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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtatgctgtatttttgcacgatacacatatgttactgcgaatcctgcctcttatgcaatgtaatatactgaatcttaatgcatcttgctcttcccagACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACCACGATCTTCAACAAAACTCACTGGACATCCTTCGCGGTTGTGCAACTTA

Basic information

species Zea mays
transcript GRMZM2G701689_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|50331744|gb|CO526870.1|CO526870
EST:     GATGCTCCTGCTGAAAATGTACTGACCACACCTTCCATGGTGCAGTGCAG                         ACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACC
genomic: GATGCTCCTGCTGAAAATGTACTGACCACACCTTCCATGGTGCAGTGCAGgtttgtatgc ... ctcttcccagACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACC
EST: gi|87156415|gb|DY401204.1|DY401204
EST:     GATGCTCCTGCTGAAAATGTACTGACCACACCTTCCATGGTGCAGTGCAG                         ACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACC
genomic: GATGCTCCTGCTGAAAATGTACTGACCACACCTTCCATGGTGCAGTGCAGgtttgtatgc ... ctcttcccagACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACC
EST: gi|50331743|gb|CO526869.1|CO526869
EST:     ACCTTCCATGGTGCAGTGCAG                         ACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACC
genomic: ACCTTCCATGGTGCAGTGCAGgtttgtatgc ... ctcttcccagACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACC
EST: gi|60394383|gb|DN227253.1|DN227253
EST:     GATGCTCCTGCTGAAAATGTACTGACCACACCTTCCATGGTGCAGTGCAG                         ACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACC
genomic: GATGCTCCTGCTGAAAATGTACTGACCACACCTTCCATGGTGCAGTGCAGgtttgtatgc ... ctcttcccagACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACC
EST: gi|40336440|gb|CK370510.1|CK370510
EST:     GATGCTCCTGCTGAAAATGTACTGACCACACCTTCCATGGTGCAGTGCAG                         ACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACC
genomic: GATGCTCCTGCTGAAAATGTACTGACCACACCTTCCATGGTGCAGTGCAGgtttgtatgc ... ctcttcccagACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACC
EST: gi|32833840|gb|CD973518.1|CD973518
EST:     ACTGACCACACCTTCCATGGTGCAGTGCAG                         ACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACC
genomic: ACTGACCACACCTTCCATGGTGCAGTGCAGgtttgtatgc ... ctcttcccagACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACC
EST: gi|31357051|gb|CD441408.1|CD441408
EST:     TCCTGCTGAAAATGTACTGACCACACCTTCCATGGTGCAGTGCAG                         ACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACC
genomic: TCCTGCTGAAAATGTACTGACCACACCTTCCATGGTGCAGTGCAGgtttgtatgc ... ctcttcccagACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACC
EST: gi|20512944|gb|BQ280130.1|BQ280130
EST:     GATGCTCCTGCTGAAAATGTACTGACCACACCTTCCATGGTGCAGTGCAG                         ACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGACGAGCTCCAAAAAACC
genomic: GATGCTCCTGCTGAAAATGTACTGACCACACCTTCCATGGTGCAGTGCAGgtttgtatgc ... ctcttcccagACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACC
EST: gi|32833804|gb|CD973482.1|CD973482
EST:     ACTGACCACACCTTCCATGGTGCAGTGCAG                         ACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACC
genomic: ACTGACCACACCTTCCATGGTGCAGTGCAGgtttgtatgc ... ctcttcccagACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACC
EST: gi|37393335|gb|CF633930.1|CF633930
EST:     GATGCTCCTGCTGAAAATGTACTGACCACACCTTCCATGGTGCAGTGCAG                         ACCCTTGGCTGGTCGTNNNNNNNNNAAGCTCCAAGAAAAGCTCCAAAAAAC
genomic: GATGCTCCTGCTGAAAATGTACTGACCACACCTTCCATGGTGCAGTGCAGgtttgtatgc ... ctcttcccagACCCTTGGCTTGTCGT-CCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAAC
EST: gi|31356228|gb|CD440585.1|CD440585
EST:     GATGCTCCTGCTGAAAATGTACTGACCACACCTTCCATGGTGCAGTGCAG                         ACCCTTGGCTTGTCCTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACC
genomic: GATGCTCCTGCTGAAAATGTACTGACCACACCTTCCATGGTGCAGTGCAGgtttgtatgc ... ctcttcccagACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACC
EST: gi|76915167|gb|DV165860.1|DV165860
EST:     GATGCTCCTGCTGAAAATGTACTGACCACACCTTCCATGGTGCAGTGCAG                         ACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACC
genomic: GATGCTCCTGCTGAAAATGTACTGACCACACCTTCCATGGTGCAGTGCAGgtttgtatgc ... ctcttcccagACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACC
EST: gi|7162203|gb|AW519825.1|AW519825
EST:     GATGCTCCTGCTGAAAATGTACTGACCACACCTTCCATGGTGCAGTGCAG                         ACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACC
genomic: GATGCTCCTGCTGAAAATGTACTGACCACACCTTCCATGGTGCAGTGCAGgtttgtatgc ... ctcttcccagACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACC

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: 380

AAGAGAAAAGTGAAATCGAGAAACAGCTTGTTGTCTACCAAACTCCTGATGATGCTCCTGCTGAAAATGTACTGACCACACCTTCCATGGTGCAGTGCAGgtttgtatgc ... ctcttcccagACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACCACGATCTTCAACAAAACTCACTGGACATCCTTCGCGGTTGTGCAACTTA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 262

AAGAGAAAAGTGAAATCGAGAAACAGCTTGTTGTCTACCAAACTCCTGATGATGCTCCTGCTGAAAATGTACTGACCACACCTTCCATGGTGCAGTGCAGgtttgtatgc ... ctcttcccagACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACCACGATCTTCAACAAAACTCACTGGACATCCTTCGCGGTTGTGCAACTTA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 320

AAGAGAAAAGTGAAATCGAGAAACAGCTTGTTGTCTACCAAACTCCTGATGATGCTCCTGCTGAAAATGTACTGACCACACCTTCCATGGTGCAGTGCAGgtttgtatgc ... ctcttcccagACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACCACGATCTTCAACAAAACTCACTGGACATCCTTCGCGGTTGTGCAACTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 248

AAGAGAAAAGTGAAATCGAGAAACAGCTTGTTGTCTACCAAACTCCTGATGATGCTCCTGCTGAAAATGTACTGACCACACCTTCCATGGTGCAGTGCAGgtttgtatgc ... ctcttcccagACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACCACGATCTTCAACAAAACTCACTGGACATCCTTCGCGGTTGTGCAACTTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgcctcttatgcaatgtaatatactgaatcttaatgcatcttgctcttcccagACCCTTGGCTTGTCGTCCACCCCCAAGCTCCAAGAAAAGCTCCAAAAAACCACGATCTTCAACAAAACTCACTGGACATCCTTCGCGGTTGTGCAACTTA
                              tcttaat  putative branch site (score: 248)
                                      catcttgctcttccc  CT-rich tract
              aatgtaatata  TA-rich tract