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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaaccttttgcaaagacccatgagatgaaattgctattcccaaagtaccactgttcctgtctatatggtttttatagcataatgtgtaattcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTT

Basic information

species Zea mays
transcript GRMZM2G042027_T05
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042027_T05 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g29860.1 (Oryza sativa), 3'ss of exon 4
ttaaccttttgcaaagacccatgagatgaaattgctat-tcccaaagtacc---actgttcctgtctatatggtttttatagcataatgtgtaattcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTT
     ||   | ||  | || |    | |  ||   |    ||| |  |     |   || |  ||| | |   |  ||| |  |  | | || ||  |   ||||| |||||  ||||||| ||  | || || || || ||||||||| ||||||| ||  ||||||||||| ||||||| ||||||||||||
----tctcaggtaataatccttagcttcactttttcaggctccataacatgggaatcattgcattctctttccatcatattgtttcttctctatttgcttgtagGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACTGGAGACTTTTCCTGAAAATTTGAGTGCTGTTGCCCATTTT
















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|211373757|gb|FL037585.1|FL037585
EST:     TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCC                         GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAMAATTACT
genomic: TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCCgtgagtacac ... ttcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
EST: gi|211371111|gb|FL037583.1|FL037583
EST:     TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCC                         GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
genomic: TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCCgtgagtacac ... ttcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
EST: gi|71436673|gb|DR817723.1|DR817723
EST:     TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCC                         GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
genomic: TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCCgtgagtacac ... ttcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
EST: gi|71302083|gb|DR787129.1|DR787129
EST:     TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCC                         GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
genomic: TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCCgtgagtacac ... ttcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
EST: gi|211371112|gb|FL037584.1|FL037584
EST:     TTGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCC                         GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
genomic: TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCCgtgagtacac ... ttcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
EST: gi|50325364|gb|CO520490.1|CO520490
EST:     TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCC                         GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
genomic: TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCCgtgagtacac ... ttcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
EST: gi|60342707|gb|DN209680.1|DN209680
EST:     TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCC                         GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
genomic: TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCCgtgagtacac ... ttcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
EST: gi|91054196|gb|EB164614.1|EB164614
EST:     TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCC                         GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
genomic: TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCCgtgagtacac ... ttcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
EST: gi|78083391|gb|DV511784.1|DV511784
EST:     TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCC                         GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT
genomic: TGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCCgtgagtacac ... ttcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACT

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), 47 (downstream exon)
Score: 87

GCCGCTCGAGGTGGAAGCCGGATTGAATGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCCgtgagtacac ... ttcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 86

GCCGCTCGAGGTGGAAGCCGGATTGAATGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCCgtgagtacac ... ttcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 54

GCCGCTCGAGGTGGAAGCCGGATTGAATGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCCgtgagtacac ... ttcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 36

GCCGCTCGAGGTGGAAGCCGGATTGAATGGAAAGGCTTGTATTCTGGATTAGCTGGAAATCTCACTGGCGTCCTTCCgtgagtacac ... ttcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaccactgttcctgtctatatggtttttatagcataatgtgtaattcatgacagGGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTT
                 tatatggtttttata  TA-rich tract