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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATGgtgtgtattcaacgtatcttctttttgtttctgctcttaaaggttgttccttttagtcacctttgtttgtgctttgtttttcag

Basic information

species Zea mays
transcript GRMZM2G085000_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085000_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os08g44400.3 (Oryza sativa), 5'ss of exon 6
GTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATGgtgtgtattcaacgtatcttctttttgtttctgctcttaaaggttgttccttttagtcacctttgtttgtgctttgtttttcag
|||||||||||||| ||||| |||||||||||||| |||| ||||||||||||||| || |||| ||||||||  ||||  |  | || ||| |   | ||  || |    ||    ||||  ||  | |||   ||||  | ||| |||||||
GTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATGgtgcctatttcatctctcatctgtacatctcc-ctgtccctggggcctcctactaacctcctgcatttgc-ccttgcttttcag
















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|60352714|gb|DN219687.1|DN219687
EST:     CGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATG                         GTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACA
genomic: CGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATGgtgtgtattc ... tgtttttcagGTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACA
EST: gi|211469259|gb|FL411595.1|FL411595
EST:     CGYCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATG                         GTGATGGAAGTGTTCCAATTATGCTA
genomic: CGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATGgtgtgtattc ... tgtttttcagGTGATGGAAGTGTTCCAATTATGCTA
EST: gi|60356894|gb|DN223867.1|DN223867
EST:     CGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATG                         GTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACA
genomic: CGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATGgtgtgtattc ... tgtttttcagGTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACA
EST: gi|40303424|gb|CK347811.1|CK347811
EST:     CGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATG                         GTGAGGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACA
genomic: CGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATGgtgtgtattc ... tgtttttcagGTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACA
EST: gi|148937629|gb|EC881822.2|EC881822
EST:     GAATCAGATGACATCATAAAATACCTAGCTGACACATATG                         GTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACA
genomic: GAATCAGATGACATCATAAAATACCTAGCTGACACATATGgtgtgtattc ... tgtttttcagGTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACA
EST: gi|93282046|gb|EB674310.1|EB674310
EST:     CGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATG                         GTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACA
genomic: CGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATGgtgtgtattc ... tgtttttcagGTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACA
EST: gi|32917029|gb|CF021841.1|CF021841
EST:     CGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATG                         GTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACA
genomic: CGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATGgtgtgtattc ... tgtttttcagGTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACA

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: 42 (upstream exon), 40 (downstream exon)
Score: 45

GTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATGgtgtgtattc ... tgtttttcagGTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACA


Block sizes: 42 (upstream exon), 44 (downstream exon)
Score: 179

GTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATGgtgtgtattc ... tgtttttcagGTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACA


Block sizes: 42 (upstream exon), 44 (downstream exon)
Score: 109

GTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATGgtgtgtattc ... tgtttttcagGTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACA


Block sizes: 42 (upstream exon), 44 (downstream exon)
Score: 63

GTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATGgtgtgtattc ... tgtttttcagGTGATGGAAGTGTTCCAATTATGCTATCGCTTGGTCTGTTGACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATGgtgtgtattcaacgtatcttctttttgtttctgctcttaaaggttgttccttttagtcacctttgtttgtgctttgtttttcag

- - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA