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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttattctcaacctggcatttttattatctgtttttaactttctatctgaattctgatgtgttaccatgaataaattttgcacttatttgacagGTCAAAGGCGAACCAAACATATCTTATATCTGTTCTAGGTACTATAGAGCACCTGAGCTTATATTTGGTGCAACTGAGTACACCACGGCCATTGATATCT

Basic information

species Glycine max
transcript GLYMA02G01220.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G01220.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 7
gtatgtttattctcaacctggcatttttattatctgtttttaactttctatctgaattctg--atgtgttaccatgaataaa-ttttgcacttatttgacagGTCAAAGGCGAACCAAACATATCTTATATCTGTTCTAGGTACTATAGAGCACCTGAGCTTATATTTGGTGCAACTGAGTACACCACGGCCATTGATATCT
                        | | || |    ||   |  |    |   |||   ||  ||    |    |   |||  |||||  ||  | | | |||| ||||| |||||||| || ||||| |||||||| |||||||| ||||| || ||||| ||||||||||| ||||| ||||| || || |||||| | |
-----------------------gtatgatcactcattaccagatactcacacgaacattgccattgtctgttgtacctaatcttttgttctattattatagGTAAAAGGAGAACCAAATATTTCTTACATCTGTTCAAGGTACTACAGAGCTCCAGAGCTCATATTTGGTGCTACTGAATACACAACAGCGATTGATGTTT

upper sequence: GLYMA02G01220.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g19150.4 (Oryza sativa), 3'ss of exon 6
gtatgtttattc---tcaacctggc--atttttatt---atctgttttta----actttctatctgaattctgatgtgttaccatgaat----aaattt--tgcacttatttgacagGTCAAAGGCGAACCAAACATATCTTATATCTGTTCTAGGTACTATAGAGCACCTGAGCTTATATTTGGTGCAACTGAGTACACCACGGCCATTGATATCT
||||| |   |    ||||   |    || || | |   || |||||| |    |     |  |  |  | | ||  | || |   |||    ||||||      |    |  | |||| ||||| |||||||| || || |||||||||||||| ||||| ||||| || || || |||||||| || || |||||||| || || |||||| | |
gtatgatcccttgtatcaattagagtaatcttcactcacatatgttttcataaaaaaaggtcacatatcttttataagctatctgaaattcttaaatttaccttgccgtgtccatagGTGAAAGGGGAACCAAATATTTCATATATCTGTTCTAGATACTACAGAGCCCCAGAACTCATATTTGGGGCTACAGAGTACACGACAGCTATTGATGTGT

upper sequence: GLYMA02G01220.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G155836_T01 (Zea mays), 3'ss of exon 7
gtatgtttattctcaacctggcatttttattatctgtttttaactttctatctgaattctgatgtgt-taccatgaataaattttgcacttatt-tgacagGTCAAAGGCGAACCAAACATATCTTATATCTGTTCTAGGTACTATAGAGCACCTGAGCTTATATTTGGTGCAACTGAGTACACCACGGCCATTGATATCT
                    | ||  |||| | |          | |  |   ||||  | ||   | |  | ||  |||||||||    || | |   |||| ||||||||||||||||| ||||| ||||||||||||||||| ||||| || ||||| ||||||||||| ||||| ||||| || ||||||||| | |
--------------------gtatggttataagcaagcaactgatattcacaggaatcttcatccttgttgcgtgcctaaattttgtttgtactgttttagGTAAAAGGCGAACCAAACATTTCTTACATCTGTTCTAGGTACTACAGAGCTCCAGAGCTCATATTTGGTGCTACTGAATACACAACAGCCATTGATGTTT

upper sequence: GLYMA02G01220.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0005g02100.t01 (Vitis vinifera), 3'ss of exon 7
gtatgtttattctcaacctggcatttttat-tatctgtttttaactttctatctgaattctgatgtgttaccatgaataaattttgcacttatttgacagGTCAAAGGCGAACCAAACATATCTTATATCTGTTCTAGGTACTATAGAGCACCTGAGCTTATATTTGGTGCAACTGAGTACACCACGGCCATTGATATCT
||  ||||  |  || ||||| ||  |||| || || | ||| |  |  |   |||  |||||||  |||  || | | | | ||  |   ||||  ||||| ||||| |||   ||||||||||| |||||||||||||||||| |||||||||| |||||||||||||||||||| |||||||| |||||||||||||
gttggttttcttgcatcctggaatgattatgtaactctcttttatatgttgg-tgatatctgatgattta--attagtta-tcttttaaaaattttgcagGTAAAAGGGGAATTGAACATATCTTACATCTGTTCTAGGTACTATCGAGCACCTGAACTTATATTTGGTGCAACTGAATACACCACAGCCATTGATATCT

upper sequence: GLYMA02G01220.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 7
gtatgtttattctcaacctggcatttttattatctgtttttaactttctatctgaattctgatgtgttaccatgaataaattttgcacttatttgacagGTCAAAGGCGAACCAAACATATCTTATATCTGTTCTAGGTACTATAGAGCACCTGAGCTTATATTTGGTGCAACTGAGTACACCACGGCCATTGATATCT
                  |||  |  |||  |   |  |    |||   ||       |||||   || |  |   |   |||       |    |||||| || || || || |||||||| |||||||||||  | |||||  | || || || |||||||||||||||||||| ||||| || ||||| || ||||
-----------------gtgg-gtgcttacaaataggatc---cttggaattcagcagctgat---ttgcgtttcctgcttttcctggcaaaacaacagGTGAAGGGAGAGCCCAACATATCGTATATCTGTTCCCGTTACTACCGTGCTCCGGAACTTATATTTGGTGCAACTGACTACACAACAGCCATCGACATCT

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|17023669|gb|BM094703.1|BM094703
EST:     CTCACACTCACCAGCTAAAGATTTGTGACTTTGGGAGTGCAAAAGTCTTG                         GTCAAAGGCGAACCAAACATATCTTATATCTGTTCTAGGTACTATAGAGCA
genomic: CTCACACTCACCAGCTAAAGATTTGTGACTTTGGGAGTGCAAAAGTCTTGgtatgtttat ... tatttgacagGTCAAAGGCGAACCAAACATATCTTATATCTGTTCTAGGTACTATAGAGCA
EST: gi|207706316|gb|GD686934.1|GD686934
EST:     CTCACACTCACCAGCTAAAGATTTGTGACTTTGGGAGTGCAAAAGTCTTG                         GTCAAAGGCGAACCAAACATATCTTATATCTGTTCTAGGTACTATAGAGCA
genomic: CTCACACTCACCAGCTAAAGATTTGTGACTTTGGGAGTGCAAAAGTCTTGgtatgtttat ... tatttgacagGTCAAAGGCGAACCAAACATATCTTATATCTGTTCTAGGTACTATAGAGCA
EST: gi|207846087|gb|GD820304.1|GD820304
EST:     CTCACACTCACCAGCTAAAGATTTGTGACTTTGGGAGTGCAAAAGTCTTG                         GTCAAAGGCGAACCAAACATATCTTATATCTGTTCTAGGTACTA
genomic: CTCACACTCACCAGCTAAAGATTTGTGACTTTGGGAGTGCAAAAGTCTTGgtatgtttat ... tatttgacagGTCAAAGGCGAACCAAACATATCTTATATCTGTTCTAGGTACTA
EST: gi|12773476|gb|BG238403.1|BG238403
EST:     CTCACACTCACCAGCTAAAGATTTGTGACTTTGGGAGTGCAAAAGTCTTG                         GGCAAAGGCGAACCAAACATATCTTATATCTGTTCT
genomic: CTCACACTCACCAGCTAAAGATTTGTGACTTTGGGAGTGCAAAAGTCTTGgtatgtttat ... tatttgacagGTCAAAGGCGAACCAAACATATCTTATATCTGTTCT
EST: gi|4396096|gb|AI495093.1|AI495093
EST:     CTCACACTCACCAGCTAAAGATNTGTGACTTTTGGAGTGCANAAGTCTTG                         GTCAAAGGCGAACCAAACATATCTTATATCTGTTCTAGGTACTATAGAGCA
genomic: CTCACACTCACCAGCTAAAGATTTGTGACTTTGGGAGTGCAAAAGTCTTGgtatgtttat ... tatttgacagGTCAAAGGCGAACCAAACATATCTTATATCTGTTCTAGGTACTATAGAGCA
EST: gi|27425418|gb|CA936938.1|CA936938
EST:     GTGACTTTGGGAGTGCAAAAGTCTTG                         GTCAAAGGCGAACCAAACATATCTTATATCTGTTCTAGGTACTATAGAGCA
genomic: GTGACTTTGGGAGTGCAAAAGTCTTGgtatgtttat ... tatttgacagGTCAAAGGCGAACCAAACATATCTTATATCTGTTCTAGGTACTATAGAGCA
EST: gi|207807268|gb|GD779339.1|GD779339
EST:     CTCACACTCACCAGCTAAAGATTTGTGACTTTGGGAGTGCAAAAGTCTTG                         GTCAAAGGCGAACCAAACATATCTTATATCTGTTCTAGGTACTATAGAGCA
genomic: CTCACACTCACCAGCTAAAGATTTGTGACTTTGGGAGTGCAAAAGTCTTGgtatgtttat ... tatttgacagGTCAAAGGCGAACCAAACATATCTTATATCTGTTCTAGGTACTATAGAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctatctgaattctgatgtgttaccatgaataaattttgcacttatttgacagGTCAAAGGCGAACCAAACATATCTTATATCTGTTCTAGGTACTATAGAGCACCTGAGCTTATATTTGGTGCAACTGAGTACACCACGGCCATTGATATCT
            ttctgat  putative branch site (score: 3)
                                           cttattt  putative PPT
                           atgaataaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttattctcaacctggcatttttattatctgtttttaactttctatctgaattctgatgtgttaccatgaataaattttgcacttatttgacagGTCAAAGGCGAACCAAACATATCTTATATCTGTTCTAGGTACTATAGAGCACCTGAGCTTATATTTGGTGCAACTGAGTACACCACGGCCATTGATATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT