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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatttttttatcacttgacaatgtgttccatggtatttgtccgtgagggaagatcccacttttactgacacgattattacgctcatgtcatactcgtgatctttttctccacatgtagCATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAA

Basic information

species Zea mays
transcript GRMZM2G028535_T02
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os01g62900.1 (Oryza sativa), 3'ss of exon 19
gtacatttttttatcacttgacaatgtgttccatggtatttgtccgtgagggaagatcc-cacttttactgacacgattattacgctcatgtcatactcgtg-atc--tttttctccacatgtagCATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAA
                        ||| |   ||  || |   | |   |  || |||   | ||||      || | || ||   |||||| |||   ||| ||   ||||||   | || ||||||||| || || ||||||||||| ||||| || ||||||||||| ||||||||||||| ||| || |||||||| ||||    
------------------------tgt-tattatcatactaaacagatggaaaaaatcagtagttttgtatttactactagtatcttcatgtaatatgtgtgcattggtttttcgttatatatagCATTTTACGAGGAAGTGGACAAGTAGTGAACGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAG----

upper sequence: GRMZM2G028535_T02 (Zea mays), 3'ss of exon 19
lower sequence: AT3G55610.1 (Arabidopsis thaliana), 3'ss of exon 19
gtacatttttttatcacttgacaat-gtgttccatggtatttgtccgtgagggaagatcccacttttactgacacgattattacgctcatgtcatactcgtgatctttttctccacatgtagCATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAA----------------
                    ||||| | |||   | || | | ||  |     | | || |   |||    | |    | | | | | |  |  |  | |||||          |     || ||  || | || |  |||||||| ||| |||| ||||| ||| | ||||||||||| |||||||||||| |   |  | | |                 
---------------gtactacaattgagttattttgtttctctctcttccata-gttcactgatttgtcaaaa--gctgtgaagtttaaatggttgtggtgatg---------aatgacagGATAATGAGAGGAAAGGGACAAGTTGTGGATGGAGACAATGGAATCGTTTACACCCATAAGGATCTTCCTGTCTTACAAAGGACAGAGGCTGTTGAGAAT
















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|32930909|gb|CF035721.1|CF035721
EST:     ATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTG                         CATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTA
genomic: ATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTGgtacattttt ... ccacatgtagCATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTA
EST: gi|6022040|gb|AW066983.1|AW066983
EST:     ATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTG                         CATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTA
genomic: ATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTGgtacattttt ... ccacatgtagCATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTA
EST: gi|61118748|gb|DN559709.1|DN559709
EST:     ATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTG                         CATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTA
genomic: ATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTGgtacattttt ... ccacatgtagCATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTA
EST: gi|60344250|gb|DN211223.1|DN211223
EST:     ATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTG                         CATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTA
genomic: ATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTGgtacattttt ... ccacatgtagCATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTA
EST: gi|60355192|gb|DN222165.1|DN222165
EST:     ATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTG                         CATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTA
genomic: ATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTGgtacattttt ... ccacatgtagCATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTA
EST: gi|211181077|gb|FL441225.1|FL441225
EST:     ATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTG                         CATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTA
genomic: ATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTGgtacattttt ... ccacatgtagCATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTA
EST: gi|101391685|gb|EB817779.1|EB817779
EST:     ATACATGCCCGCGGCCCTGTTGGAGTTGATGGACTTCTAACTACTCGCTG                         CATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTA
genomic: ATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTGgtacattttt ... ccacatgtagCATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTA
EST: gi|149066719|gb|EE286860.2|EE286860
EST:     ATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTG                         CATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTA
genomic: ATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTGgtacattttt ... ccacatgtagCATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTA
EST: gi|67017479|gb|CO446228.1|CO446228
EST:     ATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTG                         CATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTA
genomic: ATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTGgtacattttt ... ccacatgtagCATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTA

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: 204

GTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTGgtacattttt ... ccacatgtagCATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAA


Block sizes: 41 (upstream exon), 45 (downstream exon)
Score: 14

GTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTGgtacattttt ... ccacatgtagCATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAA


Block sizes: 40 (upstream exon), 47 (downstream exon)
Score: 6

GTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTGgtacattttt ... ccacatgtagCATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 595

GTTGGCATAAGTACAGAGCGCATACATGCCCGCGGACCTGTTGGAGTTGATGGACTTCTAACTACTCGCTGgtacattttt ... ccacatgtagCATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgacacgattattacgctcatgtcatactcgtgatctttttctccacatgtagCATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGGCAA
 tactgac  putative branch site (score: 595)
                                    tctttttctccacat  putative PPT
         attatta  TA-rich tract