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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggttaattaacttgctgaatgtatggtctataaataccaaaggacttatagactaacttggctttatccccagTGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTG

Basic information

species Zea mays
transcript GRMZM2G167886_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G167886_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os09g12550.1 (Oryza sativa), 3'ss of exon 4
gtaggttaattaacttgctgaatgtatggtctataaataccaaaggacttatagactaacttggctttatccccagTGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTG
||| | |||   |  |||||||| |||| |||   ||    |||  |||||  ||||||||   |||| || | ||||||||||||||||| |||||||| ||||| |||||||||||||| ||||| ||  |||||||||||   |||||||||||||||
gtaagctaaaggatatgctgaatatatgttctg--aacggaaaaaaactta--gactaactacacttt-tctctagTGGTGACCATACTGTTAAAATAATCGATTGCCAAACTGGGAAATGTTTGAAAGTGTTGCTTGGACATTGGCGCACTCCATGGGTG
















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|18384883|gb|BM418082.1|BM418082
EST:     ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACA                         TGGTGACCATACTGCCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAA
genomic: ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaat ... ttatccccagTGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAA
EST: gi|18385319|gb|BM418518.1|BM418518
EST:     ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACA                         TGGTGACCATACTGTCCAAATAATTGATTGGCAAACTGGGAAATGCTTGAA
genomic: ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaat ... ttatccccagTGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAA
EST: gi|18384882|gb|BM418081.1|BM418081
EST:     ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACA                         TGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAA
genomic: ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaat ... ttatccccagTGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAA
EST: gi|76015702|gb|DT942872.1|DT942872
EST:     ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACA                         G
genomic: ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaat ... ttatccccag-
EST: gi|76015702|gb|DT942872.1|DT942872
EST:     ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACA                         G
genomic: ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaat ... ttatccccag-
EST: gi|22489334|gb|BU049257.1|BU049257
EST:     ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACA                         TGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAA
genomic: ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaat ... ttatccccagTGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAA
EST: gi|87298785|gb|DY470788.1|DY470788
EST:     ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACA                         TGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAA
genomic: ACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaat ... ttatccccagTGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAA

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: 14 (upstream exon), 44 (downstream exon)
Score: 13

TGCATTGGTGGATTCCCAAATATTGCCCTCTCACGCCTTCTTCGAAGGCAACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaat ... ttatccccagTGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTG


Block sizes: 36 (upstream exon), 41 (downstream exon)
Score: 13

TGCATTGGTGGATTCCCAAATATTGCCCTCTCACGCCTTCTTCGAAGGCAACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaat ... ttatccccagTGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 12

TGCATTGGTGGATTCCCAAATATTGCCCTCTCACGCCTTCTTCGAAGGCAACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaat ... ttatccccagTGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTG


Block sizes: 34 (upstream exon), 49 (downstream exon)
Score: 16

TGCATTGGTGGATTCCCAAATATTGCCCTCTCACGCCTTCTTCGAAGGCAACTATTGCAGCTGCATTTAGTACAGATGGGAGAGTACTTGCATCTACACAgtaggttaat ... ttatccccagTGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtatggtctataaataccaaaggacttatagactaacttggctttatccccagTGGTGACCATACTGTCAAAATAATTGATTGGCAAACTGGGAAATGCTTGAATGTACTGCTTGGACATCACCGCACTCCATGGGTG
                                gactaac  putative branch site (score: 16)
                                           ctttatcccc  putative PPT
        tctataaata  TA-rich tract