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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactaacaattaacatcaatattagctatagcctattttcttcgttgtcatcaaaatatcagtttagcataaagataactcttaattctaacaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAGCTATTTACATGAAGCTTACG

Basic information

species Glycine max
transcript GLYMA16G06850.3
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G06850.3 (Glycine max), 3'ss of exon 12
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 12
tactaacaatt---aacatcaatattagctatagcctattttcttcgttgtcatcaaaatatcagtttagcataaagataactcttaatt--ctaacaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAGCTATTTACATGAAGCTTACG
|| |||| | ||| || ||| | | ||| | | || |||||| | | |||| || ||| | | | | ||||||| ||| ||||||||||||||| | ||| || ||||| || |||| ||| || ||||||||||||||||||
tattaactgctttagtcataaacattggttcaagcagagatctttaa-----atcaaattgttgctttaatattttattaatattcagatggtttctgtgtttagGTCAAAGGCAGGGGAGAAATGAATTTGTAATACGCCTCCAACCTTTAGAGGCCATTTACATGAAGCTTACG
















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|6566164|gb|AW233801.1|AW233801
EST:     GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT                         GTAAAAAGCAGGGGAGAAATGAGTTTGTTATCCGCCTACAGCCTTCAGAAG
genomic: GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
EST: gi|37994251|gb|CF805997.1|CF805997
EST:     TGTCCCTGGTGATATTCTCAAGT                         GTAAAAAGCAGGGGAGAAATGAGTTTGTTATCCGCCTACAGCCTTCAGAAG
genomic: TGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
EST: gi|15815763|gb|BI788038.1|BI788038
EST:     GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCGAGT                         GTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
genomic: GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
EST: gi|7925329|gb|AW831416.1|AW831416
EST:     GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT                         GTAAAAAGCAGGGGAGAAATGAGTTTGTTATCCGCCTACAGCCTTCAGAAG
genomic: GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
EST: gi|19053614|gb|BM732281.1|BM732281
EST:     GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT                         GTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
genomic: GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
EST: gi|16343150|gb|BI968745.1|BI968745
EST:     GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT                         GTAAAAAGCAGGGGAGAAATGAGTTTGTTATCCGCCTACAGCCTTCAGAAG
genomic: GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
EST: gi|58023690|gb|CX710431.1|CX710431
EST:     GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT                         GTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
genomic: GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
EST: gi|37995859|gb|CF807448.1|CF807448
EST:     GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT                         GTAAAAAGCAGGGGAGAAATGAGTTTGTTATCCGCCTACAGCCTTCAGAAG
genomic: GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
EST: gi|16346631|gb|BI972226.1|BI972226
EST:     GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT                         GTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
genomic: GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
EST: gi|37995462|gb|CF807051.1|CF807051
EST:     GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT                         GTAAAAAGCAGGGGAGAAATGAGTTTGTTATCCGCCTACAGCCTTCAGAAG
genomic: GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
EST: gi|192310376|gb|FK002256.1|FK002256
EST:     GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT                         GTAGAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
genomic: GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
EST: gi|33390426|gb|CA853621.1|CA853621
EST:     GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT                         GTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
genomic: GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
EST: gi|16346044|gb|BI971639.1|BI971639
EST:     GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT                         GTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
genomic: GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
EST: gi|15661712|gb|BI699083.1|BI699083
EST:     GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT                         GTAAAAAGCAGGGGAGAAATGAGTTTGTTATCCGCCTACAGCCTTCAGAAG
genomic: GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
EST: gi|58020056|gb|CX706798.1|CX706798
EST:     GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT                         GTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
genomic: GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
EST: gi|151395248|gb|EV265119.1|EV265119
EST:     GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT                         GTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
genomic: GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
EST: gi|7693442|gb|AW761534.1|AW761534
EST:     GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT                         GTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
genomic: GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG
EST: gi|37994622|gb|CF806296.1|CF806296
EST:     GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGT                         GTAAAAAGCAGGGGAGAAATGAGTTTGTTATCCGCCTACAGCCTTCAGAAG
genomic: GGCAGAGATAAGGGTTCAATTCAAGGATGTCCCTGGTGATATTTTCAAGTgtatgccatt ... acaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcatcaaaatatcagtttagcataaagataactcttaattctaacaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAGCTATTTACATGAAGCTTACG
                                        ttctaac  putative branch site (score: 1)
 ttaattctaacaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactaacaattaacatcaatattagctatagcctattttcttcgttgtcatcaaaatatcagtttagcataaagataactcttaattctaacaattttagGTAAAAAGCAGGGGAGAAATGAGTGTGTTATCCGCCTACAGCCTTCAGAAGCTATTTACATGAAGCTTACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
-actaaca
- - - - - - - - - - - - - - - - - - - - - - -tgtcatc