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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAAAATCTTGAGCAAAATGGGAGAAGgtttgggttttctgcaatctgtcgtctcctcttctgctgggtatctccgttattattctaatgaagagggctacgagttggattttcgtag

Basic information

species Zea mays
transcript GRMZM2G094039_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094039_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g40840.2 (Oryza sativa), 5'ss of exon 3
ATAAAATCTTGAGCAAAATGGGAGAAGgtttgggttttctgcaatctgtcgtctcctcttctgctgggtatctccgttattattctaatgaagagggctacgag-----ttggattttcg-tag
| |||||||||||||||||||||||||||| || |||||||||||||||      | ||  | |  ||| |||  | ||||||| ||||| | ||    | ||      ||  |||||   |||
ACAAAATCTTGAGCAAAATGGGAGAAGgtt-ggattttctgcaatctgtt-----ccctagtacctggtgtctttgctattattgtaatgtaaagcaacaggaatcattttaaatttttaatag
















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|211511150|gb|FL155933.1|FL155933
EST:     ATAAAATCTTGAGCAAAATGGGAGAAG                         GTACATTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATG
genomic: ATAAAATCTTGAGCAAAATGGGAGAAGgtttgggttt ... attttcgtagGTACATTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATG
EST: gi|211511148|gb|FL155931.1|FL155931
EST:     ATAAAATCTTGAGCAAAATGGGAGAAG                         GTACATTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATG
genomic: ATAAAATCTTGAGCAAAATGGGAGAAGgtttgggttt ... attttcgtagGTACATTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATG
EST: gi|71442566|gb|DR823616.1|DR823616
EST:     ATAAAATCTTGAGCAAAATGGGAGAAG                         GTACATTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATG
genomic: ATAAAATCTTGAGCAAAATGGGAGAAGgtttgggttt ... attttcgtagGTACATTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATG
EST: gi|74234529|gb|DT642443.1|DT642443
EST:     ATAAAATCTTGAGCAAAATGGGAGAAG                         GTACATTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATG
genomic: ATAAAATCTTGAGCAAAATGGGAGAAGgtttgggttt ... attttcgtagGTACATTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATG
EST: gi|22546678|gb|BU098989.1|BU098989
EST:     ATAAAATCTTGAGCAAAATGGGAGAAG                         GTACATTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATG
genomic: ATAAAATCTTGAGCAAAATGGGAGAAGgtttgggttt ... attttcgtagGTACATTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATG
EST: gi|87155804|gb|DY400593.1|DY400593
EST:     ATAAAATCTTGAGCAAAATGGGAGAAG                         GTACATTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATG
genomic: ATAAAATCTTGAGCAAAATGGGAGAAGgtttgggttt ... attttcgtagGTACATTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATG
EST: gi|26559327|gb|CA831562.1|CA831562
EST:     GAGCAAAATGGGAGAAG                         GTACATTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATG
genomic: GAGCAAAATGGGAGAAGgtttgggttt ... attttcgtagGTACATTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATG
EST: gi|148999517|gb|EE036485.2|EE036485
EST:     ATAAAATCTTGAGCAAAATGGGAGAAG                         GTACATTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATG
genomic: ATAAAATCTTGAGCAAAATGGGAGAAGgtttgggttt ... attttcgtagGTACATTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATG

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: 29 (upstream exon), 49 (downstream exon)
Score: 189

ATAAAATCTTGAGCAAAATGGGAGAAGgtttgggttt ... attttcgtagGTACATTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATGTTGCCATAAAAGTTGTTCGCAGTATCCGCAAGTACCGTGATGCTGCAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

ATAAAATCTTGAGCAAAATGGGAGAAGgtttgggttt ... attttcgtagGTACATTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATGTTGCCATAAAAGTTGTTCGCAGTATCCGCAAGTACCGTGATGCTGCAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 88

ATAAAATCTTGAGCAAAATGGGAGAAGgtttgggttt ... attttcgtagGTACATTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATGTTGCCATAAAAGTTGTTCGCAGTATCCGCAAGTACCGTGATGCTGCAAT


Block sizes: 27 (upstream exon), 49 (downstream exon)
Score: 100

ATAAAATCTTGAGCAAAATGGGAGAAGgtttgggttt ... attttcgtagGTACATTTGGGCGTGTTTTGGAATGCTGGGACCGTGAAACACATGAATATGTTGCCATAAAAGTTGTTCGCAGTATCCGCAAGTACCGTGATGCTGCAAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAAAATCTTGAGCAAAATGGGAGAAGgtttgggttttctgcaatctgtcgtctcctcttctgctgggtatctccgttattattctaatgaagagggctacgagttggattttcgtag

- - - - - - - - - - GGAGAA