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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT

Basic information

species Zea mays
transcript GRMZM2G000645_T02
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 16
gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatag--cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT
|| |||||||| || || | ||| | |||    |  | |    |||| | ||||   ||||||| ||    |||| | ||||||||| ||||||||||||||||| |||||||||||||||||||| |||||||||||||||||| | || | ||||||  | |||||| |||||||||| 
gtgtgttttcttgataatactgcctgcttattgtc-tgg----tgttgaattcttgaactaacatatttttcttgttgcagTGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCA

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 16
------gtatgttttctcgaaaacaatgcttcctttcctttgtagca--tctgttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT
      | |  || |      |  | |      |||   ||| || |    ||   | || ||||  || ||| |   ||  | |||||| || || |||||| | ||| | || ||||||||||||||||| |||||||||||||| ||||||||    || ||  ||||| || |||| || || 
gtaagtgaaacttctgcttggattattcaaagttttaaattgcagtaatcttgactacttttctgtttatcaattttttttct-cagTGTTATGGGATACACACTGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATCCCC

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 16
gtatgttttctcgaaaacaatgcttcctttcctttgtagcatct------gttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT
        |      | ||||| ||    |  ||   |  ||||        ||||     | | |    ||  | ||    |||||| || || |||||  ||||| | ||||||||||| |||||||| ||||| |||||||| ||||||||    || ||  ||||| || |||| || |||
-------gtaagtggatcaatggtttgcattattcaaaatatctcaatgcagtaatcctgattattttttaactgttttactcagTGTTATGGGATACACGCTACTTTTAAGTTTGATTGAATACAAGACACTTGTCATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATTCCT

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 16
------gtatgttttctcgaaaacaatgcttcctttcctttgtagca--tctgttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT
      | |  || |      |  | |      |||   ||| |  |    ||   |||| ||||  || ||| | | ||    |||||| || || |||||| | ||| | || ||||||||||||||||| |||||||||||||| ||||||||    || ||  | ||| |  |||| || || 
gtaagtgaaacttctgcttggattattcaaagttttaaattgcaataatcttgactatttttctgtttatcaa-ttgtttttctcagTGTTATGGGATACACACTGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGATATTCTGCCATCAATCCCC

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 16
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 16
--------------gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT
               |||||||  | || |    || ||  | |    |  |  || || |||  | | |  ||      | |     | ||||||||| || || ||  | || || ||  ||||||| |||||||| ||||||||||| || |||||||||   || ||  |||||||| |  | || |||
gtacgttcctttatatatgtttatttgaga---ctgttttatcttgcatacataatttgctaacatatttccctttttcttgg--gaatgcagTGTCATAGGATATACCCTGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCT

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 16
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 16
gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagctt----ggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT
||| ||  | | ||      || ||   |   |  |     |||   | |||||    ||        | ||    | | |||||| || |||||||| ||  | || ||  |||||||||||||||| ||||||||||| || ||||| ||  | || |   |||| ||| |  | || |||
gtaagtgct-tagatttgtgtgtttatataattgagattgttctagaagtttctgatgctgttcccctgttttgtggatgcagTGTTATAGGGTACACCTTGTTGCTAAGCCTGATTGAGTACAAGACTCTTGTGATGCGGGGTGATTTAGACAAAGCCAGTGAAATCTTACCTACAATTCCT

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 16
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 20
------gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT
        |||||||   |  |  | ||||  |  |  ||||||  |  |  | | |||| || | |    ||   |    ||||||| ||||| ||||| |||||| | |||||||||||||||||||| |||||||||||||| |||||||| || || ||  || | ||| | || || |||
gtaagcagatgttttactgttatgattgctaacaatgttttgta--acttactgacttctgtgtccactttatgatt----acagTGTTATTGGATACACTTTACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCT

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 16
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 16
------gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagctt----------ggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT
      | |  |||    ||||       |         |||| | || || |||  ||| | | ||  || | | ||            | ||||||||| || ||||| |||||||| |||||||||||||||||||| |||||||||||||| ||  |||| |  || ||  || ||||| | || || || 
gtgagtggacttttggcagaaagggggagtggagggtggttgttgtat-tgctaacatcttt-attattaagttggtttttccttttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCC

upper sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 16
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 16
gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctga-ctaa-------caaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT
||  |    || |  | |    ||||       |    || | ||||  | |   ||| ||||        |  |    |  | |||||| || || || || |||||||| | |||||||||||||||||| ||||| |||||||| || ||  | | |||||   |||||||| | |  || |||
gtgagggagcttgggagctgcacttctgcaatctgactgcttttgttcttgtaattgatctaaatttatttatgttatcttatgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT

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|18965038|gb|BM661357.1|BM661357
EST:     GGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA                         TGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGT
genomic: GGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttc ... cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGT
EST: gi|89106492|gb|DY576709.1|DY576709
EST:     GGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA                         TGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGT
genomic: GGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttc ... cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGT
EST: gi|22490520|gb|BU050443.1|BU050443
EST:     GGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA                         TGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTT
genomic: GGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttc ... cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTT

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: 241

GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttc ... cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 181

GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttc ... cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 118

GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttc ... cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 252

GTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAAgtatgttttc ... cttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctttcctttgtagcatctgttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT
                                gactaac  putative branch site (score: 252)
                   tgttaattt  TA-rich tract