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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcggtattgtttatttttctaaaataaaaatagctggtgtcaacctagtgtgtaagaaattgcttggttttttaactagcctactttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTT

Basic information

species Zea mays
transcript GRMZM2G134738_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134738_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 4
gtaagtcggtattgtttatttttctaaaataaaaatagctggtgtcaacctagtgtgtaagaaattgcttggttttttaactagcctactttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTT---
|| |||| || |||   | ||  || |   |||| |      || |||  || | || || |      |     ||||   |  | |  || |||  ||||||| || |||||||||||||||||||||||||||||||| || ||||||||||| |||||||| || ||||| |||   
gtcagtcagtgttg---acttggctcagcgaaaactctaaactgccaaa-tattatgcaatactggtatcaacatttt--ttcacttctttcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG
















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|60340144|gb|DN207117.1|DN207117
EST:     TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTG                         AGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
genomic: TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
EST: gi|18173629|gb|BM349017.1|BM349017
EST:     TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTG                         AGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
genomic: TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
EST: gi|76288216|gb|DV027784.1|DV027784
EST:     TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGGGAGGGTG                         AGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
genomic: TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
EST: gi|31354094|gb|CD438451.1|CD438451
EST:     CTCAGAGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG
genomic: CTCAGAGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG
EST: gi|21759837|gb|BQ635378.1|BQ635378
EST:     CGGATAGTCGGTTGTCCTGGTGGCGAGGGTG                         AGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
genomic: CGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
EST: gi|18450555|gb|BM428833.1|BM428833
EST:     CTCAGAGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCCAG
genomic: CTCAGAGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCT-CCAG
EST: gi|211038526|gb|FL455206.1|FL455206
EST:     TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTG                         AGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAASMCGASCCGCATG
genomic: TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
EST: gi|28985245|gb|BQ538397.2|BQ538397
EST:     TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTG                         AGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
genomic: TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
EST: gi|29130310|gb|CB381014.1|CB381014
EST:     TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTG                         AGGACGAACATGATG
genomic: TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATG
EST: gi|18450528|gb|BM428806.1|BM428806
EST:     CTCAGAGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG
genomic: CTCAGAGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG
EST: gi|60352341|gb|DN219314.1|DN219314
EST:     CAGAGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG
genomic: CAGAGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG
EST: gi|161588036|gb|EY962533.1|EY962533
EST:     TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTG                         AGGACGAACATGA
genomic: TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGA
EST: gi|37382992|gb|CF628470.1|CF628470
EST:     CTCAGAGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG
genomic: CTCAGAGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG
EST: gi|24770192|gb|CA405321.1|CA405321
EST:     TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTG                         AGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
genomic: TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
EST: gi|60348157|gb|DN215130.1|DN215130
EST:     TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTG                         AGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
genomic: TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
EST: gi|60357675|gb|DN224648.1|DN224648
EST:     TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTG                         AGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
genomic: TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
EST: gi|18649503|gb|BM498322.1|BM498322
EST:     CTCAGAGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG
genomic: CTCAGAGGACAAGCCGGCGAGGGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTAGAGGCCGAGCTCCAG
EST: gi|76288217|gb|DV027785.1|DV027785
EST:     TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTG                         AGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG
genomic: TGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATG

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: 176

GAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 310

GAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 276

GAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 278

GAGGAACCAGCTGTCATTGAGTCATACTATAACAAGCGGATAGTCGGTTGTCCTGGTGGCGAGGGTGgtaagtcggt ... ttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caacctagtgtgtaagaaattgcttggttttttaactagcctactttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTT
                             ttttaac  putative branch site (score: 278)
                                       cctacttt  putative PPT
                           ttttttaacta  TA-rich tract