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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatgaaccggatatttgttgtccagttacaacaaaactgcaacagcctgtcacccaacctgaactctgcattttcagCTTCCACAAAACTTACTGAAAGACTGCACGGCTCTTCAGAGTTTATCCCTGCACGACAACCCAATCACAATGGACCAGTTCCAACAA

Basic information

species Zea mays
transcript GRMZM5G890241_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G890241_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g11360.2 (Oryza sativa), 3'ss of exon 7
-----------------------------------------------------------------------------------------------------gtattatgaaccggatat-ttgttgtccagttacaa----caaaactgcaa-cagcctgtcacccaacctgaactctgcattttcagCTTCCACAAAACTTACTGAAAGACTGCACGGCTCTTCAGAGTTTATCCCTGCACGACAACCCAATCACAATGGACCAGTTCCAACAA
                                                                                                      |   ||   | || ||  |||||| | | ||  ||    |||||    || ||     || || ||| |  ||||| |  |  |||||||| |||||| ||||||||||||||| |||||||||||   ||||  |||| ||||| |||||| | ||||||||||| ||||||
gtacgaacttatgaatatgcttttccctcgtcgattacttctgtgtttgaacctggaggctctagggtcaaagtcagtgaataatgactattcatttagatttgaaatatcctggttacattgttgccaacttgtaacgtacaaaataataagcaaagattctccgaactttgactctcc-ctgacagCTTCCCCAAAACCTACTGAAAGACTGCAAGGCTCTTCAGAACATATCGTTGCATGACAATCCAATCTCGATGGACCAGTTTCAACAA
















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|211051530|gb|FL405966.1|FL405966
EST:     ACCTAGTTTGCCTGAAATCCTTATCACTGAACGGCAACAAAATTCGTCAG                         CTTCCACAAAACTTACTGAAAGACTGCACGGCTCTTCAGAGTTTATCCCTG
genomic: ACCTAGTTTGCCTGAAATCCTTATCACTGAACGGCAACAAAATTCGACAGgtattatgaa ... gcattttcagCTTCCACAAAACTTACTGAAAGACTGCACGGCTCTTCAGAGTTTATCCCTG
EST: gi|14243691|gb|BG841341.2|BG841341
EST:     ACCTAGTTTGCCTGAAATCCTTATCACTGAACGGCAACAAAATTCGACAG                         CTTCCACAAAACTTACTGAAAGACTGCACGGCTCTTCAGAGTTTATCCCTG
genomic: ACCTAGTTTGCCTGAAATCCTTATCACTGAACGGCAACAAAATTCGACAGgtattatgaa ... gcattttcagCTTCCACAAAACTTACTGAAAGACTGCACGGCTCTTCAGAGTTTATCCCTG
EST: gi|31909393|gb|CD650896.1|CD650896
EST:     ACCTAGTTTGCCTGAAATCCTTATCACTGAACGGCAACAAAATTCGACAG                         CTTCCACAAAACTTACTGAAAGACTGCACGGCTCTTCAGAGTTTATCCCTG
genomic: ACCTAGTTTGCCTGAAATCCTTATCACTGAACGGCAACAAAATTCGACAGgtattatgaa ... gcattttcagCTTCCACAAAACTTACTGAAAGACTGCACGGCTCTTCAGAGTTTATCCCTG
EST: gi|60351302|gb|DN218275.1|DN218275
EST:     ACCTAGTTTGCCTGAAATCCTTATCACTGAACGGCAACAAAATTCGTCAG                         CTTCCACAAAACTTACTGAAAGACTGCACGGCTCTTCAGAGTTTATCCCTG
genomic: ACCTAGTTTGCCTGAAATCCTTATCACTGAACGGCAACAAAATTCGACAGgtattatgaa ... gcattttcagCTTCCACAAAACTTACTGAAAGACTGCACGGCTCTTCAGAGTTTATCCCTG
EST: gi|60340411|gb|DN207384.1|DN207384
EST:     ACCTAGTTTGCCTGAAATCCTTATCACTGAACGGCAACAAAATTCGTCAG                         CTTCCACAAAACTTACTGAAAGACTGCACGGCTCTTCAGAGTTTATCCCTG
genomic: ACCTAGTTTGCCTGAAATCCTTATCACTGAACGGCAACAAAATTCGACAGgtattatgaa ... gcattttcagCTTCCACAAAACTTACTGAAAGACTGCACGGCTCTTCAGAGTTTATCCCTG
EST: gi|31909395|gb|CD650897.1|CD650897
EST:     ACCTAGTTTGCCTGAAATCCTTATCACTGAACGGCAACAAAATTCGACAG                         CTTCCACAAAACTTACTGAAAGACTGCACGGCTCTTCAGAGTTTATCCCTG
genomic: ACCTAGTTTGCCTGAAATCCTTATCACTGAACGGCAACAAAATTCGACAGgtattatgaa ... gcattttcagCTTCCACAAAACTTACTGAAAGACTGCACGGCTCTTCAGAGTTTATCCCTG
EST: gi|211247057|gb|FL482035.1|FL482035
EST:     ACCTAGTTTGCCTGAAATCCTTATCACTGAACGGCAACAAAATTCGTCAG                         CTTCCACAAAACTTACTGAAAGACTGCACGGCTCTTCAGAGTTTATCCCTG
genomic: ACCTAGTTTGCCTGAAATCCTTATCACTGAACGGCAACAAAATTCGACAGgtattatgaa ... gcattttcagCTTCCACAAAACTTACTGAAAGACTGCACGGCTCTTCAGAGTTTATCCCTG
EST: gi|10191716|gb|BE761792.1|BE761792
EST:     ACCTAGTTTGCCTGAAATCCTTATCAATAAACGGCACCAAAATTCGACAG                         CTTCCACAAAACTTACTGAAAGACTGCACGGCTCTTCAGAGTTTATCCCTG
genomic: ACCTAGTTTGCCTGAAATCCTTATCACTGAACGGCAACAAAATTCGACAGgtattatgaa ... gcattttcagCTTCCACAAAACTTACTGAAAGACTGCACGGCTCTTCAGAGTTTATCCCTG

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: 38 (upstream exon), 44 (downstream exon)
Score: 28

GAAATGCTATTGAAGATGTGCCAGCGTCAATTTGCAACCTAGTTTGCCTGAAATCCTTATCACTGAACGGCAACAAAATTCGACAGgtattatgaa ... gcattttcagCTTCCACAAAACTTACTGAAAGACTGCACGGCTCTTCAGAGTTTATCCCTGCACGACAACCCAATCACAATGGACCAGTTCCAACAA


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 63

GAAATGCTATTGAAGATGTGCCAGCGTCAATTTGCAACCTAGTTTGCCTGAAATCCTTATCACTGAACGGCAACAAAATTCGACAGgtattatgaa ... gcattttcagCTTCCACAAAACTTACTGAAAGACTGCACGGCTCTTCAGAGTTTATCCCTGCACGACAACCCAATCACAATGGACCAGTTCCAACAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 117

GAAATGCTATTGAAGATGTGCCAGCGTCAATTTGCAACCTAGTTTGCCTGAAATCCTTATCACTGAACGGCAACAAAATTCGACAGgtattatgaa ... gcattttcagCTTCCACAAAACTTACTGAAAGACTGCACGGCTCTTCAGAGTTTATCCCTGCACGACAACCCAATCACAATGGACCAGTTCCAACAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 49

GAAATGCTATTGAAGATGTGCCAGCGTCAATTTGCAACCTAGTTTGCCTGAAATCCTTATCACTGAACGGCAACAAAATTCGACAGgtattatgaa ... gcattttcagCTTCCACAAAACTTACTGAAAGACTGCACGGCTCTTCAGAGTTTATCCCTGCACGACAACCCAATCACAATGGACCAGTTCCAACAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagttacaacaaaactgcaacagcctgtcacccaacctgaactctgcattttcagCTTCCACAAAACTTACTGAAAGACTGCACGGCTCTTCAGAGTTTATCCCTGCACGACAACCCAATCACAATGGACCAGTTCCAACAA
                                              cattttc  CT-rich tract
       aacaaaa  TA-rich tract