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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatggacaaaactacttattgagatgattaattttatcatcattgttggtgtgcttattcatttagttttgaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTATTCAGTTTGTTGATGGTTTCTTTAGTCCAATATACTCCAGGCTCGGCATA

Basic information

species Glycine max
transcript GLYMA06G15360.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G15360.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g36110.4 (Oryza sativa), 3'ss of exon 2
-------------gtaatggacaaaactacttattgagatgattaattttatcatcattgttggtgtgcttattcatttagttttgaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTATTCAGTTTGTTGATGGTTTCTTTAGTCCAATATACTCCAGGCTCGGCATA
               |||  |   |   |  |    ||| | | ||  ||||   ||    |  |   ||  || ||     |||  || ||||||||||||||||| || ||||||||||| |||||||| || ||||||||| || ||||||||||||| || || |||||| | ||  | | ||| ||  | 
gtatgttttttcaacaattaatctagacatatcacaaga-gctaaagattatatccaagcctattaacctgttttatccctcttttgatttgcagCGTAGTTCTTTTCCCTGTTGCTGTTACATTCTTCATCACCTGGTGGTTTGTTAAGTTTGTTGATGGATTTTTCAGTCCACTGTATGCAAAGCTTGGATTT

upper sequence: GLYMA06G15360.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 2
----gtaatggacaaaa--ctacttattgagatgattaattttatcatcattgttggtgtgct--tattcatttagttttgaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTATTCAGTTTGTTGATGGTTTCTTTAGTCCAATATACTCCAGGCTCGGCATA
     |  | ||||  |  | | |||   |  | |  ||    |   | |    |  ||   |  | ||| |    ||||   | |||||||| ||||| ||||| |||||||| || |||||||| ||||||||||||||||| ||||||||||| || || || ||| ||||  | |  || || || 
gtacatctttgacaggaaccaagttaagcatgttaccaaacaaaaagtaaaaaatcatgcattgttcttcttccctttttttttttgcagCGTCGTTCTGTTTCCTGTTGCTGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGCTTTTTCAGCCCACTATATGCAAAACTTGGGATC

upper sequence: GLYMA06G15360.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G048150_T04 (Zea mays), 3'ss of exon 2
---------gtaatggacaaaactactta--ttgagatgatta-attttatcatcattgttggtgtgcttattcatttagttttgaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTATTCAGTTTGTTGATGGTTTCTTTAGTCCAATATACTCCAGGCTCGGCATA
           || |||| ||   |  ||  |||   ||| || | | ||||     |  |    || ||   |       ||||  ||||||| ||||||||||| ||| ||||||| || |||||| | || |||||||||||||| |||||||||||||| || || ||| | ||  | |  || ||  | 
gtatgcttcacaa-ggaccaattcagatactttgcagtgactacaatatatctatgctaatatcctgttttggctgcctactttgtctctgcagTGTAGTTCTTTTCCCAATTGCTGTCACATTCTTCCTCACGTGGTGGTTTATTCAATTTGTTGATGGTTTTTTCAGCCCACTCTATGCAAAACTGGGGTTT

upper sequence: GLYMA06G15360.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G149662_T01 (Zea mays), 3'ss of exon 2
-----------gtaatggacaaaact--acttattgagatgattaattttatcatc-attgttggtgtgcttattcatttagttttgaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTATTCAGTTTGTTGATGGTTTCTTTAGTCCAATATACTCCAGGCTCGGCATA
             || | |   | ||  || | |||  ||   ||  | || | |  |||  ||       ||||  ||  |||||   | ||||| ||||| |||||||| ||||| || || |||||||| ||||||||||||||||| ||||||||||| || || |||||  ||||  | |   | || || 
gtacacccttcacaa-gaattgagctaaacctgttgccatatctatgtataccttttatttatgcctgatctatttcttgtgttttatgtatgcagTGTAGTCCTTTTTCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGGTTTTTCAGTCCCCTATATGCAAAAATTGGAATC

upper sequence: GLYMA06G15360.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G052855_T01 (Zea mays), 3'ss of exon 2
-----------------gtaatggacaaaact-acttattgagatgattaattttat----catcattgttggtgtgcttattcattta---gttttgaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTATTCAGTTTGTTGATGGTTTCTTTAGTCCAATATACTCCAGGCTCGGCATA
                   ||||   ||  |  ||   |||  |||  ||    ||      ||   || |  | |  |  ||  | |      |||   | ||||| ||||||||||| ||| ||||||| || |||||||| || ||||||||||| || |||||||||||||| || || ||| | ||  | |  || ||  | 
gtatgcttcacaagttcacaatgactaattcagacactttgcaatggctacaactacaatatattgatgctaatatcttcttttgtctccctactttttctttgcagTGTAGTTCTTTTGCCAATTGCTGTCACATTCTTCATCACTTGGTGGTTTATCCAATTTGTTGATGGTTTTTTCAGCCCACTCTATGCAAAACTGGGGTTT

upper sequence: GLYMA06G15360.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G046098_T02 (Zea mays), 3'ss of exon 2
-----------gtaatggacaaaact--acttattgagatgattaattttatcatcattgttggtgtgct-tattcatttagttttgaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTATTCAGTTTGTTGATGGTTTCTTTAGTCCAATATACTCCAGGCTCGGCATA
             |||  ||  | ||  || | |||  ||   ||  | || | |   |||  |  || | ||||  ||  |||||   ||||||| ||||| ||||| || ||||| || || |||||||| ||||||||||||||||| ||||||||||| || || |||||  ||||  | |  || || || 
gtacgcccttcacaata-actgagctaaacatgttgccatagctatatataccttttatgtatgcatgatatatttcttgtgttttatgtctgcagTGTAGTCCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGGTTTTTCAGTCCCCTATATGCAAAACTTGGAATC

upper sequence: GLYMA06G15360.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G046098_T04 (Zea mays), 3'ss of exon 2
-----------gtaatggacaaaacta--cttattgagatgattaattttatcatcattgttggtgtgct-tattcatttagttttgaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTATTCAGTTTGTTGATGGTTTCTTTAGTCCAATATACTCCAGGCTCGGCATA-----
             |||  ||  | |||  | | |||  ||   ||  | || | |   |||  |  || | ||||  ||  |||||   ||||||| ||||| ||||| || ||||| || || |||||||| ||||||||||||||||| ||||||||||| || || |||||  ||||  | |  || || ||      
gtacgcccttcacaata-actgagctaaacatgttgccatagctatatataccttttatgtatgcatgatatatttcttgtgttttatgtctgcagtgtagTCCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGGTTTTTCAGTCCCCTATATGCAAAACTTGGAATCAACAT

upper sequence: GLYMA06G15360.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 2
gtaatggacaaaacta---cttattg------agatgattaat--tttatcatcattgttggtgtgcttattcatttagttttgaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTATTCAGTTTGTTGATGGTTTCTTTAGTCCAATATACTCCAGGCTCGGCATA
|||||   |  | |||   |||| |       ||||| ||| |  ||| | || ||| |          ||| | ||  |||||||  ||||| || ||||||||||||||||| ||||| || ||  |||||||||||||||||||||| |||||||||||||| |||||| ||||     |||| ||||| 
gtaatatgcttacctatgccttaatatattctagatgtttactcattttttattattttccagcctaacattgagttgattttgaaattgcagTGTTGTTCTTTTTCCAGTTGCAGTTACATTTTTTGTTACATGGTGGTTTATTCAGTTCGTTGATGGTTTCTTCAGTCCATTATATGAACGGCTTGGCATC

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|192295732|gb|FG990826.1|FG990826
EST:     TGCTGCTTTGTTCTCCAGAGTTGGGTCTCTAAGAAATTTATGACTGGATG                         CGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTAT
genomic: TGCTGCTTTGTTCTCCAGAGTTGGGTCTCTAAGAAATTTATGACTGGATGgtaatggaca ... gaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattaattttatcatcattgttggtgtgcttattcatttagttttgaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTATTCAGTTTGTTGATGGTTTCTTTAGTCCAATATACTCCAGGCTCGGCATA
 gattaat  putative branch site (score: 3)
                             ttattcatttagtttt  TA-rich tract