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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggcaacaccaccagcaaatggcataaccttttgcacttcagtttctttattttgaaagatgatgttcctctttcaacctgttactttaaatcttgtcagATTGGTCTGGCGATGTCCCCATTGAGCAACAACTCCTTATTTCTTGACTATCATCGCAACCCTTTTCCAACGTTCTTCCAACGAGGTCTGAATGTCTCAT

Basic information

species Zea mays
transcript GRMZM2G416667_T03
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G416667_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 7
---------------------------------------------------aggcaacaccaccagcaaatggcataac------------cttttgcacttcagtttcttt-------attttgaaagatgatgttcctctttcaacctgttactttaaatcttgtcagATTGGTCTGGCGATGTCCCCATTGAGCAACAACTCCTTATTTCTTGACTATCATCGCAACCCTTTTCCAACGTTCTTCCAACGAGGTCTGAATGTCTCAT
                                                     | ||    |  || |||  |||| ||             |  |||| ||  ||||  ||       | |||  |||    | |   |  ||||| ||||| |||| ||| || ||||||||||||||| ||||||||||| |||||||||||||| |||||||| || || || || ||||| |||| ||| ||||||||||| |||||||| ||  
gtaattcttcatattttcataatccagcatgatttttaaaaacctctgtagctgtaattttatgagtaaaaagcatgacagatttatctaattagtgcagtttggtttgcttttaagaaactttttaagtcactatcatttcttcaatctgttgctttcaattttatcagATTGGTCTGGCAATGTCCCCATTAAGCAACAACTCCTTGTTTCTTGATTACCACCGGAATCCTTTCCCAATGTTTTTCCAACGAGGCCTGAATGTTTCCC

upper sequence: GRMZM2G416667_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA03G07460.1 (Glycine max), 3'ss of exon 15
aggcaacaccaccagcaaatggcataaccttttgcact-tcagtttctttattttgaaagatgatgttcctc--tttcaacctgttactttaaatcttgtcagATTGGTCTGGCGATGTCCCCATTGAGCAACAACTCCTTATTTCTTGACTATCATCGCAACCCTTTTCCAACGTTCTTCCAACGAGGTCTGAATGTCTCAT
                     | || ||| |||   |  |   || |||  || ||| |  ||  |||      ||| |      |  |||     || | ||||||| ||||| ||||| || |||||||| |||||| ||||  | ||||| ||||| || |||||||||| |||||||  ||| ||||||||||| ||| 
---------------------gtatgacccttttttcaattgattacttggttgtgagatttgtagtttgctaattttagttgaatgtttt-----ttattagATTGGGCTGGCAATGTCTCCTTTGAGCAATAACTCCCTATTCTTAGACTACCATCGGAATCCTTTTCCAATGTTCTTCTTACGGGGTCTGAATGTGTCAC

upper sequence: GRMZM2G416667_T01 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA01G29470.1 (Glycine max), 3'ss of exon 16
aggcaacaccaccagcaaatggcataaccttttgcact-tcagtttctttattttgaaagatgatgttcctctttcaacctgttactttaaatcttgtcagATTGGTCTGGCGATGTCCCCATTGAGCAACAACTCCTTATTTCTTGACTATCATCGCAACCCTTTTCCAACGTTCTTCCAACGAGGTCTGAATGTCTCAT
                     | ||  || |||   |  |   || |||  || ||| |  ||  ||| ||  ||  |    ||| |||     || | ||||||| ||||| ||||| || |||||||| |||||| ||||  | ||||| ||||| || |||||||||| |||||||  ||| ||||||||||| ||| 
---------------------gtatggcccttttttcaattgattacttggttgtgatatttgtagttgctaattttagt--ttatttt----tttattagATTGGGCTGGCAATGTCTCCTTTGAGCAATAACTCCCTATTCTTAGACTACCATCGGAATCCTTTTCCAATGTTCTTCTTACGGGGTCTGAATGTGTCAC

upper sequence: GRMZM2G416667_T01 (Zea mays), 3'ss of exon 15
lower sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 15
aggcaacaccaccagcaaatggcataaccttttgcacttcagtttctttattttgaaaga--tgatgttcctctttcaacctgttactttaaatcttgtcagATTGGTCTGGCGATGTCCCCATTGAGCAACAACTCCTTATTTCTTGACTATCATCGCAACCCTTTTCCAACGTTCTTCCAACGAGGTCTGAATGTCTCAT
                             | | |    |   |   | ||||    | |   |  |||| || ||  ||   |  | ||    | ||| |||||||||||||| ||||| ||| ||||||||||||| || ||||| || || || || ||||| |||||   ||| |||  | ||||||| ||||| ||  
--------------------------gtttgtggagactgcctgcatgtattacatatgtattattgtttctgttctaagaagacatttc---ttttgacagATTGGTCTGGCCATGTCACCACTGAGCAACAACTCTTTGTTTCTAGATTACCACCGGAACCCGTTTCCTGTGTTTTTCTTAAGAGGTCTCAATGTTTCTC

upper sequence: GRMZM2G416667_T01 (Zea mays), 3'ss of exon 15
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 3'ss of exon 15
aggcaacaccaccagcaaatggcataa--ccttttgcacttcagtttctttattttgaaagatgatgttcctctttcaacctgttactttaaatcttgt-cagATTGGTCTGGCGATGTCCCCATTGAGCAACAACTCCTTATTTCTTGACTATCATCGCAACCCTTTTCCAACGTTCTTCCAACGAGGTCTGAATGTCTCAT
             |  ||  |  || |  |  |||  | |  |  | |  |   ||||    |        |||      |||| | |  |  |    | |||||||||||||| ||||| ||  |||||||||| ||||| ||| | ||||||||||| || |||||||| | ||| ||||  || || || ||||| ||  
-----------gtaaaaagggagatgatgctgttttgaatatatctacactgacttgattattccatagtatctgattggctgtgattgcatgttggttacagATTGGTCTGGCTATGTCTCCTCTGAGCAACAATTCCTTGTTTTTGGACTATCATCGGAATCCTTTTCCTATGTTTTTCCTTCGGGGCCTCAATGTTTCCC

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|18661413|gb|BM501264.1|BM501264
EST:     TTAATCTAAGGAAGTCTCCTGTGCTTCAGTACTTGTACTATCTTGGTCAG                         ATTGGTCTNGCGATGTNCCCATTGAGCAACAA-TCCTNAATNCTTGACTAT
genomic: TTAATCTAAGGAAGTCTCCTGTGCTTCAGTACTTGTACTATCTTGGTCAGgtaatatgtt ... atcttgtcagATTGGTCTGGCGATGTCCCCATTGAGCAACAACTCCTTATTTCTTGACTAT
EST: gi|33101472|gb|CF061432.1|CF061432
EST:     GTACTATCTTGGTCAG                         ATTGGTCTGGCGATGTCCCCATTGAGCAACAACTCCTTATTTCTTGACTAT
genomic: GTACTATCTTGGTCAGgtaatatgtt ... atcttgtcagATTGGTCTGGCGATGTCCCCATTGAGCAACAACTCCTTATTTCTTGACTAT
EST: gi|5871432|gb|AW017903.1|AW017903
EST:     TTAATCTAAGGAAGTCTCCTGTGCTTCAGTACTTGTACTATCTTGGTCAG                         ATTGGTCTGGCGATGTCCCCATTGAGCAACAACTCCTTATTTCTTGACTAT
genomic: TTAATCTAAGGAAGTCTCCTGTGCTTCAGTACTTGTACTATCTTGGTCAGgtaatatgtt ... atcttgtcagATTGGTCTGGCGATGTCCCCATTGAGCAACAACTCCTTATTTCTTGACTAT

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), 45 (downstream exon)
Score: 11

TGATCACTTGGCAGCGACATTTCTTCTCTGTCACAACATATCACATGGAATTAATCTAAGGAAGTCTCCTGTGCTTCAGTACTTGTACTATCTTGGTCAGgtaatatgtt ... atcttgtcagATTGGTCTGGCGATGTCCCCATTGAGCAACAACTCCTTATTTCTTGACTATCATCGCAACCCTTTTCCAACGTTCTTCCAACGAGGTCTGAATGTCTCAT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 22

TGATCACTTGGCAGCGACATTTCTTCTCTGTCACAACATATCACATGGAATTAATCTAAGGAAGTCTCCTGTGCTTCAGTACTTGTACTATCTTGGTCAGgtaatatgtt ... atcttgtcagATTGGTCTGGCGATGTCCCCATTGAGCAACAACTCCTTATTTCTTGACTATCATCGCAACCCTTTTCCAACGTTCTTCCAACGAGGTCTGAATGTCTCAT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 28

TGATCACTTGGCAGCGACATTTCTTCTCTGTCACAACATATCACATGGAATTAATCTAAGGAAGTCTCCTGTGCTTCAGTACTTGTACTATCTTGGTCAGgtaatatgtt ... atcttgtcagATTGGTCTGGCGATGTCCCCATTGAGCAACAACTCCTTATTTCTTGACTATCATCGCAACCCTTTTCCAACGTTCTTCCAACGAGGTCTGAATGTCTCAT


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 15

TGATCACTTGGCAGCGACATTTCTTCTCTGTCACAACATATCACATGGAATTAATCTAAGGAAGTCTCCTGTGCTTCAGTACTTGTACTATCTTGGTCAGgtaatatgtt ... atcttgtcagATTGGTCTGGCGATGTCCCCATTGAGCAACAACTCCTTATTTCTTGACTATCATCGCAACCCTTTTCCAACGTTCTTCCAACGAGGTCTGAATGTCTCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttattttgaaagatgatgttcctctttcaacctgttactttaaatcttgtcagATTGGTCTGGCGATGTCCCCATTGAGCAACAACTCCTTATTTCTTGACTATCATCGCAACCCTTTTCCAACGTTCTTCCAACGAGGTCTGAATGTCTCAT
                                              tcttgtc  CT-rich tract
                                    ttactttaaatctt  TA-rich tract