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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccatcctccgtttgtatgtatgcaatttccatttcaaatcggtactgatgaattggctgcctctctgcagCTTTACAAAATCTTGGAAAATAATGGTGGACTCGCATGAAACCCAGAGGCAGATTATGTTCGAGGTGAATTCATTTACATGCCCTGCTTATGGCAAATTC

Basic information

species Zea mays
transcript GRMZM2G440831_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G440831_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g37040.1 (Oryza sativa), 3'ss of exon 3
gtaagcc-atcctccgtttgtatgta--------tgcaatttccatttcaa--atcggtactgatgaattggctgcctctctg-cagCTTTACAAAATCTTGGAAAATAATGGTGGACTCGCATGAAACCCAGAGGCAGATTATGTTCGAGGTGAATTCATTTACATGCCCTGCTTATGGCAAATTC
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gtaagctgaccttacatccgtgtgtggtaagttctgctagtcccattcctgttgttaaaactgatggtttgcttgcctccttggcagGCTGACAAGAACTTGGAAAATAATGGTGGACTCACATGAAACCCAGAGACAGATAATGTTTGAGGTGAATTCGTTCACCTGCCCTGCTTATGGCAAATTC
















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|78116819|gb|DV535206.1|DV535206
EST:     AAGTTACGGGACGAGGAACTGCAGCCACAACTCGTCGAGCTGTTGCAGGG                         CTTTACAAAATCTTGGAAAATAATGGTGGACTCGCATGAAACCCAGAGGCA
genomic: AAGTTACGGGACGAGGAACTGCAGCCACAACTCGTCGAGCTGTTGCAGGGgtaagccatc ... ctctctgcagCTTTACAAAATCTTGGAAAATAATGGTGGACTCGCATGAAACCCAGAGGCA
EST: gi|26558650|gb|CA830885.1|CA830885
EST:     AAGTTACGGGACGAGGAACTGCAGCCACAACTCGTCGAGCTGTTGCAGGG                         CTTTACAAAATCTTGGAAAATAATGGTCGACTCGCATGAAACCCAGAGGCA
genomic: AAGTTACGGGACGAGGAACTGCAGCCACAACTCGTCGAGCTGTTGCAGGGgtaagccatc ... ctctctgcagCTTTACAAAATCTTGGAAAATAATGGTGGACTCGCATGAAACCCAGAGGCA
EST: gi|87155625|gb|DY400414.1|DY400414
EST:     AAGTTACGGGACGAGGAACTGCAGCCACAACTCGTCGAGCTGTTGCAGGG                         CTTTACAAAATCTTGGAAAATAATGGTCGACTCGCATGAAACCCAGAGGCA
genomic: AAGTTACGGGACGAGGAACTGCAGCCACAACTCGTCGAGCTGTTGCAGGGgtaagccatc ... ctctctgcagCTTTACAAAATCTTGGAAAATAATGGTGGACTCGCATGAAACCCAGAGGCA
EST: gi|78116820|gb|DV535207.1|DV535207
EST:     AAGTTACGGGACGAGGAACTGCAGCCACAACTCGTCGAGCTGTTGCAGGG                         CTTTACAAAATCTTGGAAAATAATGGTGGACTCGCATGAAACCCAGAGGCA
genomic: AAGTTACGGGACGAGGAACTGCAGCCACAACTCGTCGAGCTGTTGCAGGGgtaagccatc ... ctctctgcagCTTTACAAAATCTTGGAAAATAATGGTGGACTCGCATGAAACCCAGAGGCA
EST: gi|30270747|gb|BQ280273.1|BQ280273
EST:     AAGTTACGGGACGAGGAACTGCAGCCACAACTCGTCGAGCTGTTGCAGGG                         CTTTACAAAATCTTGGAAAATAATGGTCGACTCGCATGAAACCCAGAGGCA
genomic: AAGTTACGGGACGAGGAACTGCAGCCACAACTCGTCGAGCTGTTGCAGGGgtaagccatc ... ctctctgcagCTTTACAAAATCTTGGAAAATAATGGTGGACTCGCATGAAACCCAGAGGCA
EST: gi|21331755|gb|BQ487136.1|BQ487136
EST:     AAGTTACGGGACGAGGAACTGCAGCCACAACTCGTCGAGCTGTTGCAGGG                         CTTTACAAAATCTTGGAAAATAATGGTCGACTCGCATGAAACCCAGAGGCA
genomic: AAGTTACGGGACGAGGAACTGCAGCCACAACTCGTCGAGCTGTTGCAGGGgtaagccatc ... ctctctgcagCTTTACAAAATCTTGGAAAATAATGGTGGACTCGCATGAAACCCAGAGGCA
EST: gi|22472567|gb|BU037047.1|BU037047
EST:     AAGTTACGGGACGAGGAACTGCAGCCACAACTCGTCGAGCTGTTGCAGGG                         CTTTACAAAATCTTGGAAAATAATGGTCGACTCGCATGAAACCCAGAGGCA
genomic: AAGTTACGGGACGAGGAACTGCAGCCACAACTCGTCGAGCTGTTGCAGGGgtaagccatc ... ctctctgcagCTTTACAAAATCTTGGAAAATAATGGTGGACTCGCATGAAACCCAGAGGCA

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), 46 (downstream exon)
Score: 104

GAATCTGGGTTTCTCTACGAGCAGCGGAATCCATATCTGATAGAATACAAAAGTTACGGGACGAGGAACTGCAGCCACAACTCGTCGAGCTGTTGCAGGGgtaagccatc ... ctctctgcagCTTTACAAAATCTTGGAAAATAATGGTGGACTCGCATGAAACCCAGAGGCAGATTATGTTCGAGGTGAATTCATTTACATGCCCTGCTTATGGCAAATTC


Block sizes: 43 (upstream exon), 45 (downstream exon)
Score: 15

GAATCTGGGTTTCTCTACGAGCAGCGGAATCCATATCTGATAGAATACAAAAGTTACGGGACGAGGAACTGCAGCCACAACTCGTCGAGCTGTTGCAGGGgtaagccatc ... ctctctgcagCTTTACAAAATCTTGGAAAATAATGGTGGACTCGCATGAAACCCAGAGGCAGATTATGTTCGAGGTGAATTCATTTACATGCCCTGCTTATGGCAAATTC


Block sizes: 43 (upstream exon), 45 (downstream exon)
Score: 10

GAATCTGGGTTTCTCTACGAGCAGCGGAATCCATATCTGATAGAATACAAAAGTTACGGGACGAGGAACTGCAGCCACAACTCGTCGAGCTGTTGCAGGGgtaagccatc ... ctctctgcagCTTTACAAAATCTTGGAAAATAATGGTGGACTCGCATGAAACCCAGAGGCAGATTATGTTCGAGGTGAATTCATTTACATGCCCTGCTTATGGCAAATTC


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 49

GAATCTGGGTTTCTCTACGAGCAGCGGAATCCATATCTGATAGAATACAAAAGTTACGGGACGAGGAACTGCAGCCACAACTCGTCGAGCTGTTGCAGGGgtaagccatc ... ctctctgcagCTTTACAAAATCTTGGAAAATAATGGTGGACTCGCATGAAACCCAGAGGCAGATTATGTTCGAGGTGAATTCATTTACATGCCCTGCTTATGGCAAATTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtatgcaatttccatttcaaatcggtactgatgaattggctgcctctctgcagCTTTACAAAATCTTGGAAAATAATGGTGGACTCGCATGAAACCCAGAGGCAGATTATGTTCGAGGTGAATTCATTTACATGCCCTGCTTATGGCAAATTC
                           tactgat  putative branch site (score: 49)
                                         ctgcctctct  putative PPT
               atttcaaat  TA-rich tract