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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgaaccttatgatttttcgcatattgtacgctaataaaaaagctagaaataagggggagatgatactactaaacgtgtatgctttacttcattcttcgtaacctcgtgcttgtcttgtttagGTATATTTTGAACCGGATGAGGTCCACGCATGCATTGTCACTTGTGGAGGATTGTGCCCTGGACTTAATACTGTGATTAGGGAAATTGTATGTGGCTTAT

Basic information

species Zea mays
transcript GRMZM2G443985_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 4
gtatatgaaccttatgatttttcgcatattgtacgctaataaaaaagctagaaataagggggagatgatactactaaacgtgtatgctttacttcattcttcgtaacctcgtgcttgtcttgtttagGTATATTTTGAACCGGATGAGGTCCACGCATGCATTGTCACTTGTGGAGGATTGTGCCCTGGACTTAATACTGTGATTAGGGAAATTGTATGTGGCTTAT
                                       || | ||  | | | | |        | | || | |||    | |        ||| || ||  | || || |  |  || || | |||| | ||||||| ||||||||||||| |||||||||||||| ||||||||| ||||||||||||| || ||||| |||||||||||||||||||||||||
--------------------------------------gtatataacattgtattcatatac---taacacaaataagttggaaaaaaactattctttttttctcacttcatattattcctggtcagGTGTTTTTTGAATCGGATGAGGTCCATGCATGCATTGTCACATGTGGAGGACTGTGCCCTGGACTGAACACTGTCATTAGGGAAATTGTATGTGGCTTAT

upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 4
gtatatgaaccttatgatttttcgcatattgtacgctaataaaaaagctagaa-ataagggggagatgatactactaaacgtgtat---gctttacttc-attcttcgtaacctcgtgcttgtcttgtttagGTATATTTTGAACCGGATGAGGTCCACGCATGCATTGTCACTTGTGGAGGATTGTGCCCTGGACTTAATACTGTGATTAGGGAAATTGTATGTGGCTTAT
              | ||||  |   | ||||  |   ||| | |   || |  || | |     |  ||| ||  ||| || ||      |||  ||| | ||  |   ||||  | | | |  |||| ||||||| ||| || ||||||| || || |||||||||||||| ||||| ||| | |||||||| || || ||||| || ||||||||||| |||||  | |
-------------gtcatttcccttgt-ttgtctgtgcatatatattatatattattaagaactaagaatattaaaaaatgtataattaattttgtttccactcaccaacacctaat-catatgctgttcagGTATACTTTAAATCGGATGAAGTGCATGCATGCATTGTCACGTGTGGTGGACTCTGCCCTGGCCTCAACACTGTCATAAGGGAAATTGTCTGTGGTCTTT

upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 3
-gtatatgaaccttatgatttttcgcatattgtacgctaataaaaaagctagaaataagggggagatgatactactaaacgtgtatgctttacttcattcttcgtaacctcgtgcttgtcttgtttagGTATATTTTGAACCGGATGAGGTCCACGCATGCATTGTCACTTGTGGAGGATTGTGCCCTGGACTTAATACTGTGATTAGGGAAATTGTATGTGGCTTAT
   || |      | ||  | | || ||||| ||   || ||| ||   ||  ||||      | ||| ||  | |||   |||||          | ||  |   ||||  | | | |  |||| ||||||| ||| || ||||||| || || |||||||||||||| ||||| ||| | |||||||| || || ||||| || ||||||||||| |||||  | |
gtcatttcccttgtttgtctgtgcgtatattatatattattaagaa--ttaagaatatta--aaaatg-tataattaattttgtat--------caactcaccaacacctaat-catatgctgttcagGTATACTTTAAATCGGATGAAGTGCATGCATGCATTGTCACGTGTGGTGGACTCTGCCCTGGCCTCAACACTGTCATAAGGGAAATTGTCTGTGGTCTTT

upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 4
gtatatgaaccttatgatttttcgcatattgtacgctaataaaaaagctagaaataagggggagatgatactactaaacgtgtatgctttacttcattcttcgtaacctcgtgcttgtcttgtttagGTATATTTTGAACCGGATGAGGTCCACGCATGCATTGTCACTTGTGGAGGATTGTGCCCTGGACTTAATACTGTGATTAGGGAAATTGTATGTGGCTTAT
              | | | || |  | || ||  |     |   |  | ||||| |     |||  |||         |  | |   |||    ||||||       | | | ||   || |  |||| ||||||||  | ||||| || || ||||| ||||| || ||||| || || |||||||| || || || |||||||||||||| |||||||||||  
-------------gtaagtctttgtttgttatattc-----atggaatttgaaatgataaa-agacaata---------ggttttctcttaacatattctt-------ttgggttt---ttttccagGTGTATTTTGAGTCTGATGAAGTTCATGCATGTATTGTGACATGTGGTGGTTTATGCCCTGGCCTCAACACAGTGATTAGGGAAATAGTATGTGGCTTGA

upper sequence: GRMZM2G443985_T04 (Zea mays), 3'ss of exon 4
lower sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 5
gtatatgaaccttatgatttttcgcat-attgtacgctaataaaaaagctagaaataagggggagatgatactactaaacg--tgtatgctttacttcattcttcgtaacctcgtg-----cttgtcttgttt--agGTATATTTTGAACCGGATGAGGTCCACGCATGCATTGTCACTTGTGGAGGATTGTGCCCTGGACTTAATACTGTGATTAGGGAAATTGTATGTGGCTTAT
||   | |     || | | ||| | | ||| |  | ||||   ||   || | |  | |   |  |  |   |  ||  |  | | |   | |||||    || |  |  |||||     |||  |||||    || |||| ||  |  |||| || ||  | ||||||||||| |||||||||||||| ||||| ||| | |||||||||||| | || ||||| |||||  | |
gttcttaatatccattactcttctcttgatttttaggtaatttgaa---tacataccaagctaatttactgtcaagaagtgcctttttaagtgacttccacttttgacatttcgtgacactctttccttgtccgcagATATACTTCCAGTCGGAGGATGTGAAGGCATGCATTGTAACTTGTGGAGGATTATGCCCCGGAATCAATACTGTGATTCGTGAGATTGTCTGTGGTCTGT

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|148972520|gb|EE023481.2|EE023481
EST:     AGGATGGGCCCAGAGGTAACCATTTCCGTCGTGCTGGACCTCGCCAAAAG                         GTATATTTTGAACCGGATGAGGTCCACGCATGCATTGTCACTTGTGGAGGA
genomic: AGGATGGGCCCAGAGGTAACCATTTCCGTCGTGCTGGACCTCGCCAAAAGgtatatgaac ... tcttgtttagGTATATTTTGAACCGGATGAGGTCCACGCATGCATTGTCACTTGTGGAGGA
EST: gi|211132977|gb|FL170882.1|FL170882
EST:     AGGATGGGCCCAGAGGGAACCACTTCCGTCGTGCTGGACCTCGCCAAAAG                         GTATATTTTGAACCAGATGAGGTCCATGCATGCATTGTCACTTGTGGAGGA
genomic: AGGATGGGCCCAGAGGTAACCATTTCCGTCGTGCTGGACCTCGCCAAAAGgtatatgaac ... tcttgtttagGTATATTTTGAACCGGATGAGGTCCACGCATGCATTGTCACTTGTGGAGGA
EST: gi|13557855|gb|BG549211.1|BG549211
EST:     CCAGAGGTAACCATTTCCGTCGTGCTGGACCTCGCCAAAAG                         GTATATTTTGAACCGGATGAGGTCCACGCATGCATTGTCACTTGTGGAGGA
genomic: CCAGAGGTAACCATTTCCGTCGTGCTGGACCTCGCCAAAAGgtatatgaac ... tcttgtttagGTATATTTTGAACCGGATGAGGTCCACGCATGCATTGTCACTTGTGGAGGA
EST: gi|211132967|gb|FL170872.1|FL170872
EST:     AGGATGGGCCCAGAGGGAACCACTTCCGTCGTGCTGGACCTCGCCAAAAG                         GTATATTTTGAACCAGATGAGGTCCATGCATGCAT
genomic: AGGATGGGCCCAGAGGTAACCATTTCCGTCGTGCTGGACCTCGCCAAAAGgtatatgaac ... tcttgtttagGTATATTTTGAACCGGATGAGGTCCACGCATGCAT

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: 49 (upstream exon), 47 (downstream exon)
Score: 79

ATTGTTGTTCACAAGGATGGGCCCAGAGGTAACCATTTCCGTCGTGCTGGACCTCGCCAAAAGgtatatgaac ... tcttgtttagGTATATTTTGAACCGGATGAGGTCCACGCATGCATTGTCACTTGTGGAGGATTGTGCCCTGGACTTAATACTGTGATTAGGGAAATTGTATGTGGCTTAT


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 91

ATTGTTGTTCACAAGGATGGGCCCAGAGGTAACCATTTCCGTCGTGCTGGACCTCGCCAAAAGgtatatgaac ... tcttgtttagGTATATTTTGAACCGGATGAGGTCCACGCATGCATTGTCACTTGTGGAGGATTGTGCCCTGGACTTAATACTGTGATTAGGGAAATTGTATGTGGCTTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 107

ATTGTTGTTCACAAGGATGGGCCCAGAGGTAACCATTTCCGTCGTGCTGGACCTCGCCAAAAGgtatatgaac ... tcttgtttagGTATATTTTGAACCGGATGAGGTCCACGCATGCATTGTCACTTGTGGAGGATTGTGCCCTGGACTTAATACTGTGATTAGGGAAATTGTATGTGGCTTAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 114

ATTGTTGTTCACAAGGATGGGCCCAGAGGTAACCATTTCCGTCGTGCTGGACCTCGCCAAAAGgtatatgaac ... tcttgtttagGTATATTTTGAACCGGATGAGGTCCACGCATGCATTGTCACTTGTGGAGGATTGTGCCCTGGACTTAATACTGTGATTAGGGAAATTGTATGTGGCTTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actaaacgtgtatgctttacttcattcttcgtaacctcgtgcttgtcttgtttagGTATATTTTGAACCGGATGAGGTCCACGCATGCATTGTCACTTGTGGAGGATTGTGCCCTGGACTTAATACTGTGATTAGGGAAATTGTATGTGGCTTAT
                                         cttgtctt  CT-rich tract
               tttactt  TA-rich tract