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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtacattttgtaatgcatctctctgctttatgtgttcatgtagatcagtacagaaaatgatttcattattttgactccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAGGTTCCAGGGTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACT

Basic information

species Zea mays
transcript GRMZM2G376727_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G376727_T05 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g01307.2 (Oryza sativa), 3'ss of exon 2
gtgagtacattttgtaatgcatctctctgctttatgtgttcatgtagatcagtacagaaaatgatttcattattttgactccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAGGTTCCAGGGTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACT
|||||| |||||  |   ||||||||||||| | ||  |   | ||      ||||| |||||| || ||  || |  || ||  ||||||| ||||||| | ||  ||| |||| |||||||||||  |||||||||||| || |||||||| ||  ||||||| || ||||||||||||||| ||
gtgagtgcatttcatgcagcatctctctgctatgtgattcattataaggtgttacaggaaatgactttatctttgttgcttct--agTGGTGTCACTGCTTCGCATGCATTTGTCTTGGAGACCAAAGTACAGGGCAGGTTTCAAGGTTCACCTGCGGTTATTACCTATCGTGTTCCCACAAAGGCT
















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|5006027|gb|AI712089.1|AI712089
EST:     TTGTCCCTGGAGAGAAATCGAAGCCATTGGAAAGGCTTGACCC                         TGGTGCCACTGGTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|15590113|gb|BI674729.1|BI674729
EST:     TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|31611983|gb|CD568605.1|CD568605
EST:     TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|9255123|gb|BE345591.1|BE345591
EST:     TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGGTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|60347158|gb|DN214131.1|DN214131
EST:     TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|7137614|gb|AW499182.1|AW499182
EST:     CTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGGTACACACACATATGTCCTGTATACCAAAACACAGGGCAG
genomic: CTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|78080233|gb|DV508645.1|DV508645
EST:     TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|149106143|gb|EE291820.2|EE291820
EST:     TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|60346405|gb|DN213378.1|DN213378
EST:     TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|60355754|gb|DN222727.1|DN222727
EST:     TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|89249519|gb|DY621305.1|DY621305
EST:     GAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: GAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|30706031|gb|CD059006.1|CD059006
EST:     TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|78107599|gb|DV526017.1|DV526017
EST:     TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|60354184|gb|DN221157.1|DN221157
EST:     TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|211379488|gb|FL165247.1|FL165247
EST:     TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|21987232|gb|BQ778760.1|BQ778760
EST:     TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGGTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|211340832|gb|FL479597.1|FL479597
EST:     TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|24769483|gb|CA404612.1|CA404612
EST:     TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|78081691|gb|DV510103.1|DV510103
EST:     TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|211354951|gb|FL243591.1|FL243591
EST:     TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|87156435|gb|DY401224.1|DY401224
EST:     TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGGTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|60356569|gb|DN223542.1|DN223542
EST:     TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|74243940|gb|DT651854.1|DT651854
EST:     TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|211354953|gb|FL243593.1|FL243593
EST:     TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|16919381|gb|BM074163.1|BM074163
EST:     TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|24765720|gb|CA400879.1|CA400879
EST:     TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|60347341|gb|DN214314.1|DN214314
EST:     GAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGGTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: GAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
EST: gi|211130311|gb|FL066378.1|FL066378
EST:     TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC                         TGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG
genomic: TTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAG

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), 49 (downstream exon)
Score: 340

GACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAGGTTCCAGGGTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 312

GACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAGGTTCCAGGGTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 391

GACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAGGTTCCAGGGTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 290

GACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCCgtgagtacat ... actccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAGGTTCCAGGGTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtgttcatgtagatcagtacagaaaatgatttcattattttgactccttcagTGGTGCCACTGCTACACACACATATGTCCTGGAGACCAAAACACAGGGCAGGTTCCAGGGTTCACCAGCTATTATTACGTACCGTGTTCCCACAAAGACT
                                        ttttgac  putative branch site (score: 290)
                                              ctccttc  CT-rich tract
                       agaaaatgatttcatt  TA-rich tract