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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaacatcagtctcttgtatagtatcctcttttttggatagaagttttgaatactattttcctttatgtatcattggacttgatttttactttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTTCTTGGATATGCTGATGAGGTTGTTGAGGAGCGAATTTCTGATGATGCTG

Basic information

species Glycine max
transcript GLYMA08G12970.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G12970.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os04g46620.1 (Oryza sativa), 3'ss of exon 11
--------------------------------------------------------------------------------gcaacatcagtctcttgtatagtatcctctt--ttttggatagaagttt-tgaatactattttcc---tttatgtatcattgg--acttgat----ttttactttgaca--------cagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTTCTTGGATATGCTGATGAGGTTGTTGAGGAGCGAATTTCTGATGATGCTG
                                                                                |    | |    ||   |    || ||   |  |||| |    |||||| |   | ||| |       || |||   ||        ||| |    |  || ||||  |        ||||| || |||||||||||||||||||| || || ||||| ||  |||| || |||||| |||||||||| |||||||||||  ||||| ||||||||| ||
gtatgcctcaccttttgtttatcgagttgtaaccacattggaatacataattgtgcagatgactaatagaattaataaatgatgaagcgacttcccttgcgatacccctgtaattttagtcttaagtttgttgcttctagtcctaatattaatgctacaccaactgtttggtgctgtcctaatttggtagtaaattgcagGTATCTACATTTGCTGATATGGAAGGTGAAGAGACATTCGATTCATCGTTCCTTGGACATGCTGATGAAGTTGTTGAGGAAAGAATTGCTGATGATGATG

upper sequence: GLYMA08G12970.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G110626_T01 (Zea mays), 3'ss of exon 11
gcaacatcagtctcttgtatagtatcctcttttttggatagaagt--tttgaatactattttcctttatgtatcattggacttgatttttactttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTTCTTGGATATGCTGATGAGGTTGTTGAGGAGCGAATTTCTGATGATGCTG
| ||  |||     |  |||| | |     |||| | | ||| |      ||     |   |  ||    | | |     |||||   ||         |||||    |||||||| || |||||||| || |||||||||||  |||| || |||||| |||||||||| ||||| |||||  ||||| ||||||||| ||
gaaatgtcaaaacgtcttataat-ttgaaattttggaacagagggagcacgacagaaaacgttattaggatttaaggtagcttgacaattgaaccttt-cagGTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTCCTTGGACATGCTGATGAAGTTGTGGAGGAAAGAATTGCTGATGATGATG

upper sequence: GLYMA08G12970.1 (Glycine max), 3'ss of exon 11
lower sequence: AT3G20050.1 (Arabidopsis thaliana), 3'ss of exon 11
gcaacatcagtctcttgtatagtatcctcttttttggatagaagttttgaatactattttcctttatgtatcattggacttgat----ttttactttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTTCTTGGATATGCTGATGAGGTTGTTGAGGAGCGAATTTCTGATGATGCTG
                            |||  |  | |||   |||| |||||   | |  |  |  ||  |||  |  | ||    || | ||||     ||||| | || |||||||| ||||| || || ||||||||||| ||| ||   ||||||| |||||||||||||||||| ||| ||||  | ||||||| ||
-------------------------gtacttcctgcgctaggctttttcaatacccatgttgtcaaactaaaatttcaactaatatatttatcctttattttagGTCACCACTTTTGCTGACATGGAGGGCGAAGAAACATTTGATCCAGCTCACCTTGGATCTGCTGATGAGGTTGTTGAAGAGAGAATCGCAGATGATGATG

upper sequence: GLYMA08G12970.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 11
gcaacatcagtctcttgtatagtatcctctt-ttttggatagaagttttgaatact-attttcctttatgtatcattggacttgatttttactttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTTCTTGGATATGCTGATGAGGTTGTTGAGGAGCGAATTTCTGATGATGCTG
 ||     | | | || |      |   ||| | ||  ||   |||     ||||  |  ||   || | |||| ||    ||    ||   | |    ||||| ||||| |||||||| ||||||||||| || ||||||||  |||| |||||||||||||| ||||| ||||| ||||| || ||| | ||||||| ||
-catggatattatgttatgctacttgtgcttatcttttatgatagtcaaagatacccaacttatcttgtttatcgttatg-ttacccttcgatgttctgcagGTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTTCTTGGATATGCAGATGAAGTTGTGGAGGAACGCATTGCAGATGATGATG

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|13562760|gb|BG550980.1|BG550980
EST:     TGCGGAAAGAGGACATGCGCCATGTTGCCAATGCTACTGGTGCAACATTG                         GTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTT
genomic: TGCGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTGgtaggatttt ... tttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTT
EST: gi|14011018|gb|BG725940.1|BG725940
EST:     TGCGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTG                         GTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTT
genomic: TGCGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTGgtaggatttt ... tttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTT
EST: gi|208072471|gb|GD871887.1|GD871887
EST:     TGCGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTG                         GTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTT
genomic: TGCGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTGgtaggatttt ... tttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTT
EST: gi|14125209|gb|BG789656.1|BG789656
EST:     GCCATGTTGCCAAGGCTACTGGTGCAACATTG                         GTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTT
genomic: GCCATGTTGCCAAGGCTACTGGTGCAACATTGgtaggatttt ... tttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTT
EST: gi|20497727|gb|BQ272657.1|BQ272657
EST:     GCCAAGGCTACTGGTGCAACATTG                         GTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTT
genomic: GCCAAGGCTACTGGTGCAACATTGgtaggatttt ... tttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTT
EST: gi|15200044|gb|BI424143.1|BI424143
EST:     GCGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTG                         GTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTT
genomic: GCGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTGgtaggatttt ... tttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTT
EST: gi|18040540|gb|BM308834.1|BM308834
EST:     AAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTG                         GTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTT
genomic: AAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTGgtaggatttt ... tttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTT
EST: gi|193607044|gb|FK556943.1|FK556943
EST:     GACGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTG                         GTCTCAACATTTGCTGATATGGAAGGGGAAGGAAACATTTGAACCAT
genomic: G-CGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTGgtaggatttt ... tttgacacagGTCTCAACATTTGCTGATATGGAAGGGGA-GGAAACATTTGAACCAT
EST: gi|254323555|gb|GR836001.1|GR836001
EST:     TGCGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTG                         GTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTT
genomic: TGCGGAAAGAGGACATGCGCCATGTTGCCAAGGCTACTGGTGCAACATTGgtaggatttt ... tttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgaatactattttcctttatgtatcattggacttgatttttactttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTTCTTGGATATGCTGATGAGGTTGTTGAGGAGCGAATTTCTGATGATGCTG
                                            ctttgac  putative branch site (score: 4)
                                      tttttacttt  CT-rich tract
                                  ttgatttttacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaacatcagtctcttgtatagtatcctcttttttggatagaagttttgaatactattttcctttatgtatcattggacttgatttttactttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTTCTTGGATATGCTGATGAGGTTGTTGAGGAGCGAATTTCTGATGATGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
-caacatc