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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcattatttttttctctctatcaaaattgttttatttattcatttaagtttctggaggtgttgattttattggaagctgatttttttttttttcttcagATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCT

Basic information

species Glycine max
transcript GLYMA04G12890.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G12890.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 1
agcattatttttttctctctatcaaaatt-gttttatttattcatttaagtttctggaggtgttgatttta--ttggaagctgattt--ttttttttttcttcagATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCT
                 |     |||  |   | | |||||||       ||  || |   ||  |||  |  ||| |   | || |  |||| || ||  | ||||||||||||||||||  | |||||||| ||||| ||||| || || || |||||||| |||||||| || |||||||| || ||||||
----------------gtaagctaaagctcactctttttattctcaactattgatgcaatcgtaaattaaagtttgaacttttatctggttttattgtttattagATAAGAAGGTGTTCCCTGATTTCTATATTCTGGGATGGTACTCTACGGGAAGTGATGCTGAGGAATCTGATATGCATATCCATAAAGCT

upper sequence: GLYMA04G12890.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 1
--------------------------------------------------------------agcattatttttttctctctatcaaaattgttttatttattc--------atttaagtttctggaggtgttga--ttttattggaa-----gctgatttttttttttttcttcagATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCT
                                                              ||  || || || |   | | |     || |||| ||| ||          |||| ||||  ||   || |||  ||| | ||  |       ||||| | ||  | |   | |||||||||||| || ||| |||| |||||||| || ||||| || || || ||||||||  | |||||||| ||||||||||| ||||||
gttagtctttctctacctcccttcccctatatatctctcagtgtttagtcatgattcaagttagggtttttcttgttcgtttgttttgttttttttttttttttttcatgtggtttaggttttagggtttggtgaactttgaatgttacgctgagtgattctcttgatgtggattagATAAGAAGGTCTTTCCGAACTTTTATATACTTGGATGGTACTCCACCGGAAGTGATGCCCAAGAATCAGATATGCATATTCATAAAGCT
















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|298179134|gb|HO027605.1|HO027605
EST:     TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCT                         ATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGG-A
genomic: TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCTgttcagtatt ... ttttcttcagATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGA
EST: gi|298185593|gb|HO030806.1|HO030806
EST:     TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCT                         ATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGA
genomic: TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCTgttcagtatt ... ttttcttcagATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGA
EST: gi|298165455|gb|HO011504.1|HO011504
EST:     TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCT                         ATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGA
genomic: TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCTgttcagtatt ... ttttcttcagATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGA
EST: gi|9986533|gb|BE660641.1|BE660641
EST:     TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCT                         ATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGA
genomic: TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCTgttcagtatt ... ttttcttcagATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGA
EST: gi|298173272|gb|HO016608.1|HO016608
EST:     TTCCTCCCACTCCCTCGATCGCACCTTCCTCGGGAAGAAGCAAGAACTCT                         ATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGA
genomic: TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCTgttcagtatt ... ttttcttcagATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGA
EST: gi|7587867|gb|AW703674.1|AW703674
EST:     TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCT                         ATAAGAAAGTGTTCCCGCACTTCTATATACTAGGGTGGTATTCGACTGAGA
genomic: TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCTgttcagtatt ... ttttcttcagATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGA
EST: gi|18041126|gb|BM309420.1|BM309420
EST:     TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCT                         ATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGA
genomic: TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCTgttcagtatt ... ttttcttcagATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGA
EST: gi|298192702|gb|HO033136.1|HO033136
EST:     TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCT                         ATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGA
genomic: TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCTgttcagtatt ... ttttcttcagATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGA
EST: gi|298199097|gb|HO042460.1|HO042460
EST:     TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCT                         ATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCAACTGGGA
genomic: TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCTgttcagtatt ... ttttcttcagATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGA
EST: gi|15203210|gb|BI425978.1|BI425978
EST:     TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCT                         ATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGA
genomic: TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCTgttcagtatt ... ttttcttcagATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGA
EST: gi|14992076|gb|BI317749.1|BI317749
EST:     TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCT                         ATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGA
genomic: TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCTgttcagtatt ... ttttcttcagATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGA
EST: gi|15662488|gb|BI699859.1|BI699859
EST:     TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCT                         ATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGA
genomic: TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCTgttcagtatt ... ttttcttcagATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGA
EST: gi|298172080|gb|HO021672.1|HO021672
EST:     TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCT                         ATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGA
genomic: TTCCTCCCACTCCCTCGATCGCACCTTCCTCGAGAAGAAGCAAGAACTCTgttcagtatt ... ttttcttcagATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagtttctggaggtgttgattttattggaagctgatttttttttttttcttcagATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCT
                              agctgat  putative branch site (score: 4)
                                ctgatttttttttttt  CT-rich tract
                                 tgattttttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcattatttttttctctctatcaaaattgttttatttattcatttaagtttctggaggtgttgattttattggaagctgatttttttttttttcttcagATAAGAAGGTGTTCCCGCACTTCTATATACTGGGGTGGTATTCGACTGGGAGTGATGCAGAGGAATCAGACATGCATATTCACAAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - ggaggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaagctg