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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaatttttggactcttgattgtccttaggttgccagtatttggctaatttaatgagttgtgatttgacatttacttggtctgttgattggtatacacagGCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACAT

Basic information

species Zea mays
transcript GRMZM2G057408_T02
intron # 6
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|71428976|gb|DR810026.1|DR810026
EST:     GTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGATATTGAAACG                         GCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTT
genomic: GTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGATATTGAAACGgtacatattg ... gtatacacagGCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTT
EST: gi|78118281|gb|DV536668.1|DV536668
EST:     GTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGATATTGAAACG                         GCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTT
genomic: GTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGATATTGAAACGgtacatattg ... gtatacacagGCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTT
EST: gi|148939135|gb|EC883572.2|EC883572
EST:     GTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGATATTGAAACG                         GCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTT
genomic: GTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGATATTGAAACGgtacatattg ... gtatacacagGCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTT
EST: gi|60336979|gb|DN203952.1|DN203952
EST:     GTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGATATTGAAACG                         GCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTT
genomic: GTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGATATTGAAACGgtacatattg ... gtatacacagGCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTT
EST: gi|161590039|gb|EY962031.1|EY962031
EST:     GTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGATATTGAAACG                         GCACTACTACTTATGAGGAATCTT-CCATGAACC
genomic: GTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGATATTGAAACGgtacatattg ... gtatacacagGCACTACTACTTATGAGGAATCTTTCCATGAACC
EST: gi|91876491|gb|EB406448.1|EB406448
EST:     GTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGATATTGAAACG                         GCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTT
genomic: GTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGATATTGAAACGgtacatattg ... gtatacacagGCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTT
EST: gi|60397572|gb|DN230388.1|DN230388
EST:     GTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGATATTGAAACG                         GCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTT
genomic: GTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGATATTGAAACGgtacatattg ... gtatacacagGCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTT
EST: gi|110220916|gb|EC902814.1|EC902814
EST:     GTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGATATTGAAACG                         GCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTT
genomic: GTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGATATTGAAACGgtacatattg ... gtatacacagGCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTT
EST: gi|50322593|gb|CO517719.1|CO517719
EST:     GTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGATATTGAAACG                         GCCCTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTT
genomic: GTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGATATTGAAACGgtacatattg ... gtatacacagGCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTT
EST: gi|71763063|gb|DR961000.1|DR961000
EST:     GTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGATATTGAAACG                         GCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTT
genomic: GTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGATATTGAAACGgtacatattg ... gtatacacagGCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTT

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 3 RNA-Seq libraries.


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 2

TTTTGCCCAAGTATACAACTTCCTGGGAAGCATATTTGATCCGGATACAAGTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGATATTGAAACGgtacatattg ... gtatacacagGCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACAT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 8

TTTTGCCCAAGTATACAACTTCCTGGGAAGCATATTTGATCCGGATACAAGTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGATATTGAAACGgtacatattg ... gtatacacagGCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 11

TTTTGCCCAAGTATACAACTTCCTGGGAAGCATATTTGATCCGGATACAAGTGGGCATTTGCAGAGGTTAAAAGCGATGGATCCAGTTGATATTGAAACGgtacatattg ... gtatacacagGCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatttaatgagttgtgatttgacatttacttggtctgttgattggtatacacagGCACTACTACTTATGAGGAATCTTTCCATGAACCTTAGGAGTCCCGACTTTGAGCAACAT
                        atttactt  TA-rich tract