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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttacatctcttacaataagattattcatggttttctattctcctgttatgttattacttcaatattccttgatgtagaccaaaatgggtaaacaagaacatctctttttcatttttcttttctagGTTGGGTACTTGTGGTATGAATACATATACAAGCTGGACAAGGTCTCATACAACAAGCTCCACCCCTACACCTCTTGGATTCCAATTAC

Basic information

species Glycine max
transcript GLYMA05G25780.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G458538_T01 (Zea mays), 3'ss of exon 5
gtgagttacatctcttacaataagat-tattcatggttttctattctcctgttatgttattacttcaatattccttgatgtagaccaaaatgggtaaacaagaacatctctttttcatttttctt-ttctagGTTGGGTACTTGTGGTATGAATACATATACAAGCTGGACAAGGTCTCATACAACAAGCTCCACCCCTACACCTCTTGGATTCCAATTAC
|| ||||      |  |||||    |   ||  | ||| |  |  ||  ||  || |  |||  ||||   | |||||     ||     ||   | ||   |    ||   | |  | |||||| ||||||||||| |   ||||||||||||| ||||||||||| ||||| ||  |||||||||||  ||| |||||||| || ||||| || || ||
gtaagtt------cccacaatctcttacctttgttgttgtggaaactgttgg-atttctttaaatcaag--tacttgacacc-actgtgttgttaatactgtactgactaggtgttgtgtttcttcttctagGTTGGCTTTCTGTGGTATGAATATATATACAAGCTAGACAAAGTTACATACAACAAGTACCATCCCTACACATCATGGATCCCTATAAC

upper sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G29890.2 (Arabidopsis thaliana), 3'ss of exon 9
gtgagttacatctcttacaataagattattcatggttttctattctcctgttatgttattacttcaatattccttgatgtagaccaaaatgggtaaacaagaacatctctttttcatttttcttttctagGTTGGGTACTTGTGGTATGAATACATATACAAGCTGGACAAGGTCTCATACAACAAGCTCCACCCCTACACCTCTTGGATTCCAATTAC
                            |   | |||  || |||||   || || |    | |  ||| || |         ||| |||   ||  |       | | |  |   ||     | |  ||| ||| ||| | |||||||||||||| |||||||||||||||||  | ||||||||    || |||||||| |||||||||||||| ||
---------------------------gtgagttgttagcttttctcggcttctggttcatcatatatagtcttct-------ccacaat---tattctgatgtttgtgtcgtggtttccaaatgttcagGCTGGTTACCTTTGGTATGAATACATCTACAAGCTGGACAAGGTTACGTACAACAAATATCATCCCTACACATCTTGGATTCCAATAAC

upper sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 11
lower sequence: AT2G34410.3 (Arabidopsis thaliana), 3'ss of exon 10
gtgagttacatctcttacaataagattattcatggttttctattctcctgttatgttattacttcaatattccttgatgtagaccaaaatgggtaaacaagaacatctctttttcatttttcttttctagGTTGGGTACTTGTGGTATGAATACATATACAAGCTGGACAAGGTCTCATACAACAAGCTCCACCCCTACACCTCTTGGATTCCAATTAC
                                ||  |||   |||||    |   ||||   |   || |   ||||| |    |  |     |   ||||         || |    | | || |  ||||||| ||| | ||||||||||||||||||||||| ||||||||  ||||||||||    || |||||||| || ||||||||||| ||
-------------------------------gtgagtttgggttctct--ctggcttatggatcttatgtat-ttgatattattctga-----tgcccaag---------ttgttccctatattgttcagGTTGGTTACCTATGGTATGAATACATATACAAGCTTGACAAGGTTACATACAACAAATATCATCCCTACACATCGTGGATTCCAATAAC

upper sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv10s0003g02830.t01 (Vitis vinifera), 3'ss of exon 5
gtgagttacatc-tcttacaataagattattcatggttttctattctcctgttatgttattacttcaatattccttgatgtagaccaaaatgggtaaacaagaacatctctttttcatttttcttttctagGTTGGGTACTTGTGGTATGAATACATATACAAGCTGGACAAGGTCTCATACAACAAGCTCCACCCCTACACCTCTTGGATTCCAATTAC
|| |||| |||  || |   || | | |||| ||  || ||| ||    | ||| || | |  || | |  | |||  | |         |   ||      ||  |   | | |  | | || | | |||||||| || ||||||||||||||||| |||||||||||||| ||  |||| || ||| |||| |||||||| || ||||||||||| ||
gtaagttgcatgatcctgtgatcacagtatt-attcttatctgtttagattttaagtgacttttttatttatactttctttttctt---ttttttagtttttaatttaattgtctactctgtcctctatagGTTGGTTATTTGTGGTATGAATACATTTACAAGCTGGACAAAGTTACATATAATAAGTTCCATCCCTACACATCATGGATTCCAATAAC

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|24136282|gb|BU926792.1|BU926792
EST:     CCAAGAGGAGAGTTACCATCAAAACTGGCATCGTTTCTGTTGCATTATTT                         GTTGGGTACTTGTGGTATGAATACATATACAAGCTGGACAAGGTCTCATAC
genomic: CCAAGAGGAGAGTTACCATCAAAACTGGCATCGTTTCTGTTGCATTATTTgtgagttaca ... tcttttctagGTTGGGTACTTGTGGTATGAATACATATACAAGCTGGACAAGGTCTCATAC
EST: gi|207740974|gb|GD714352.1|GD714352
EST:     CATCGTTTCTGTTGCATTATTT                         GTTGGGTACTTGTGGTATGAATACATATACAAGCTGGACAAGGTCTCATAC
genomic: CATCGTTTCTGTTGCATTATTTgtgagttaca ... tcttttctagGTTGGGTACTTGTGGTATGAATACATATACAAGCTGGACAAGGTCTCATAC
EST: gi|208161302|gb|GD963476.1|GD963476
EST:     CCAAGAGGAGAGTTACCATCAAAACTGGCATCGTTTCTGTTGCATTATTT                         GTTGGGTACTTGTGGTATGAATACA
genomic: CCAAGAGGAGAGTTACCATCAAAACTGGCATCGTTTCTGTTGCATTATTTgtgagttaca ... tcttttctagGTTGGGTACTTGTGGTATGAATACA
EST: gi|192300083|gb|FG991873.1|FG991873
EST:     CCAAGAGGAGAGTTACCATCAAAACTGGCATCGTTTCTGTTGCATTATTT                         GTTGGGTACTTGTGGTATGAATACATATACAAGCTGGACAAGGTCTCATAC
genomic: CCAAGAGGAGAGTTACCATCAAAACTGGCATCGTTTCTGTTGCATTATTTgtgagttaca ... tcttttctagGTTGGGTACTTGTGGTATGAATACATATACAAGCTGGACAAGGTCTCATAC
EST: gi|208336761|gb|GE135151.1|GE135151
EST:     CATCGTTTCTGTTGCATTATTT                         GTTGGGTACTTGTGGTATGAATACATATACAAGCTGGACAAGGTCTCATAC
genomic: CATCGTTTCTGTTGCATTATTTgtgagttaca ... tcttttctagGTTGGGTACTTGTGGTATGAATACATATACAAGCTGGACAAGGTCTCATAC
EST: gi|192332805|gb|FK026806.1|FK026806
EST:     CCAAGAGGAGAGTTACCATCAAAACTGGCATCGTTTCTGTTGCATTATTT                         GTTGGGTACTTGTGGTATGAATACATATACAAGCTGGACAAGGTCTCATAC
genomic: CCAAGAGGAGAGTTACCATCAAAACTGGCATCGTTTCTGTTGCATTATTTgtgagttaca ... tcttttctagGTTGGGTACTTGTGGTATGAATACATATACAAGCTGGACAAGGTCTCATAC
EST: gi|193676073|gb|FK618281.1|FK618281
EST:     CCAAGAGGAGAGTTACCATCAAAACTGGCATCGTTTCTGTTGCATTATTT                         GTTGGGTACTTGTGGTATGAATACATATACAAGCTGGACAAGGTCTCATAC
genomic: CCAAGAGGAGAGTTACCATCAAAACTGGCATCGTTTCTGTTGCATTATTTgtgagttaca ... tcttttctagGTTGGGTACTTGTGGTATGAATACATATACAAGCTGGACAAGGTCTCATAC
EST: gi|207760949|gb|GD731990.1|GD731990
EST:     CCAAGAGGAGAGTTACCATCAAAACTGGCATCGTTTCTGTTGCATTATTT                         GTTGGGTACTTGTGGTATGAATACATAT
genomic: CCAAGAGGAGAGTTACCATCAAAACTGGCATCGTTTCTGTTGCATTATTTgtgagttaca ... tcttttctagGTTGGGTACTTGTGGTATGAATACATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgtagaccaaaatgggtaaacaagaacatctctttttcatttttcttttctagGTTGGGTACTTGTGGTATGAATACATATACAAGCTGGACAAGGTCTCATACAACAAGCTCCACCCCTACACCTCTTGGATTCCAATTAC
 ccttgat  putative branch site (score: 5)
                            catctctttttcattt  putative PPT
                                  tttttcatttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttacatctcttacaataagattattcatggttttctattctcctgttatgttattacttcaatattccttgatgtagaccaaaatgggtaaacaagaacatctctttttcatttttcttttctagGTTGGGTACTTGTGGTATGAATACATATACAAGCTGGACAAGGTCTCATACAACAAGCTCCACCCCTACACCTCTTGGATTCCAATTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT