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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCATTTGGGTCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAATAAATCGTTTCAGgtacatggtctgctttagtttattgtttttctatatattaattgcttaatcagatgcaaatttctcatttcttccatagttacctaaacattgcctctgg...

Basic information

species Zea mays
transcript GRMZM2G000645_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 12
ATCATTTGGGTCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAATAAATCGTTTCAGgtacatggtctgctttagtttattgtttttctatatattaatt-gcttaatcagatgcaaatttctcatttcttccatagttac-ctaaacattgcctctgg-
 |||||||| |||||| |||| ||||||||||||||||||||||| ||||| || ||||||||||||||||||||||||||||||| |||||| ||||||||   ||| |  | ||  ||  | |  ||||  | ||| |||| | | | | | |    | | | |||||||||| ||    || ||  | | |||  |    
GTCATTTGGATCTGCATTGGAGTTTGTTTGGTCATCAGAAGGAGAGTATGCTATCAGGGAAAGTACATCAAGAATAAAGATTTTCAGTAAATCATTTCAGgtt--tggcccacattgatt-gtagcctttccttttatgaatttgatcagtaaaactgtagtgtttcatttcttcaatcaccactctggagaatgcaccatct

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 12
ATCATTTGGGTCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAATAAATCGTTTCAGgtacatggtctgctttagtttattgtttttctatatattaattgcttaatcagatgcaaatttctcatttcttccatagttacctaaacattgcctctgg------
||||||||| || |||||||||||||||||||| ||||| || || |||||  | || ||||||||||| |   | || |||||||  |||   || |||||   || |   ||||   ||| |  || ||  | |||   |||  | ||  || | || |            | | | ||  ||||| | |   |          
ATCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCAGATGGGGAGTATGCTGTAAGAGAAAGTACATCGAAGGTTAAAATTTTCAGCAAAAATTTCCAGgt-tgtgcttcactttcagttact-cttatcattttatactttgtcttat--gacgaaagtgatggtgacaacctacaatt--ctaaataatttgttaaaaggata

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 12
ATCATTTGGGTCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAATAAATCGTTTCAGgtacatggtctgctttagtttattgttttt-ctatatattaattgcttaatcagatgcaaatttctcatttcttccatagttacctaaacattgcctctgg-----
||||||||| || || ||||||||||||||||| ||||| || || |||||  | || ||||||||||| |   | || |||||||  |||   || |||||   || |    | |   ||| | || |   | |||| |   |  | |  |  | |  |  |  | |   | | || | |   ||||| | |   |         
ATCATTTGGTTCAGCTCTGGAATTTGTTTGGTCTTCAGATGGGGAGTATGCTGTAAGAGAAAGTACATCGAAGGTCAAAATTTTCAGCAAAAATTTCCAGgt-tgtgcttcattatcagttactcttatcattttatactttgtattaagacgaaagtga--tggtgacagcctacaaatt---ctaaataatttgttaaaaggat

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 12
ATCATTTGGGTCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAATAAATCGTTTCAGgtacatggtctgctttag--tttattgtttttcta-tatattaattgcttaatcag-atgcaaatttctcatttcttcc-atagttacctaaacattgcctctgg
 |||||||| || |||||||||||||||||||| || || |||||||||||  | || |||||||||||||  || || |||||||  |||   || |||||   |  | |  |  |   ||| ||   | |||| | |  |     |||  || |  || ||    |  |    |||      || | ||||            
GTCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCTGAGGGAGAATATGCTGTCAGAGAAAGTACATCAAAGATTAAAATTTTCAGCAAAAATTTCCAGgtttgtacttttttaaaaactttgtttcctctctaatctcgtgcaatcttgttctgtgtgtaatgaaccaacaagttcttgctatttcttaaaaggaaaa-----

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 12
ATCATTTGGGTCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAATAAATCGTTTCAGgtacatggtctgctttag--tttattgtttttcta----tatattaattgcttaatcagatgcaaatttctcatttcttccatagttacctaaacattgcctctgg
 |||||||| || |||||||||||||||||||| || || |||||||||||  | || |||||||||||||  || || |||||||  |||   || |||||   |  | |  ||||   || |||   | ||||    | | | |  |  ||  |    |    |     ||  |  |   || ||    |||            
GTCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCTGAGGGAGAATATGCTGTCAGAGAAAGTACATCAAAGATTAAAATTTTCAGCAAAAATTTCCAGgtttgtacttttttttaaacttcatttcctctctaatcttgtgtgatcttgttctttgtgtaatgaaccaacaagttcttgctatttcttaaaaggaaaa------

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 12
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 12
ATCATTTGGGTCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAATAAATCGTTTCAGgtacatgg-----------tctgctttagtttattgttttt--ctatatattaattgcttaatcagatgcaaatttctcatttcttccatagttacctaaacattgcctctgg------------------------
 |||||||| |||| ||||||||||||||||||||| || || || | |||  |||| |||||  ||||||  || || || || |  |||   || |||||   |             |||| | ||     || | ||   |  | |||  || | |   |  || | |   ||   | |  |     || || ||| |  | |  |||||                        
GTCATTTGGTTCTGGACTGGAATTTGTTTGGTCATCCGAGGGGGAGTGTGCGGTTAGAGAAAGCTCATCAAAGATTAAAATATTTAGCAAAAATTTCCAGgtttctaaatctttttctctctgatctaagccgttctgttcaaccctgtatctatggtt--gttggaagtattattgatactggtcatggagatagctatat-tcggatctggctcattcagaaaatacattttcag

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 12
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 12
ATCATTTGGGTCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAATAAATCGTTTCAGgtacatggtct--------gctttagtt-tattgtttttctatatattaattgcttaatcagatgcaaatttctcatttcttccatagttac--ctaaacattgcctctgg-------------------------
||| ||||||||||  |||||||||||||||||||| || || |||| |||  |||| |||||  ||||||  |||||||| |||| ||||   || |||||      |          || ||| |  || | ||||  |  |   | |||      |   |   ||||| |  ||   | | ||||  ||  |||    | || | |                           
ATCTTTTGGGTCTGGCCTGGAATTTGTTTGGTCATCTGAGGGGGAATGTGCGGTTAGAGAAAGCTCATCAAAGATAAAGATATTCAGTAAAAATTTCCAGgtttgctattctcattatggccttactcatactattttgttggagtatgattctagggttgaa--gaaattgcagatgcttgcaatagagacagctattactggcttattatattaataaaaggtggtgttttcag

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 12
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 12
ATCATTTGGGTCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAATAAATCGTTTCAGgtacatggtctgctttagtttattgtttttctatatattaattgcttaatcagatgcaaatttctcatttct-tccatagttacctaaacat-tgcctctgg-------
 || ||||| || ||| |||||||||| ||||||||||| || ||||||||  | || |||||||||||||   | |||||||||| |||    || |||||   ||  |     |      |||||| ||| |  || |     |  || || |||||  |    || | | | |||   |   |     | |||  |||        
GTCTTTTGGTTCGGCATTGGAATTTGTATGGTCATCAGATGGTGAATATGCTGTCAGAGAAAGTACATCAAAGGTTAAGATTTTCAGTAAGAATTTCCAGgtttgtgtcccctcct------ttgtttctctctg-atgag--aatagattaggtgcaatatatatatatatatgcatgtgtgtgtgtgtgtgtgctgctgaaaacatt

upper sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 12
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 12
ATCATTTGGGTCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAATAAATCGTTTCAGgtacatggtctgctttagtttattgtttttctatatattaattg---cttaatcagatgcaaatttctcatttcttccatagttacctaaacattgcctctgg
||||||||| || || ||||||||||||||||||||||| | |||||||||  | ||||||||||||||||| || ||||||||||  ||| | || |||||       ||     ||||||   | |  | |  |||| || |   |||      | |||||||   || | ||||  | ||| |  |    ||     |  
ATCATTTGGCTCAGCGCTGGAATTTGTTTGGTCATCAGATGCAGAATATGCTGTGAGGGAAAGTACATCAAGGATTAAGATTTTCAGCAAAACATTCCAGgttttgatcctttcaaagtttagattctcacgacttattgatgggggcttttctccaagcaaattag-caatgcttcttttgttgcaaagttgtttatctt--

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|32865242|gb|CF004924.1|CF004924
EST:     CAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAATAAATCGTTTCAG                         GAGAAGAAAACTATCCGCCCTTCATTTTCAGCAGAGCGTATTTATGGTGGG
genomic: CAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAATAAATCGTTTCAGgtacatggtc ... gattttttagGAGAAGAAAACTATCCGCCCTTCATTTTCAGCAGAGCGTATTTATGGTGGG
EST: gi|31353243|gb|CD437600.1|CD437600
EST:     CAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAATAAATCGTTTCAG                         GAGAAGAAAACTATCCGCCCTTCATTTTCAGCAGAGCGTATTTATGGTGGG
genomic: CAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAATAAATCGTTTCAGgtacatggtc ... gattttttagGAGAAGAAAACTATCCGCCCTTCATTTTCAGCAGAGCGTATTTATGGTGGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 209

ATCATTTGGGTCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAATAAATCGTTTCAGgtacatggtc ... gattttttagGAGAAGAAAACTATCCGCCCTTCATTTTCAGCAGAGCGTATTTATGGTGGGGTATTGTTGGCAATGTGTTCTAGTGACTTCATCTGCTTTTATGACTGGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 84

ATCATTTGGGTCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAATAAATCGTTTCAGgtacatggtc ... gattttttagGAGAAGAAAACTATCCGCCCTTCATTTTCAGCAGAGCGTATTTATGGTGGGGTATTGTTGGCAATGTGTTCTAGTGACTTCATCTGCTTTTATGACTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 56

ATCATTTGGGTCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAATAAATCGTTTCAGgtacatggtc ... gattttttagGAGAAGAAAACTATCCGCCCTTCATTTTCAGCAGAGCGTATTTATGGTGGGGTATTGTTGGCAATGTGTTCTAGTGACTTCATCTGCTTTTATGACTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 170

ATCATTTGGGTCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAATAAATCGTTTCAGgtacatggtc ... gattttttagGAGAAGAAAACTATCCGCCCTTCATTTTCAGCAGAGCGTATTTATGGTGGGGTATTGTTGGCAATGTGTTCTAGTGACTTCATCTGCTTTTATGACTGGG