTGGTGACTA
                  | ||| | |  |||||  ||||      ||    ||||| |   |   | ||| |   |       |||  |     |  ||||| || ||||| |||||||| |||||||||||||| ||||||||||||||||| ||||| || || ||| ||||    ||| || | |||||||| |   
------------------gtaaaatga--tttgt-taattttgaggtgtgagattttgtagctgaggattggacgatgaaaaagtttggatttg-atccagGAAACGGCACTCAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTTGGCTCCACACCAGAGATGAGTAAACGAAACTTGTTCTGGGTGGTTAGCC

upper sequence: GLYMA06G23560.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G140298_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------------aatggga-aaaacacctatggaaactaag--ttttgtacaattgca-tattgatttattttattttattgtttgaattgtttgtttatttaaaaaaacaaacagGAGACTGCACTTAATCATGTTAAGACCGCTGGGCTTCTAGGTGATGGATTTGGTTCCACGCCTGAAATGTGTAAGAAGAACCTGATATGGGTGGTGACTA
                                                   |||   | || |||  | | |  ||||  |||  |||| |||   | |    || || |   | |  | ||| | | |       |||  |     |  ||||| ||  ||||||||||||| |||||||||||||| |||||||||||||| || ||||| || || ||| ||||   |||| || | |||||||| |   
gtatatgcccgtgtatccatagaaatcctaatgttcggggggctcttttgttggtttagaataccatttgcaggtaaggatttgttacatttgaggtgtgagattgttgtggctgag-gattggactatgaaaaagtttggatttg-atccagGAAACGACACTTAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTCGGCTCCACACCAGAGATGAGTAAACGGAACTTGTTCTGGGTGGTTAGCC

upper sequence: GLYMA06G23560.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G700221_T01 (Zea mays), 3'ss of exon 4
--aatgggaaaaacacctatggaaactaagttttgtacaattgca-tattgatttattttattttattgtttgaattgtttgtttatttaaaaaaacaaacagGAGACTGCACTTAATCATGTTAAGACCGCTGGGCTTCTAGGTGATGGATTTGGTTCCACGCCTGAAATGTGTAAGAAGAACCTGATATGGGTGGTGACTA
    |  ||| | ||  |   |  |   | || | |||| |||   | |    || || |  || |  | ||| | | |       |||  |     |  ||||| ||  ||||||||||||| |||||||||||||| |||||||||||||| || ||||| ||  | ||| ||||   |||| || | |||||||| |   
tggtttagaataccatttgcaggtaaggatttgt-tacatttgaggtgtgagattgttgtggttgag-gattggactatgaaaaagtttggatttg-atccagGAAACGACACTTAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTCGGGTCCACACCAAAGATGAGTAAACGGAACTTGTTCTGGGTGGTTAGCC

upper sequence: GLYMA06G23560.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G330521_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------------aatggga-aaaacacc-tatggaaactaagttttgt-acaattgca-tattgatttattttattttattgtttgaattgtttgtttatttaaaaaaacaaacagGAGACTGCACTTAATCATGTTAAGACCGCTGGGCTTCTAGGTGATGGATTTGGTTCCACGCCTGAAATGTGTAAGAAGAACCTGATATGGGTGGTGACTA
                                                   |||   | || ||| | || |    | | ||||| ||| |||   | |    || || |   | |  | ||| | | |       |||  |     |  ||||| ||  ||||||||||||| |||||||||||||| |||||||||||||| || ||||| || || ||| ||||   |||| || | ||||||       
gtatatgcccgtgtatccatagaaatcctaatgttcgaggggctcttttgttggtttagaataccatttgcaggtaaggatttgtcacatttgaggtgtgagattgttgtggctgag-gattggactatgaaaaagtttggatttg-atccagGAAACGACACTTAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTCGGCTCCACACCAGAGATGAGTAAACGGAACTTGTTCTGGGTG-------

upper sequence: GLYMA06G23560.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G025211_T01 (Zea mays), 3'ss of exon 6
aatgggaaaaacacctatggaaactaagttttgt-acaattgca-tattgatttattttattttattgtttgaattgtttgtttatttaaaaaaacaaacagGAGACTGCACTTAATCATGTTAAGACCGCTGGGCTTCTAGGTGATGGATTTGGTTCCACGCCTGAAATGTGTAAGAAGAACCTGATATGGGTGGTGACTA
                         | | ||||| ||| |||   | |    || || |   | |  | ||| | | |       |||  |     |  ||||| || |||||||||||||| ||||||| |||||| |||||||||||||| || ||||| |  || ||| ||||   |||| || | | |||||| |   
----------------------gtaaggatttgttacatttgaggtgtgagattgttgtggctgag-gattggactatgaaaaagtttggatttg-atccagGAAACAGCACTTAATCATGTGAAGACCGTTGGGCTACTAGGTGATGGATTCGGCTCCACACTAGAGATGAGTAAATGGAACTTGTTCTAGGTGGTTAGCC

upper sequence: GLYMA06G23560.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G08510.1 (Arabidopsis thaliana), 3'ss of exon 2
aatgggaaaaacacctatggaaactaagttttgtacaattgcatattg--atttattttattttattgtttgaattgtttgtttatttaaaaaaacaaacagGAGACTGCACTTAATCATGTTAAGACCGCTGGGCTTCTAGGTGATGGATTTGGTTCCACGCCTGAAATGTGTAAGAAGAACCTGATATGGGTGGTGACTA
            |||  | ||   || | ||   ||  || | | |||  | |  ||| |||    ||| ||||     | ||    | |  |      ||||| || || ||||||||||||||||| |||||  | || || ||||| ||||| || || ||||| |||| |||||||||| |||||||||| || ||| 
----------gtaccatttga--ttatgatt---acggttacctgttgtcactggtttaattgatatgtatgaacaagctcttatgctcatga------cagGAAACGGCGCTTAATCATGTTAAGACTGCTGGATTGCTTGGAGATGGGTTTGGCTCTACACCTGAGATGTTTAAGAAGAACTTGATATGGGTTGTCACTC

upper sequence: GLYMA06G23560.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0016g04480.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------------------aatgggaaaaacacctat--ggaaactaagttttgta---caattgcatattgatttattttattttattgtttgaat-tgtttgtttatttaaaaaaacaaa------------------cagGAGACTGCACTTAATCATGTTAAGACCGCTGGGCTTCTAGGTGATGGATTTGGTTCCACGCCTGAAATGTGTAAGAAGAACCTGATATGGGTGGTGACTA
                                       |  |  || || ||| |    |||  ||   |  ||   ||  ||  | || ||    || |||    ||| | |   || ||| |  || | ||     ||                  ||||| ||||||||||| ||||||| ||| ||||| ||||| |||||||| |||||||| ||||| || ||| | |  | |||||| ||||||||||| ||| 
gtatgaacaattaattcatcacatttatgtggccaaaagaaagagaatacccctgtttaaaaatgaacactcataaggcatctggttgtttatcatcttgattggtgtgtgtaagcctgcttgctccttcacaagcttgaagtttctctccttgtatcgcagGAAACTGCACTTAACCATGTTAGGACTGCTGGTCTTCTGGGTGATGGTTTTGGTTCAACGCCAGAGATGAGCATAAGGAACCTAATATGGGTGGTCACTC

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|15286252|gb|BI470143.1|BI470143
EST:     TTGGCGCAGACAAAACTGCGTCAATAGAGACCTTAATGAATCATTTGCAG                         GAGACTGCACTTAATCATGTTAAGACCGCTGGGCTTCTAGGTGATGGA
genomic: TTGGCGCAGACAAAACTGCGTCAATAGAGACCTTAATGAATCATTTGCAGgtaagatcaa ... aaacaaacagGAGACTGCACTTAATCATGTTAAGACCGCTGGGCTTCTAGGTGATGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatttattttattttattgtttgaattgtttgtttatttaaaaaaacaaacagGAGACTGCACTTAATCATGTTAAGACCGCTGGGCTTCTAGGTGATGGATTTGGTTCCACGCCTGAAATGTGTAAGAAGAACCTGATATGGGTGGTGACTA
 tattgat  putative branch site (score: 3)
     ttattttattttattg  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgggaaaaacacctatggaaactaagttttgtacaattgcatattgatttattttattttattgtttgaattgtttgtttatttaaaaaaacaaacagGAGACTGCACTTAATCATGTTAAGACCGCTGGGCTTCTAGGTGATGGATTTGGTTCCACGCCTGAAATGTGTAAGAAGAACCTGATATGGGTGGTGACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - aaaaaca
- - - - - - - - - -gaaactaa
- - - - - - - - - - - - - - - - - - - -tgcatat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt