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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccagctgtttgatgttctccatcttaattgatatttcaagttttaggtatctcataattcaactttctttgatacagTAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCCTGGTATCAACCCTGTCATGATTGATGAACTTACAGAGTGTAATGCCATGCTTTCAGC

Basic information

species Zea mays
transcript GRMZM2G324540_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G324540_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g32880.1 (Oryza sativa), 3'ss of exon 4
--------gtaccagctgtttgatgttctccatcttaattgatatttcaagttttaggtatctcataattcaactttctttgatacagTAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCCTGGTATCAACCCTGTCATGATTGATGAACTTACAGAGTGTAATGCCATGCTTTCAGC
         | |   |||||||| ||| |  |  | ||||  ||  |  | ||| ||   ||||||| |||  | || || ||| ||| | ||||||||||| |||| || |||||||||||||| |||||||||||||||||||| |||||||||||||| |||||||||||| ||||||| || ||
gtacctactttctgactgtttgaagttgttgaagtaaatttctacatataatttcagccttctcatagttctgcattgttggattcagCATTTGAAGATGAAGTTGGACCAGACGGGAAGAAGATTCGTCCTGGTATCAACCCTGTGATGATTGATGAACTAACAGAGTGTAATACCATGCTCTCTGC
















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|211137349|gb|FL244356.1|FL244356
EST:     GTCAGTTGCAGGAGCTGCTCCTGCAGCTGTTGTTTCCAATGGAAAAAGAG                         TAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCC
genomic: GTCAGTTGCAGGAGCTGCTCCTGCAGCTGTTGTTTCCAATGGAAAAAGAGgtaccagctg ... tttgatacagTAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCC
EST: gi|211125236|gb|FL005609.1|FL005609
EST:     TGTTGTTTTCAATGGAAAAAGAG                         TAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCCTGGTATCA
genomic: TGTTGTTTCCAATGGAAAAAGAGgtaccagctg ... tttgatacagTAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCCTGGTATCA
EST: gi|60400048|gb|DN232855.1|DN232855
EST:     GTTGTTTCCAATGGAAAAAGAG                         TAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCCTGGTATCA
genomic: GTTGTTTCCAATGGAAAAAGAGgtaccagctg ... tttgatacagTAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCCTGGTATCA
EST: gi|211137353|gb|FL244360.1|FL244360
EST:     GTCAGTTGCAGGAGCTGCTCCTGCAGCTGTTGTTTCCA-TGGAAAA-GAG                         TAATTGAAGATGAAATTGGCCCTGACG
genomic: GTCAGTTGCAGGAGCTGCTCCTGCAGCTGTTGTTTCCAATGGAAAAAGAGgtaccagctg ... tttgatacagTAATTGAAGATGAAATTGGCCCTGACG

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: 121

AGAGATGACGCTAGAGCACTTTTGGCTCAAGCTGAGAGACAGATTCCTGCGTCAGTTGCAGGAGCTGCTCCTGCAGCTGTTGTTTCCAATGGAAAAAGAGgtaccagctg ... tttgatacagTAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCCTGGTATCAACCCTGTCATGATTGATGAACTTACAGAGTGTAATGCCATGCTTTCAGC


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 50

AGAGATGACGCTAGAGCACTTTTGGCTCAAGCTGAGAGACAGATTCCTGCGTCAGTTGCAGGAGCTGCTCCTGCAGCTGTTGTTTCCAATGGAAAAAGAGgtaccagctg ... tttgatacagTAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCCTGGTATCAACCCTGTCATGATTGATGAACTTACAGAGTGTAATGCCATGCTTTCAGC


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 27

AGAGATGACGCTAGAGCACTTTTGGCTCAAGCTGAGAGACAGATTCCTGCGTCAGTTGCAGGAGCTGCTCCTGCAGCTGTTGTTTCCAATGGAAAAAGAGgtaccagctg ... tttgatacagTAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCCTGGTATCAACCCTGTCATGATTGATGAACTTACAGAGTGTAATGCCATGCTTTCAGC


Block sizes: 40 (upstream exon), 48 (downstream exon)
Score: 35

AGAGATGACGCTAGAGCACTTTTGGCTCAAGCTGAGAGACAGATTCCTGCGTCAGTTGCAGGAGCTGCTCCTGCAGCTGTTGTTTCCAATGGAAAAAGAGgtaccagctg ... tttgatacagTAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCCTGGTATCAACCCTGTCATGATTGATGAACTTACAGAGTGTAATGCCATGCTTTCAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaattgatatttcaagttttaggtatctcataattcaactttctttgatacagTAATTGAAGATGAAATTGGCCCTGACGGGAAGAAGATCCGTCCTGGTATCAACCCTGTCATGATTGATGAACTTACAGAGTGTAATGCCATGCTTTCAGC
                                        ctttcttt  CT-rich tract
        atatttcaagtttta  TA-rich tract