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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttatattaaactttatctacctctttctttatatttatgatttatctcaccatcttcatcctgtttgatattttgcctctactgatgctatgcattttatccctgcagAGGAACAGTTTTGAACAGTTCTGCATAAATTATGCAAATGAGAGATTACAGCAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG

Basic information

species Glycine max
transcript GLYMA20G00320.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 13
gtatgtttatattaaactttatctacctctttctttatatttatgatttatctcaccatcttcatcctgtttgatattttgcctctactgatgctatgcattttatccctgcagAGGAACAGTTTTGAACAGTTCTGCATAAATTATGCAAATGAGAGATTACAGCAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG
                              |  | ||  |  ||     ||     |||| | ||  |  |||  |  | |  |||  ||     |  ||   |     |||||||||||||||||||||||||||| || || ||||| ||||| ||  | || ||||| |||||||| ||||| || ||| | ||||| |||
-----------------------------gtaatgtacttccatttgacatgctgtcatcat-attttaattggcaaatggtttctcatgtcataacacaaaat-----tgcagAGGAACAGTTTTGAACAGTTCTGTATTAACTATGCTAATGAAAGGCTCCAACAACATTTCAATCGCCATTTGTTTAAGCTTGAACAAGAG

upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 13
gtatgtttatattaaactttatctacctctttctttatatttatgatttatctcaccatcttcatcctgtttgatattttgcctctactgatgctatgcatt-ttatccctgcagAGGAACAGTTTTGAACAGTTCTGCATAAATTATGCAAATGAGAGATTACAGCAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG
                                     || |     ||| | |  | |   |  || | | |  ||  || | | || | |       |||| | ||   |||||| |||||||||||||||||||||||| |||||||| ||||| || || |||||||| |||||||||||||| || ||| | || || |||
------------------------------------gtaatgcacttttctttacctaaagttgtcatatatattaaattccatatagttacttctgacattatcatatttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG

upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G139583_T02 (Zea mays), 3'ss of exon 13
gtatgtttatattaaactttatctacctct--ttctttatatttatgatttatctcaccatcttcatcctgtttgatattttgcctctactgatgctatgcattttatccctgcagAGGAACAGTTTTGAACAGTTCTGCATAAATTATGCAAATGAGAGATTACAGCAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG
             | ||   |      |    | ||       || |  |   | ||   |  ||||  | ||  ||    ||    |||||  |  ||   | |||    |||||| |||||||||||||||||||||||| |||||||| ||||| || || || ||||| ||||||||||||||||| ||| | || || |||
------------cagaccccactcgtttgggatcctccggcactaggtctgcccccaaagttgtcata-tattaaattgcatgtacttactggcgacat---tattacatttgcagAAGAACAGTTTTGAACAGTTCTGCATCAATTATGCTAATGAAAGGTTGCAACAACATTTCAATCGTCATTTATTTAAGCTTGAGCAAGAG

upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 14
lower sequence: AT1G50360.1 (Arabidopsis thaliana), 3'ss of exon 14
gtatgtttatattaaa-ctttatctacctctttctttata----tttatgatttatct-caccatcttcatcctgtttgatattttgcctc--tactgat-------gct--atgcattttatcc---ctgcagAGGAACAGTTTTGAACAGTTCTGCATAAATTATGCAAATGAGAGATTACAGCAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG
||||| |  | || |  ||   | | | | || ||  ||     |  || |  ||||| |||  |     | |||| | | ||||||   |  |  | ||       |||  ||  ||  ||| |    ||||||  || |||||||| |||||||| ||||||||||||||||||||||| |||||||||||||| |||||| | |||||| | || ||||||
gtatgctggtttttagtctccctttgcgttttactgcatgaacttacataagctatctgcacattacatcttctgtgttacattttgtaccaatgttaatttggtttgctgaataaatactatacatgttgcagAAAAATAGTTTTGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTCAACCGTCATCTCTTCAAGCTTGAGCAGGAG

upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 14
lower sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 14
--------------------------------------------------------------------------------gtatgtttatattaaactttatctacctcttt--ctttatatttatgatttatctcaccatcttcatcctgtttgatattttgcctctactgatgctatgcattttatccct--gcagAGGAACAGTTTTGAACAGTTCTGCATAAATTATGCAAATGAGAGATTACAGCAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG
                                                                                 |    | |||  ||||  |  | |    |    || ||||| ||||   | |        | |  || || || || | |    |  | |     || |  ||| || |||  |||||  || || || || |||||||| ||||||||||||||||||||||| ||||||||||| || |||||| |||||||| | || || |||
gtatgttcctgttctctggctctctgagctttctcctgaaaaagattacaattgctaccagctatcattagaccttcagtttgcaatgataccaaacagtgccaaatagtagaactctatatctatgtgcttttgtgtttccatt-tcttgatttatgtgtcttattgatttgctatacgactttcattcctctgcagAAAAATAGCTTCGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTTAACCGTCATCTATTCAAGCTGGAGCAAGAG

upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 13
gtatgtttatattaaactttatctacctctttctttatatttatgatttatctcaccat-cttcatcctgtttgatattttgcctctactgatgctatgcattttatccctgcagAGGAACAGTTTTGAACAGTTCTGCATAAATTATGCAAATGAGAGATTACAGCAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG
           |   |  |||| ||  |  | || || ||   |  |   || | |||| |  |||  |       | |||     || | ||| ||   ||| | |   | ||||| || || ||||| ||||||||||||||||||||||||||||| || ||||| ||||| || |||||||||||||||||||| || |||
----------gtatgatattatttagtttctgctgtaaataatttttcattccccccattccccattgtccccctaaatttataaatattcatgttacatattctgtttttccagAGAAATAGCTTTGAGCAGTTCTGCATAAATTATGCAAATGAGAGGTTGCAGCAGCACTTTAACCGTCATTTATTCAAGTTAGAGCAAGAG

upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 14
lower sequence: PP1S174_120V6.1 (Physcomitrella patens), 3'ss of exon 13
-------------gtatgtttatattaaactttatctacctctttctttata--tttatgattta-tctcaccatcttcatcctgtttgata-ttttgcctctactgatgct-atgcattttatccctg----cagAGGAACAGTTTTGAACAGTTCTGCATAAATTATGCAAATGAGAGATTACAGCAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG
              ||   |   || | | | ||   |  |  || || ||   ||  |||| || ||  | | |     ||  | |||||   | | | | |  |   ||| | ||||||    ||||    |||| |||||||||||| ||||| |||||||| |||||||| || || || || ||||| |||||||| ||| | || ||| | || || |||
gtgaaatcttctcatacactagaatgagattgtaagcagtttattattaattgtttcctgatctagtcaaagctttgatttctggattgatggctcttcttatggtctagcttaagcatttccctcctgattgcagAAGAACAGTTTTGAGCAGTTATGCATAAACTATGCAAACGAAAGGTTGCAACAACATTTCAATCGCCATCTGTTTAAGCTTGAGCAAGAG

upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 14
lower sequence: PP1S228_18V6.1 (Physcomitrella patens), 3'ss of exon 13
gtatgtttatattaaactttatctacctctttctttatatttatgatttatctcaccatcttcatcctgtttgatattttgcctctactgatgctatgcattttatccctgcagAGGAACAGTTTTGAACAGTTCTGCATAAATTATGCAAATGAGAGATTACAGCAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG
         ||| |     |  | |  |||||    || |  |   |  |  || |  | ||| |    |||    ||||| ||| |    | |||||       | | ||||||  ||||||||||| || || || ||||||||||| ||||| || || || ||||| |||||||||||| | |||||| | || || |||
----aggggtatcaggacctgaccaggtcttttacaatgtccactgtcgaaatc-cacttttcgtagaattt---tttttgtctcaagctttactatg------gttcttgcagAAAAACAGTTTTGAGCAATTATGTATAAATTATGCGAATGAAAGGTTGCAACAACATTTCAATCGTCATCTGTTCAAGCTTGAGCAAGAG

upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 14
lower sequence: EFJ20281 (Selaginella moellendorffii), 3'ss of exon 12
gtatgtttatattaaactttatctacctctttctttatatttatgatttatctcaccatcttcatcctgtttgata-ttttgcctctactgatgctatgcattttatccctgcagAGGAACAGTTTTGAACAGTTCTGCATAAATTATGCAAATGAGAGATTACAGCAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG
                                                                  | ||  | || ||||   | |   |||  ||   | |||    |||||||| || |||||||| ||  | |||||||| ||||||||||| |||||||||||||| ||||| || ||  | |||||  | || || |||
----------------------------------------------------------------gtcggtgcgctagttttagttttcgcgattttactgagttttctactgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG

upper sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 14
lower sequence: EFJ23280 (Selaginella moellendorffii), 3'ss of exon 12
gtatgtttatattaaactttatctacctctttctttatatttatgatttatctcaccatcttcatcctgtttgat-attttgcctctactgatgctatgcattttatccctgcagAGGAACAGTTTTGAACAGTTCTGCATAAATTATGCAAATGAGAGATTACAGCAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG
                                                                  | ||  | | |||||   | |   |||  ||   | |||    |||||||| || |||||||| ||  | |||||||| ||||||||||| |||||||||||||| ||||| || ||  | |||||  | || || |||
----------------------------------------------------------------gtcggtgcgctcattttagttttcgcgattttactgagttttctactgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG

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|208104539|gb|GD904530.1|GD904530
EST:     CCGGCAGATCAATCAGTATTCTAGATATCTATGGCTTTGAATCTTTCAAT                         AGGAACAGTTTTGAGCAGTTCTGCATAAATTATGCAAATGAGAGATTACAG
genomic: CCGGCAGATCAATCAGTATTCTAGATATCTACGGCTTTGAATCTTTCAATgtatgtttat ... atccctgcagAGGAACAGTTTTGAACAGTTCTGCATAAATTATGCAAATGAGAGATTACAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcatcctgtttgatattttgcctctactgatgctatgcattttatccctgcagAGGAACAGTTTTGAACAGTTCTGCATAAATTATGCAAATGAGAGATTACAGCAACACTTCAATCGTCATTTATTCAAGTTAGAACAGGAG
                          tactgat  putative branch site (score: 2)
                                         ttttatccct  putative PPT
          tttgatatttt  TA-rich tract