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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcccttcacaataactgagctaaacatgttgccatagctatatataccttttatgtatgcatgatatatttcttgtgttttatgtctgcagtgtagTCCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGGTTTTTCAGTCCCCTATATGCAAAACTTGGAATCAACAT

Basic information

species Zea mays
transcript GRMZM2G046098_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046098_T04 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 2
gtacgcccttcacaataactgagctaaacatgttgccatagctatatataccttttatgtatgcatgatatatttcttgtgttttatgtctgcagtgtagTCCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGGTTTTTCAGTCCCCTATATGCAAAACTTGGAATCAACAT
||||  | || |||  |||  || ||| |||||| ||| | | | |  ||     |    ||||||  | | ||  |    |||| | | ||||| || || || || |||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||| || ||||||||||||||||| |||     
gtacatctttgacaggaaccaagttaagcatgttacca-aacaaaaagtaaaaaat---catgcattgt-tcttcttccctttttttttttgcagCGTCGTTCTGTTTCCTGTTGCTGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGCTTTTTCAGCCCACTATATGCAAAACTTGGGATC-----

upper sequence: GRMZM2G046098_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G39490.1 (Glycine max), 3'ss of exon 2
gtacgcccttcacaat-aactgagctaaacatgttgccatagctatatat-accttttatgtatgcatgatatatttcttgtgttttatgtctgcagtgtagTCCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGGTTTTTCAGTCCCCTATATGCAAAACTTGGAATCAACAT
             ||| |||  | |||  | | |||  ||   || || | | | |   |||  |  || | ||||  ||  |||||   ||||||| ||||| ||||| || ||||| || || |||||||| ||||||||||||||||| ||||||||||| || || |||||  ||||  | |  || || ||      
-----------gtaatgaacaaaacta--cttattgagatgattaaattttatcatcattgttggtgtgct-tattcatttagttttgaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTATTCAGTTTGTTGATGGTTTCTTTAGTCCAATATACTCCAGGCTCGGGATA-----

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

upper sequence: GRMZM2G046098_T04 (Zea mays), 3'ss of exon 2
lower sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 2
gtacgcccttcacaataactgagc-taaacatgttgccatagctatatataccttttatgtatgcatgat---atatttcttgtgttttatgtctgcagtgtagTCCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGGTTTTTCAGTCCCCTATATGCAAAACTTGGAATCAACAT
    |   |   |  || ||  || | || || || | | |  | ||   |  ||||||   |          | |||   |   ||||     |||||||| || ||||| || |||||||| || || ||  | ||||||||||||||||| || |||||||| || ||||||||  |||||| |   ||||| |||     
----gtaatatgct-tacctatgccttaatatatt-ctagatgtttactcattttttattattttccagcctaacattgagttgattttgaaattgcagTGTTGTTCTTTTTCCAGTTGCAGTTACATTTTTTGTTACATGGTGGTTTATTCAGTTCGTTGATGGTTTCTTCAGTCCATTATATGAACGGCTTGGCATC-----

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|42491828|gb|CK700874.1|CK700874
EST:     TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATG                         TGTAGTCCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTAT
genomic: TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATGgtacgccctt ... tgcagtgtagT-----CCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTAT
EST: gi|40287177|gb|CK327569.1|CK327569
EST:     TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATG                         TGTAGTCCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTAT
genomic: TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATGgtacgccctt ... tgcagtgtagT-----CCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTAT
EST: gi|42491878|gb|CK700924.1|CK700924
EST:     TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATG                         TGTAGTCCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTAT
genomic: TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATGgtacgccctt ... tgcagtgtagT-----CCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTAT
EST: gi|40287192|gb|CK327584.1|CK327584
EST:     TGCTGTGCTGTTCTTCAAAGNTGGGTCNNAAGAAAATTTATGACTGGATGTGTAG                     
genomic: TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA----T-Ggtacgccctt ... tgcagt
EST: gi|76293651|gb|DV033219.1|DV033219
EST:     TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATGTGTAG                     
genomic: TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA----T-Ggtacgccctt ... tgcagt
EST: gi|51871146|gb|CV126030.1|CV126030
EST:     TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATGTGTAG                     
genomic: TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA----T-Ggtacgccctt ... tgcagt
EST: gi|51871157|gb|CV126041.1|CV126041
EST:     TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATGTGTAG                     
genomic: TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA----T-Ggtacgccctt ... tgcagt
EST: gi|148949550|gb|EC895017.2|EC895017
EST:     TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATGTGTAG                     
genomic: TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA----T-Ggtacgccctt ... tgcagt
EST: gi|50336995|gb|CO532121.1|CO532121
EST:     TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATG                         TGTAGTCCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTAT
genomic: TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATGgtacgccctt ... tgcagtgtagT-----CCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTAT
EST: gi|28910665|gb|CB331552.1|CB331552
EST:     TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATG                         TGTAGTCCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTAT
genomic: TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATGgtacgccctt ... tgcagtgtagT-----CCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTAT
EST: gi|74239462|gb|DT647376.1|DT647376
EST:     TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATGTGTAG                     
genomic: TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA----T-Ggtacgccctt ... tgcagt
EST: gi|148944675|gb|EC889811.2|EC889811
EST:     TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATGTGTAG                     
genomic: TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA----T-Ggtacgccctt ... tgcagt
EST: gi|50323815|gb|CO518941.1|CO518941
EST:     TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATGTGTAG                     
genomic: TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA----T-Ggtacgccctt ... tgcagt
EST: gi|88755429|gb|DY539570.1|DY539570
EST:     TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATG                         TCCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTATTCAAT
genomic: TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATGgtacgccctt ... tgcagtgtagTCCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTATTCAAT
EST: gi|91053372|gb|EB163790.1|EB163790
EST:     TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATGTGTAG                     
genomic: TGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGA----T-Ggtacgccctt ... tgcagt

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: 27 (upstream exon), 49 (downstream exon)
Score: 11

GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATGgtacgccctt ... tgcagtgtagTCCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGGTTTTTCAGTCCCCTATATGCAAAACTTGGAATCAACAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 6

GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATGgtacgccctt ... tgcagtgtagTCCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGGTTTTTCAGTCCCCTATATGCAAAACTTGGAATCAACAT


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 12

GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATGgtacgccctt ... tgcagtgtagTCCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGGTTTTTCAGTCCCCTATATGCAAAACTTGGAATCAACAT


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 8

GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATGgtacgccctt ... tgcagtgtagTCCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGGTTTTTCAGTCCCCTATATGCAAAACTTGGAATCAACAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atataccttttatgtatgcatgatatatttcttgtgttttatgtctgcagtgtagTCCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGGTTTTTCAGTCCCCTATATGCAAAACTTGGAATCAACAT
                   atgatatatttctt  TA-rich tract