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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcagcatgcagcatacctacttctgatcttcttacatgatgtgtttttgggttatgacaacaatttttttattacagTGTGGTGGGTTATACTTTACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCA

Basic information

species Zea mays
transcript GRMZM2G443953_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 16
gtaagcagca-tgcagcatacctacttctgatcttc---ttaca-tgatgtgtttttgggttatgacaacaatttttttattacagTGTGGTGGGTTATACTTTACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCA
|||||    | | | || |   |  |||  |  ||    || || | || |    |    || ||   |  | |||||| |  ||||||  |||| || ||  | ||  | || |||||||||||||| ||||||||||||||||| |||||||||   || |||   ||| ||||||| || || 
gtaagtgaaacttctgcttggattattcaaagttttaaattgcagtaatcttgactacttttctgtttatcaattttttttctcagTGTTATGGGATACACACTGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATCCCC

upper sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 16
gtaagcagcatg-cagcatacctacttctgatcttcttacatgatgtgtttttgggttatgacaacaatttttttattacagTGTGGTGGGTTATACTTTACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCA
|||||  |       |  | | |  |||  |   ||| | |||  ||  |  ||  ||||      || | ||||| | ||||||  |||| || ||  ||||  | ||||||||||| ||||| |||||||| |||||||| |||||||||   || |||   ||| ||||||| || || 
gtaagtggatcaatggtttgcattattcaaaatatctca-atgcagtaatcctga-ttatt-ttttaactgttttact-cagTGTTATGGGATACACGCTACTTTTAAGTTTGATTGAATACAAGACACTTGTCATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATTCCT

upper sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 17
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 16
gtaagcagca-tgcagcatacctacttctgatcttc---ttaca-tgatgtgtttttgggttatgacaacaatttttttattacagTGTGGTGGGTTATACTTTACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCA
|||||    | | | || |   |  |||  |  ||    || || | || |    |    || ||   |  | || ||| |  ||||||  |||| || ||  | ||  | || |||||||||||||| ||||||||||||||||| |||||||||   || |||  |||| | ||||| || || 
gtaagtgaaacttctgcttggattattcaaagttttaaattgcaataatcttgactatttttctgtttatcaattgtttttctcagTGTTATGGGATACACACTGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGATATTCTGCCATCAATCCCC

upper sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 17
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 20
gtaagcagcatgcagcatacctacttctgatcttcttacatgatgtgtttttgggttatgacaacaatttttttattacagTGTGGTGGGTTATACTTTACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCA
|||||||| |||    |    ||    || |     |   |  |   ||  ||  || ||    | | ||| | ||||||||||  | || || ||||||||  | ||||||||||||||||| || |||||||||||||| ||||||||||| || |||    | ||||| || || || 
gtaagcag-atgttttactgttatgattgctaacaatgttttgtaacttactgacttctg-tgtccactttatgattacagTGTTATTGGATACACTTTACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCT

upper sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 17
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 16
-----------gtaagcagcatgcagca-tacctacttctgatcttcttacatgatgtgtttttgggttatgacaacaatt--tttttattacagTGTGGTGGGTTATACTTTACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCA
            |  |||| | |  | | |      |  |  |  | || | | |  | ||| |   ||| |       ||  |||| | | ||||||  |||| || || ||||| |||||||||||||||||||| || |||||||||||||| ||  ||||||  || |||    ||||||| || || || 
gtgagtggacttttggcagaaagggggagtggagggtggttgttgtattgc-taacatctttatta-ttaagttggtttttccttttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCC

upper sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 17
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 16
gtaagcagcatgcagcatacctacttctgatcttcttacatgatgtgtttttgggttatgacaacaatttttttat---------tacagTGTGGTGGGTTATACTTTACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCA
|| ||  |      | |     |||||||    ||| ||    | |||| |||   | |||    ||||| |||||         | ||||||  |||| ||||| ||||| |||| ||||||||||||||| |||||||| |||||||| || ||  ||| ||| | |   |||||||| |  || || 
gtgag-ggagcttgggagctgcacttctg-caatctgactgcttttgttcttgtaat-tgatctaaatttatttatgttatcttatgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT

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|5895850|gb|AW037096.1|AW037096
EST:     GGATATCTTGCTAACCAAAGTCGTGTATATCTTATTGACAAGGAATTTAA                         TGGGGTGGGTTATACTTTACTACTCAGTTTGATTGAGTACAAAACACTTGT
genomic: GGATATCTTGCTAACCAAAGTCGTGTATATCTTATTGACAAGGAATTTAAgtaagcagca ... tttattacagTGTGGTGGGTTATACTTTACTACTCAGTTTGATTGAGTACAAAACACTTGT
EST: gi|160481629|gb|EY254461.1|EY254461
EST:     GGATATCTTGCTAACCAAAGTCGTGTATATCTTATTGACAAGGAATTTAA                         TGTGGTGGGTTATACTTTACTACTCAGTTTGATTGAGTACAAAACACTTGT
genomic: GGATATCTTGCTAACCAAAGTCGTGTATATCTTATTGACAAGGAATTTAAgtaagcagca ... tttattacagTGTGGTGGGTTATACTTTACTACTCAGTTTGATTGAGTACAAAACACTTGT

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), 49 (downstream exon)
Score: 63

GTTACTACAATGTTTCACTTGGATCGGCCTATGTATTTATTAGGATATCTTGCTAACCAAAGTCGTGTATATCTTATTGACAAGGAATTTAAgtaagcagca ... tttattacagTGTGGTGGGTTATACTTTACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 27

GTTACTACAATGTTTCACTTGGATCGGCCTATGTATTTATTAGGATATCTTGCTAACCAAAGTCGTGTATATCTTATTGACAAGGAATTTAAgtaagcagca ... tttattacagTGTGGTGGGTTATACTTTACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 14

GTTACTACAATGTTTCACTTGGATCGGCCTATGTATTTATTAGGATATCTTGCTAACCAAAGTCGTGTATATCTTATTGACAAGGAATTTAAgtaagcagca ... tttattacagTGTGGTGGGTTATACTTTACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCA


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

GTTACTACAATGTTTCACTTGGATCGGCCTATGTATTTATTAGGATATCTTGCTAACCAAAGTCGTGTATATCTTATTGACAAGGAATTTAAgtaagcagca ... tttattacagTGTGGTGGGTTATACTTTACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatcttcttacatgatgtgtttttgggttatgacaacaatttttttattacagTGTGGTGGGTTATACTTTACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCA
      ttcttac  putative branch site (score: 22)
                                         tttttttatt  putative PPT
                             ttatgacaacaatttt  TA-rich tract