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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcattttttttttaatgttcaacacgcaagtttgttaagagttggttggtatttgggtattcaaccttttttttcccatgttgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCTGAATATGACCCTGTAGCCAAGATATCAATTATTCCTCGTGGCCAAGCTGGTGGTCTCACATTTTT

Basic information

species Glycine max
transcript GLYMA06G02200.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G02200.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g51029.1 (Oryza sativa), 3'ss of exon 2
gtatgcattttttttttaatgttcaacacgcaagttt-gttaagagttggttggtatttgggtattc--aaccttttttttcccatgttgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCTGAATATGACCCTGTAGCCAAGATATCAATTATTCCTCGTGGCCAAGCTGGTGGTCTCACATTTTT
   |  || || |    | | || |||  |  | ||  | | | | |    |||| |   |   |||  || |  |||||   | | |  |||| |||||||||| ||||| || || |||||  | |||||||||||||||||||| || ||||| || || ||||||||||| ||||||||||| |||||||| ||
--gtaaatcttgtcacca-tatt-aacttgtgacttgagctgaaattatcctggtgtgcagaggttcctaatccatttttgaacttttcaatttgcagAGGCTGGTCATGCCCTTGTTGGTGCCCTCATGCCTGAATATGACCCTGTTGCTAAGATTTCCATCATTCCTCGTGGTCAAGCTGGTGGACTCACATTCTT

upper sequence: GLYMA06G02200.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G126361_T03 (Zea mays), 3'ss of exon 3
gtatgcattttttttttaatgttcaacacgcaagtttgttaagagttggttggtatttgggtattcaaccttttttttcccatgttgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCTGAATATGACCCTGTAGCCAAGATATCAATTATTCCTCGTGGCCAAGCTGGTGGTCTCACATTTTT
|||    || |    || || ||  |  |  |||||||      | |    ||   |  |||    || || || ||   | |    ||||  ||||||||||||||| || || || ||  | ||||| || ||||| || ||||||||||| || || || ||||||||||| |||||||| |||||||| ||
gtaaatgttgtcaaatttatattataaccataagtttgactcccgcttacggg-gctcaggttcctaatctgttgttgaactttggaatttgtagAGGCTGGCCATGCCCTTGTCGGCGCCCTCATGCCAGAGTATGATCCAGTAGCCAAGATTTCCATCATCCCTCGTGGCCAGGCTGGTGGACTCACATTCTT

upper sequence: GLYMA06G02200.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G42270.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgcattttttttttaatgttcaacacgcaagtttgttaagagttggttggtat-ttgggtattcaaccttttttttcccatgttgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCTGAATATGACCCTGTAGCCAAGATATCAATTATTCCTCGTGGCCAAGCTGGTGGTCTCACATTTTT
              ||  ||  |    |  | || |  ||      |  ||  | | |||   | |||  || ||   |   ||  | |||| |||||||||| |||||| |||| |||||  | ||||| || ||||| || || ||||||||||| |||||||| ||||||||||||||||| ||||| |||||
-------------gttagatactactgatcctagctacttcttgtgttattattgtgttgaccactca--ctgttcaataaaattgtaatttgcagAGGCTGGGCATGCTTTAGTTGGTGCACTTATGCCGGAGTATGATCCAGTGGCCAAGATATCGATTATTCCACGTGGCCAAGCTGGTGGGCTCACCTTTTT

upper sequence: GLYMA06G02200.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G50250.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgcattttttttttaatgttcaacacgcaagtttgttaagagttggttggtatttgggtattcaaccttttttttcccatgttgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCTGAATATGACCCTGTAGCCAAGATATCAATTATTCCTCGTGGCCAAGCTGGTGGTCTCACATTTTT
       ||    |||||     | | | | ||    ||    || |||  | |  |||  |  | | |   |    |    | |  |||| |||||||||| |||||||||||||||||| | ||||| |||||||| || || || ||||| || || ||||||||||||||||||||||| ||||| |||||
------gttagcattttatctaactatatgtaatggagtacgcagctgg--gattcttgttttctgaccacctcaaatgaattttaaatttacagAGGCTGGTCATGCTCTAGTGGGTGCTCTTATGCCAGAATATGATCCGGTTGCAAAGATTTCTATCATTCCTCGTGGCCAAGCTGGTGGGCTCACTTTTTT

upper sequence: GLYMA06G02200.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g00190.t01 (Vitis vinifera), 3'ss of exon 2
gtatgcatttttttttta-atgttcaacacgcaagtttgttaagagttggttggtatttgggtattcaaccttttttt----tcccatgttgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCTGAATATGACCCTGTAGCCAAGATATCAATTATTCCTCGTGGCCAAGCTGGTGGTCTCACATTTTT
|||   |          | |    |      || || |  | |   ||| |     ||||||| ||  | || ||| |    |  ||  |  |||| |||||||||| |||||  | || |||||  | |||||||||||||||||||| ||||||||||| || ||||| ||||||||||| |||||||| || |||||
gtacataaaagagaacaacacaagctttgtacaggtct-ctgatgcttgttattgttttgggtgttttaactctttatgtgtttgcacttgaatttgcagAGGCTGGGCATGCATTGGTCGGTGCACTTATGCCTGAATATGACCCTGTGGCCAAGATATCCATCATTCCCCGTGGCCAAGCAGGTGGTCTTACCTTTTT

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|193305281|gb|FK273214.1|FK273214
EST:     GAAAAATGCTGTAGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATG                         AGGCTGGCCATGCT
genomic: GAAAAATGCTGTAGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATGgtatgcattt ... tgattttcagAGGCTGGCCATGCT
EST: gi|192314907|gb|FK010725.1|FK010725
EST:     GAAAAATGCTGTAGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATG                         AGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCTGAATATGGCCCTGTAG
genomic: GAAAAATGCTGTAGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATGgtatgcattt ... tgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCTGAATATGACCCTGTAG
EST: gi|151393635|gb|EV263510.1|EV263510
EST:     GAAAAATGCTGTAGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATG                         AGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCTGAATATGACCCTGTAG
genomic: GAAAAATGCTGTAGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATGgtatgcattt ... tgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCTGAATATGACCCTGTAG
EST: gi|20811366|gb|BQ295844.1|BQ295844
EST:     GAAAAATGCTGTAGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATG                         AGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCTGAATATGACCCTGTAG
genomic: GAAAAATGCTGTAGTCTCAGATGAGAAGAAGAAATTAGTAGCCTATCATGgtatgcattt ... tgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCTGAATATGACCCTGTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagagttggttggtatttgggtattcaaccttttttttcccatgttgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCTGAATATGACCCTGTAGCCAAGATATCAATTATTCCTCGTGGCCAAGCTGGTGGTCTCACATTTTT
                                          tgttgat  putative branch site (score: 4)
                            ccttttttttcccatg  CT-rich tract
                              tttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcattttttttttaatgttcaacacgcaagtttgttaagagttggttggtatttgggtattcaaccttttttttcccatgttgattttcagAGGCTGGCCATGCTCTAGTGGGTGCTTTAATGCCTGAATATGACCCTGTAGCCAAGATATCAATTATTCCTCGTGGCCAAGCTGGTGGTCTCACATTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG