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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgagaacctttaccagttattttaacatattttagtaacatttgaaatctctgacatttcttataatattaataatgataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGACCTGGGTGGCACATTGAATGCAGTGCAATGAGTGCTTGTTATTTAACTC

Basic information

species Glycine max
transcript GLYMA20G25160.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G25160.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g04960.4 (Oryza sativa), 3'ss of exon 3
gtgcgagaacctttaccagttattttaacatattttagtaacatttgaaatctctgacattt--cttataatattaataatgataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGACCTGGGTGGCACATTGAATGCAGTGCAATGAGTGCTTGTTATTTAACTC
             ||    | || |||  |||||     | |  ||| |   | | || ||   |||||  | |   || |  |   | |||||||||||   ||| || |||  |||||| ||||| ||||| | ||| ||||| || ||||| ||||||||||||||||||||||||  |||||||   |
------------gtaattttgatgttatgatattcatagatctcttgcacattgttactttctgcttatcttttctgtattattgtattcagGCTGCTAAGGAAGGCGAACCTTTCTGGGATAGCCCATGGGGCCGTGGTAGACCAGGATGGCATATTGAATGCAGTGCAATGAGTGCTCATTATTTAGGAC

upper sequence: GLYMA20G25160.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g32570.1 (Oryza sativa), 3'ss of exon 4
gtgcgagaacctttaccagttattttaacatattttagtaacatttgaaatctctgacatttcttataatattaataatgataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGACCTGGGTGGCACATTGAATGCAGTGCAATGAGTGCTTGTTATTTAACTC
        || |    |  | | ||||||  |  |||   |  |  |     |||     |||||   | | |  || ||    | |||| |||||||    ||||||||    ||||| ||||||||||||| |||||| || || ||||| ||||| |||||||| ||||| |||  ||||||   | 
-----gtgacatactgctttcactttaaccaaacttacccatttgagcctcttctctgtattcttgatagacttgtattgtctgt-gcagTCTGCTAAGGAGGGTGAGCCATCTTGGGAGAGCCCTTGGGGTCGTGGAAGGCCAGGATGGCATATTGAGTGCAGTGCGATGAGCGCTCATTATTTGGGTA

upper sequence: GLYMA20G25160.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G874500_T03 (Zea mays), 3'ss of exon 4
---gtgcgagaacctttaccagt--tattttaacatattttagtaac-atttgaaatctctgacatttcttataata----ttaataatgataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGACCTGGGTGGCACATTGAATGCAGTGCAATGAGTGCTTGTTATTTAACTC
    |   || ||   || | ||  | || | | | |   |  || | |  | |    | | || ||| || |  ||    | |||||  ||  || |||||||| ||    ||||| |||   ||||| ||||||||||| | ||||||||| || ||||| ||||||||||| ||||||||||||   ||||||   |
gaactttaagcacaaatagctgtagttttctgaaacaaactgatatctagcttattgttgtcactttttttttcttatccttcaataaccattgtttcagGCTGCAAAGGAGGGTGAACCTTTTTGGGATAGCCCTTGGGGCCGTGGAAGACCAGGTTGGCATATTGAATGCAGCGCAATGAGTGCTCACTATTTAGGAC

upper sequence: GLYMA20G25160.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G071924_T01 (Zea mays), 3'ss of exon 1
gtgcgagaacctttac-------cagttat--tttaacatattttagtaacatttgaaatctctgaca-tttcttataatatt--aataatgataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGACCTGGGTGGCACATTGAATGCAGTGCAATGAGTGCTTGTTATTTAACTC
 |  | ||| |||||         || | |  |||     | |  | | | || |   |     | || ||| || | ||| |  | |||  ||  || |||||||| ||    || || |||   ||||| ||||||||||| | ||||||||| || ||||| ||||||||||| ||||||||||||   ||||||   |
-tttgtgaaactttaggcaaaaatagctgtagttttgtgaaataaactcatatctagcagtgtggtcacttttttcttatacttcattaaccatgttt-cagGCTGCAAAGGAGGGCGAACCTTTTTGGGATAGCCCTTGGGGCCGTGGAAGACCGGGATGGCATATTGAATGCAGCGCAATGAGTGCTCACTATTTAGGAC

upper sequence: GLYMA20G25160.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G56300.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgcgagaacctttaccagttattttaa--catattttagtaac--atttgaaatctctgacatttcttataatattaataatgataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGACCTGGGTGGCACATTGAATGCAGTGCAATGAGTGCTTGTTATTTAACTC
||  || ||  || | |  ||  || ||  | ||||| ||| |   |  |  |    |||   ||| |  | | |||  ||        |||||||||| ||| | ||||| || || ||||| ||||||||||||| ||||||||| || |||||||| ||                                
gtttgacaagtttaatctttttgttcaattcttatttcagttattaaactagagcagctggagtttatgctgaaattttta--------tgcagGCTGCAAAATCTGGTGAACCAAGTTGGGAGAGCCCTTGGGGTCATGGAAGACCAGGATGGCACATCGA--------------------------------

upper sequence: GLYMA20G25160.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G38830.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgcgagaacctttaccagttattttaacatattttagt-aacatttgaaatctctgacatttcttataatattaataatgataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGACCTGGGTGGCACATTGAATGCAGTGCAATGAGTGCTTGTTATTTAACTC
||  ||  | ||||     |  |||||  |||||  | |  |   ||| |   | |   ||    |  | | | || |    |   ||||||| || || || | |||||| || ||||| |||||||||||||| |||||||| || |||||||| || |||||||||||||||| |  |||| |  |||
gtttgaatatcttttt---tctttttattatattcaatttgaggcttgcacagtatatgatgaagtgaagtttgaacataattctatgcagGCGGCAAAGCCTGATGAGCCAAGTTGGGAGAGCCCTTGGGGTCCAGGAAGACCAGGATGGCACATCGAGTGCAGTGCAATGAGTGTTCATTATCTGTCTC

upper sequence: GLYMA20G25160.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0265g00020.t01 (Vitis vinifera), 3'ss of exon 5
gtgcgagaacctttaccagttattttaacatattttagtaacatttgaaatctctgacatttcttataatattaataatgataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGACCTGGGTGGCACATTGAATGCAGTGCAATGAGTGCTTGTTATTTAACTC
                 ||  | | | ||| ||||   | | ||||    ||  |    || |   |||||||   |||     ||||||||||| || || |||||||| || ||||||||||| ||||||||||||||||| || |||||||| || |||||||||||||||||   |||||| ||  
--------------gtgagaaactgtcacaaatttcc-tgatatttatgctcattt---ttgcgcctaatatttccaat----tttgcagGCTGCAAAGCCTGGTGAGCCAAGTTGGGACAGCCCATGGGGTCCTGGAAGACCAGGATGGCACATAGAGTGCAGTGCAATGAGTGCACATTATTTGACCT

upper sequence: GLYMA20G25160.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0017g01640.t01 (Vitis vinifera), 3'ss of exon 4
gtgcgagaacctttaccagttattttaacatattttagtaacatttgaaatctctgacatttcttataatattaataatgataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGACCTGGGTGGCACATTGAATGCAGTGCAATGAGTGCTTGTTATTTAACTC
                  |  | | | ||| |||    | | ||||    ||  |    || ||  |||| ||   |||     ||||||||||| || || | |||||| || ||||||||||| ||||||||||||||||| || |||||||| || |||||||||||||||||   |||||| ||  
--------------gtgggcaactgtcacaaattgcc-tgatatttatgctcattt---ttcctcctaatttttccaat----tttgcagGCTGCAAAGCCTGATGAGCCAAGTTGGGACAGCCCATGGGGTCCTGGAAGACCGGGATGGCACATAGAGTGCAGTGCAATGAGTGCACATTATTTGACCT

upper sequence: GLYMA20G25160.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S504_12V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------------------------------gtgcgagaacctttaccagttattttaacatattttagtaacatttgaaatctctgacatttcttat---aatattaataatgataatt----gcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGACCTGGGTGGCACATTGAATGCAGTGCAATGAGTGCTTGTTATTTAACTC
                                                   || | ||    ||   |    || ||  | || |  |||     |||   ||||  |  ||   | |   ||  |   |  |   | ||    ||||  ||| ||||| || ||||||   |||||||| ||||||||||||||  | || || |||||||||||||||||||| ||||||||     |||||  ||
gtcagcgcccttgaaaatggtgagagaaaactcttctgtctgctgagttaggtcctagggaattagactaa-atcttgtcctactaaagtgggtgttggt-tctcaaattttctctctctgaaggtcgctggtatcattttctcgcagAGTGCGAAACCCGGAGAGCCTGCTTGGGACAGTCCTTGGGGTCCTGGGCGCCCGGGCTGGCACATTGAATGCAGTGCTATGAGTGCGGAGCATTTAGGTC

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|193628492|gb|FK575832.1|FK575832
EST:     TAGCTGTGGACTCAAGAAAGCGTCACCCAGCTGATTTTGCATTGTGGAAG                         GCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGA
genomic: TAGCTGTGGACTCAAGAAAGCGTCACCCAGCTGATTTTGCATTGTGGAAGgtgcgagaac ... ataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtaacatttgaaatctctgacatttcttataatattaataatgataattgcagGCTGCTAAACCAGGTGAGCCTAGCTGGGACAGCCCTTGGGGTCCTGGAAGACCTGGGTGGCACATTGAATGCAGTGCAATGAGTGCTTGTTATTTAACTC
                 tctgacatttcttata  TA-rich tract