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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgattttcgaaatccttttctttcacttgttgtttatgcttgctttattattataaaatatgcacttgattctgtcttcaaaacatgcgtgcccgctgctctttgtactgtctgccctattttattgagttcttccccctcccctcctttaaactatgtttgcttactgttaatttaacaccagAGAGCAGCAATACAGAATCTTCTGATGATGTTGGGCAACAGGAGTTGGATGAACTTTTGGATGACGATGACTATCAATTTTATGATACAAGGCAGAGTTT

Basic information

species Zea mays
transcript GRMZM5G875564_T01
intron # 4
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|211178688|gb|FL100547.1|FL100547
EST:     TATTCCAGCTCTGGACAGGGAAAATGTAGTG                         AGAGCAGCAATACAGAATCTTCTGATGATGTTGGGCAACAGGAGTTGGATG
genomic: TATTGCAGCTCTGGACAGGGAAAATGTAGTGgtacttgatt ... ttaacaccagAGAGCAGCAATACAGAATCTTCTGATGATGTTGGGCAACAGGAGTTGGATG
EST: gi|211178686|gb|FL100545.1|FL100545
EST:     GCACTTGATGAAACCTGACTATTCCAGCTCTGGACAGGGAAAATGTAGTG                         AGAGCAGCAATACAGAATCTTCTGATGATGTTGGGCAACAGGAGTTGG
genomic: GCACTTGATGAAACCTGACTATTGCAGCTCTGGACAGGGAAAATGTAGTGgtacttgatt ... ttaacaccagAGAGCAGCAATACAGAATCTTCTGATGATGTTGGGCAACAGGAGTTGG
EST: gi|211178687|gb|FL100546.1|FL100546
EST:     GCACTTGATGAAACCTGACTATTCCAGCTCTGGACAGGGAAAATGTAGTG                         AGAGCAGCAATACAGAATCTTCTGATGATGTTGGGCAACAGGAGTTGGATG
genomic: GCACTTGATGAAACCTGACTATTGCAGCTCTGGACAGGGAAAATGTAGTGgtacttgatt ... ttaacaccagAGAGCAGCAATACAGAATCTTCTGATGATGTTGGGCAACAGGAGTTGGATG
EST: gi|16137372|gb|BI894237.1|BI894237
EST:     GCACTTGATGAAACCTGACTATTGCAGCTCTGGACAGGGAAAATGTAGTG                         AGAGCAGCAATACAGAATCCTCTGATGATGTTGGGCAACAGGAGTTGGATG
genomic: GCACTTGATGAAACCTGACTATTGCAGCTCTGGACAGGGAAAATGTAGTGgtacttgatt ... ttaacaccagAGAGCAGCAATACAGAATCTTCTGATGATGTTGGGCAACAGGAGTTGGATG
EST: gi|211178685|gb|FL100544.1|FL100544
EST:     GCACTTGATGAAACCTGACTATTCCAGCTCTGGACAGGGAAAATGTAGTG                         AGAGCAGCAATACAGAATCTTCTGATGATGTTGGG
genomic: GCACTTGATGAAACCTGACTATTGCAGCTCTGGACAGGGAAAATGTAGTGgtacttgatt ... ttaacaccagAGAGCAGCAATACAGAATCTTCTGATGATGTTGGG
EST: gi|16137371|gb|BI894236.1|BI894236
EST:     GCACTTGATGAAACCTGACTATTGCAGCTCTGGACAGGGAAAATGTAGTG                         AGAGCAGCAATACAGAATCTTCTGATGATGTTGGGCAACAGGAGTTGGATG
genomic: GCACTTGATGAAACCTGACTATTGCAGCTCTGGACAGGGAAAATGTAGTGgtacttgatt ... ttaacaccagAGAGCAGCAATACAGAATCTTCTGATGATGTTGGGCAACAGGAGTTGGATG

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: 48 (upstream exon), 49 (downstream exon)
Score: 102

GTACTTAGCGCAGATGATAATGCTAATATGATTGAGCTCCACTCGCACTTGATGAAACCTGACTATTGCAGCTCTGGACAGGGAAAATGTAGTGgtacttgatt ... ttaacaccagAGAGCAGCAATACAGAATCTTCTGATGATGTTGGGCAACAGGAGTTGGATGAACTTTTGGATGACGATGACTATCAATTTTATGATACAAGGCAGAGTTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 148

GTACTTAGCGCAGATGATAATGCTAATATGATTGAGCTCCACTCGCACTTGATGAAACCTGACTATTGCAGCTCTGGACAGGGAAAATGTAGTGgtacttgatt ... ttaacaccagAGAGCAGCAATACAGAATCTTCTGATGATGTTGGGCAACAGGAGTTGGATGAACTTTTGGATGACGATGACTATCAATTTTATGATACAAGGCAGAGTTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 63

GTACTTAGCGCAGATGATAATGCTAATATGATTGAGCTCCACTCGCACTTGATGAAACCTGACTATTGCAGCTCTGGACAGGGAAAATGTAGTGgtacttgatt ... ttaacaccagAGAGCAGCAATACAGAATCTTCTGATGATGTTGGGCAACAGGAGTTGGATGAACTTTTGGATGACGATGACTATCAATTTTATGATACAAGGCAGAGTTT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 20

GTACTTAGCGCAGATGATAATGCTAATATGATTGAGCTCCACTCGCACTTGATGAAACCTGACTATTGCAGCTCTGGACAGGGAAAATGTAGTGgtacttgatt ... ttaacaccagAGAGCAGCAATACAGAATCTTCTGATGATGTTGGGCAACAGGAGTTGGATGAACTTTTGGATGACGATGACTATCAATTTTATGATACAAGGCAGAGTTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttccccctcccctcctttaaactatgtttgcttactgttaatttaacaccagAGAGCAGCAATACAGAATCTTCTGATGATGTTGGGCAACAGGAGTTGGATGAACTTTTGGATGACGATGACTATCAATTTTATGATACAAGGCAGAGTTT
                                  ttactgttaatttaa  TA-rich tract