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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctacagtacattgcttagttgctttggcatgttacagtttctgtcgaggatatgaattaaagtatgtcatgcattagtattctaggatccatcatttgtgtgagtatttgcgtgctgcatgctgtaaccagtattgtaatttttctagTTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACA

Basic information

species Zea mays
transcript GRMZM2G052880_T01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052880_T01 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os02g25580.1 (Oryza sativa), 3'ss of exon 19
--------gtatctacagtacattgcttagttgctttggcatgttacagtttctgtcgaggatatgaattaaa-gtatgtcatgcattagta----ttctaggatccatcatttgtgtgagtatttgcgtgctgcatgctgtaaccagtattgtaatttttctagTTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACA
         ||  | ||   |  | ||   ||   |||     ||    ||| | | |      | | ||  |  |   ||||   |||  |    ||| |   |  |   |||      ||           ||| | | ||||| ||| | || | | |  ||||||||||||  ||||||||| |||||||||| ||||| ||  |||| |||||||||||||| || ||||||||||||||||||||||| 
gtatattattaattgcatgcctctcctcttttaagttgtagctttgagatttattttgctttcgtaatttggatattcatcatttgttacaagaatttccaatttggaaggtttaacctcgttaaaaaaaaaagcaaggtttaaccggtaatata-tatctgcagTTACGTGCTGTGCACAAGCTTACATCCAAGCTAAAGCGGGAAGTCATACTTGGTTCATCTAGTCTGGATGATCCTCCCCAGTTCATCACG
















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|211275799|gb|FL433157.1|FL433157
EST:     TTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAG                         TTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTT
genomic: TTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAGgtatctacag ... atttttctagTTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTT
EST: gi|67022604|gb|CO451353.1|CO451353
EST:     TGGTCAGCGTATATTTGTTTTTGTA-TAAGGCG-TGCTACTCGATCAGA-                         TTACGTGCTGCACACA-GCTTT
genomic: TGGTCAGCGTATATTTGTTTTTGTAATA-GGCGGTGCTACTCGATCAGAGgtatctacag ... atttttctagTTACGTGCTGCACACAAGCTTT
EST: gi|60345833|gb|DN212806.1|DN212806
EST:     TTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAG                         TTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTT
genomic: TTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAGgtatctacag ... atttttctagTTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTT
EST: gi|60398850|gb|DN231666.1|DN231666
EST:     TTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAG                         TTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTT
genomic: TTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAGgtatctacag ... atttttctagTTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTT
EST: gi|211539100|gb|FL044736.1|FL044736
EST:     TTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAG                         TTACGTGCTKCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTT
genomic: TTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAGgtatctacag ... atttttctagTTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTT
EST: gi|50336914|gb|CO532040.1|CO532040
EST:     TTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAG                         TTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTT
genomic: TTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAGgtatctacag ... atttttctagTTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTT
EST: gi|76911270|gb|DV164216.1|DV164216
EST:     TTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAG                         TTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTT
genomic: TTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAGgtatctacag ... atttttctagTTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTT
EST: gi|6827451|gb|AW331094.1|AW331094
EST:     TTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGNGCTACTCGATCAGAG                         TTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTT
genomic: TTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAGgtatctacag ... atttttctagTTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTT
EST: gi|76908403|gb|DV162923.1|DV162923
EST:     TTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAG                         TTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTT
genomic: TTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAGgtatctacag ... atttttctagTTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTT
EST: gi|113858206|gb|DW974301.1|DW974301
EST:     CGGTGCTACTCGATCAGAG                         TTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTT
genomic: CGGTGCTACTCGATCAGAGgtatctacag ... atttttctagTTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTT
EST: gi|6194629|gb|AW146733.1|AW146733
EST:     TTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAG                         TTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTT
genomic: TTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAGgtatctacag ... atttttctagTTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTT
EST: gi|211447144|gb|FL470093.1|FL470093
EST:     TTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAG                         TTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTT
genomic: TTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAGgtatctacag ... atttttctagTTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTT

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: 47 (upstream exon), 47 (downstream exon)
Score: 77

TGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAGgtatctacag ... atttttctagTTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 210

TGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAGgtatctacag ... atttttctagTTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

TGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAGgtatctacag ... atttttctagTTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 54

TGATTCTGTGTTGAAGCATGCCTCCAGTGACTTCAGGAAACTTGGTCAGCGTATATTTGTTTTTGTAATAGGCGGTGCTACTCGATCAGAGgtatctacag ... atttttctagTTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgtgtgagtatttgcgtgctgcatgctgtaaccagtattgtaatttttctagTTACGTGCTGCACACAAGCTTTCATCCAAGCTGAAGCGAGACATCATCCTTGGTTCATCTAGCCTTGATGATCCTCCCCAGTTCATCACA
                            ctgtaac  putative branch site (score: 54)
                                              tttttct  putative PPT
                                      tattgtaatttttcta  TA-rich tract