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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatatcaactctaacagttcaatggttagttttacaatctcaaatcagatccgactttaatttgttctcgcactgtagGTGGTGGTGTTGCTCTTCTATATGCATCGAGAGAGTTGGATAAACTTCAAACTGCTAACTTCGGTCAAAAGATTGGTGTCCAGATTATCCAAAATGCTTT

Basic information

species Glycine max
transcript GLYMA20G19980.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 14
----------------gtaaaatatcaactctaacagttcaatggttagttttacaatctcaaatcagatccgactttaatttgttctcgcac-tgtagGTGGTGGTGTTGCTCTTCTATATGCATCGAGAGAGTTGGATAAACTTCAAACTGCTAACTTCGGTCAAAAGATTGGTGTCCAGATTATCCAAAATGCTTT
                 |   || | |  |    ||||| | |  ||||    | |    ||   |||| |  |   ||  |  ||||       ||||||||||| ||||| ||||| |||||||| | |||  |||||||| | || ||||| ||||| |  |||||||||||||||||||| || |||||||||||
gtactgtatgtcatcgctgctattttattttctgcagtttacta-ttagcagcatatcaccattgcagagc--atcatatctgattctaatttacgtagGTGGTGGAGTTGCCCTTCTGTATGCATCAAAAGACCTGGATAAATTGCAGACTGCGAACTTTGACCAAAAGATTGGTGTCCAGATCATTCAAAATGCTTT

upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 14
----------------------------------------------gtaaaatatcaactctaacagttcaatggttagttttacaat-ctcaaatcagatccgactttaatttgttctcgcactgtagGTGGTGGTGTTGCTCTTCTATATGCATCGAGAGAGTTGGATAAACTTCAAACTGCTAACTTCGGTCAAAAGATTGGTGTCCAGATTATCCAAAATGCTTT
                                               |  ||| |  |||    |||||      || |  |||  || | ||| |  | |   |    |  ||    |  || |  |||||| |||||||| ||||| |||||||| |  ||| |||||||| | |  ||||||||||| | ||||||||||||||| || || || || ||||||||
gtatgcagttgctccacttcagtagatttctttcaatatgttttccttgtaatgt--acttgttcagtttgcatctttgcattattatgcccaagtatgctgacatgacatctttgcattacaatacagGTGGAGGTGTTGCACTTCTTTATGCATCAAAGGAGCTGGATAAATTGCCGACTGCTAACTTTGATCAAAAGATTGGTGTACAAATCATTCAGAATGCTTT

upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G111477_T01 (Zea mays), 3'ss of exon 2
-----------------------------gtaaaatatcaactctaacagttcaatggttagttttac-aatctc-----aaatcag---atccgactttaatttgttctcgcac-tgtagGTGGTGGTGTTGCTCTTCTATATGCATCGAGAGAGTTGGATAAACTTCAAACTGCTAACTTCGGTCAAAAGATTGGTGTCCAGATTATCCAAAATGCTTT
                                  || |  |  || |          |||| |  |||  |||||       |||||     | ||   | || | |  | | |  || ||||||||||||||||||||| ||||||||||  ||| | |||||| | || || || ||||||| ||| ||||||||||| || || || || ||||||||
gtaatgtatcatttgaatatttgatgttcacgggatgttcatgctgatttcctttgtgttattcctactgatctcctgttgcatcagtatgcctgatagtcatctttaattgtatatgcagGTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTTGATAAATTGCAGACAGCGAACTTCGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTT

upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 13
------------------------------------------------------------------------------gtaaaatatcaactctaacagttcaatggttagttttacaat-ctcaaatcagatccgactttaatttgttctcgcac-tgtagGTGGTGGTGTTGCTCTTCTATATGCATCGAGAGAGTTGGATAAACTTCAAACTGCTAACTTCGGTCAAAAGATTGGTGTCCAGATTATCCAAAATGCTTT
                                                                               |  |  |  |  | |   ||||  ||   |  |||     | |   | |  |  | |   | ||| | |  | |    || ||||||||||||||||||||| ||||||||||  ||| | |||||  | || || || || || | ||| ||||||||||| || || || || ||||||||
gtaatgtatcaattaaaatttcatggggggggggtgtttatgctgatttcctgtgttatttgctcctactgattcctgttgcatcagtatttgtgttagtt--attcctgatttcctgttgcgtcagtatgcccgggagtcaatctttaattgtgtatgcagGTGGTGGTGTTGCTCTTCTCTATGCATCGAAGGAGCTCGATAAGTTGCAGACAGCAAATTTTGATCAGAAGATTGGTGTGCAAATCATTCAGAATGCTTT

upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 14
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaaaa---tatcaactctaacagttcaatggt-tagttttacaatctcaaatcagatccgactttaatttgttctcgcact-gtagGTGGTGGTGTTGCTCTTCTATATGCATCGAGAGAGTTGGATAAACTTCAAACTGCTAACTTCGGTCAAAAGATTGGTGTCCAGATTATCCAAAATGCTTT
|||      |  ||      |    ||  || | ||||  || ||  |      |  | | |    ||    |     |||| | ||| || ||||| ||||||||||| ||| | ||||||||||| ||||||| ||| || ||||| |  || |||||||||||||||||||| || || || ||
gtatgtctcttccagtgaggaagactctttgatatagtgctaaaaagtttg-ctatgtgctaaagaaacaaatcaaaacacttgcagGAGGAGGTGTGGCTCTTCTATACGCAGCAAGAGAGTTGGAAAAACTTCCAACAGCCAACTTTGACCAGAAGATTGGTGTCCAGATTATTCAGAACGCATT

upper sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 14
lower sequence: PP1S149_289V6.1 (Physcomitrella patens), 3'ss of exon 13
-------------gtaaaatatcaactctaacagttcaatggttag----ttttacaatctcaaatcagatccgacttt-aatttgttctcgcactgtagGTGGTGGTGTTGCTCTTCTATATGCATCGAGAGAGTTGGATAAACTTCAAACTGCTAACTTCGGTCAAAAGATTGGTGTCCAGATTATCCAAAATGCTTT
             ||| | | |  |    |     | ||| |  |      | |    | ||   |   |    | ||| |||||| |   |      |||||||||||| |||||| | ||||| ||  ||||| |||| ||| |||||||||| ||||| |  || ||||| || || || || ||||||||||||||
taaatttatatacgtagattttagaaggcacgtcatgaattgcgaagcccctctggtgtttcgtctggtaatgaattttcaatttgattgggtggaacagGTGGTGGTGTGGCTCTTTTGTATGCTTCTCGAGAGCTGGAGAAAGTTCAAACTGCGAACTTTGACCAGAAGATCGGAGTGCAAATCATCCAAAATGCTTT

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|16279136|gb|BI943277.1|BI943277
EST:     TGATGCATTAAATGCAACTAAGGCTGCTGTAGAGGAGGGCATAATGCCTG                         GTGGTGGTGTTGCTCTTCTATATGCATCGAGAGAGTTGGATAAACTTCAAA
genomic: TGATGCATTAAATGCAACTAAGGCTGCTGTAGAGGAGGGCATAGTGCCTGgtaaaatatc ... cgcactgtagGTGGTGGTGTTGCTCTTCTATATGCATCGAGAGAGTTGGATAAACTTCAAA
EST: gi|19268755|gb|BM885011.1|BM885011
EST:     TGATGCATTANATGCAACTAAGGCTGCTGTAGAGGAGGGCATAGTGCCTG                         GTGGTGGTGTTGCTCTTCTATATGCA
genomic: TGATGCATTAAATGCAACTAAGGCTGCTGTAGAGGAGGGCATAGTGCCTGgtaaaatatc ... cgcactgtagGTGGTGGTGTTGCTCTTCTATATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttagttttacaatctcaaatcagatccgactttaatttgttctcgcactgtagGTGGTGGTGTTGCTCTTCTATATGCATCGAGAGAGTTGGATAAACTTCAAACTGCTAACTTCGGTCAAAAGATTGGTGTCCAGATTATCCAAAATGCTTT
                               ctttaat  putative branch site (score: 4)
                                     tttgttctc  CT-rich tract
                                tttaatttgtt  TA-rich tract