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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcactattaaattggccgattttttcacaacatgaacgacaaagtaagaaaaaaaaatccttgatgtctgttcaaacagGAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAG

Basic information

species Zea mays
transcript GRMZM2G147721_T01
intron # 9
splice site 3'
intron type U2

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|148986684|gb|EE030466.2|EE030466
EST:     TCGTGCAAGCTCTTGAACACGCTGATGAGAAGCAAAAGAACATTCTGTTT                         GAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
genomic: TCGTGCAAGCTCTTGAACACGCTGATGAGAAGCAAAAGAACATTCTGTTTgtaagcacta ... gttcaaacagGAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
EST: gi|60355786|gb|DN222759.1|DN222759
EST:     TCGTGCAAGCTCTTGAACACGCTGATGAGAAGCAAAAGAACATTCTGTTT                         GAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
genomic: TCGTGCAAGCTCTTGAACACGCTGATGAGAAGCAAAAGAACATTCTGTTTgtaagcacta ... gttcaaacagGAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
EST: gi|148995918|gb|EE035161.2|EE035161
EST:     TCGTGCAAGCTCTTGAACACGCTGATGAGAAGCAAAAGAACATTCTGTTT                         GAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
genomic: TCGTGCAAGCTCTTGAACACGCTGATGAGAAGCAAAAGAACATTCTGTTTgtaagcacta ... gttcaaacagGAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
EST: gi|148972760|gb|EE023733.2|EE023733
EST:     TCGTGCAAGCTCTTGAACACGCTGATGAGAAGCAAAAGAACATTCTGTTT                         GAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
genomic: TCGTGCAAGCTCTTGAACACGCTGATGAGAAGCAAAAGAACATTCTGTTTgtaagcacta ... gttcaaacagGAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
EST: gi|211433629|gb|FL480968.1|FL480968
EST:     TCGTGCAAGCTCTTGAACGCGCTGATGAGAAACAAAAGAGCATTCTGTTT                         GAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
genomic: TCGTGCAAGCTCTTGAACACGCTGATGAGAAGCAAAAGAACATTCTGTTTgtaagcacta ... gttcaaacagGAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
EST: gi|211420061|gb|FL460750.1|FL460750
EST:     TCGTGCAAGCTCTTGAACGCGCTGATGAGAAACAAAAGAGCATTCTGTTT                         GAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
genomic: TCGTGCAAGCTCTTGAACACGCTGATGAGAAGCAAAAGAACATTCTGTTTgtaagcacta ... gttcaaacagGAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
EST: gi|148943252|gb|EC888313.2|EC888313
EST:     TCGTGCAAGCTCTTGAACACGCTGATGAGAAGCAAAAGAACATTTTGTTT                         GAAAGTTATGGAAAGTTTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
genomic: TCGTGCAAGCTCTTGAACACGCTGATGAGAAGCAAAAGAACATTCTGTTTgtaagcacta ... gttcaaacagGAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
EST: gi|111189546|gb|EE287682.1|EE287682
EST:     TCGTGCAAGCTCTTGAACACGCTGATGAGAAGCAAAAGAACATTCTGTTT                         GAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG
genomic: TCGTGCAAGCTCTTGAACACGCTGATGAGAAGCAAAAGAACATTCTGTTTgtaagcacta ... gttcaaacagGAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTG

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: 39 (upstream exon), 47 (downstream exon)
Score: 30

ATCGGAACTGACATTGAAGACTACAAGTGTTCCTGGCTAGTCGTGCAAGCTCTTGAACACGCTGATGAGAAGCAAAAGAACATTCTGTTTgtaagcacta ... gttcaaacagGAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 36

ATCGGAACTGACATTGAAGACTACAAGTGTTCCTGGCTAGTCGTGCAAGCTCTTGAACACGCTGATGAGAAGCAAAAGAACATTCTGTTTgtaagcacta ... gttcaaacagGAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAG


Block sizes: 29 (upstream exon), 48 (downstream exon)
Score: 20

ATCGGAACTGACATTGAAGACTACAAGTGTTCCTGGCTAGTCGTGCAAGCTCTTGAACACGCTGATGAGAAGCAAAAGAACATTCTGTTTgtaagcacta ... gttcaaacagGAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAG


Block sizes: 39 (upstream exon), 47 (downstream exon)
Score: 59

ATCGGAACTGACATTGAAGACTACAAGTGTTCCTGGCTAGTCGTGCAAGCTCTTGAACACGCTGATGAGAAGCAAAAGAACATTCTGTTTgtaagcacta ... gttcaaacagGAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacaacatgaacgacaaagtaagaaaaaaaaatccttgatgtctgttcaaacagGAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAG
                                  ccttgat  putative branch site (score: 59)
                                          tctgttc  CT-rich tract
                aaagtaagaaaaaaaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcactattaaattggccgattttttcacaacatgaacgacaaagtaagaaaaaaaaatccttgatgtctgttcaaacagGAAAGTTATGGAAAGTCTGATCCAGCGTGTGTTGCAAAGGTGAAGGACTTGTACAAAGAGCTTAAACTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT