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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatgtgtgagccatagtgaactgtatatgctttatatatgcaactgtttcttatactgccatgtttgcagCTTGTGCTTCGTTTTGCAAACCGCTTATTTTTGCCTCTCTGGAACCGTGATAACATAGCTAACGTACAG

Basic information

species Zea mays
transcript GRMZM2G031107_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G031107_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g38840.2 (Oryza sativa), 3'ss of exon 6
gtaatatgtgtgagccatagtgaactgtatatgctttatat---atgcaactgtttcttatactgccatgtttgcagCTTGTGCTTCGTTTTGCAAACCGCTTATTTTTGCCTCTCTGGAACCGTGATAACATAGCTAACGTACAG
||||  ||| || ||       |  |   |   |  |||||   |||| ||| |  | |||      || ||| |||||||||||||| ||||||||||| || ||  | ||||| ||||| ||||||||||| ||||| ||||||
gtaagttgtatg-gcttcgtctagttagttgaacgatatattccatgctactataacatatttcaatatattt-cagCTTGTGCTTCGCTTTGCAAACCGTTTGTTCCTACCTCTTTGGAATCGTGATAACATTGCTAATGTACAG

upper sequence: GRMZM2G031107_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA19G22690.1 (Glycine max), 3'ss of exon 6
gtaatatgtgtgagccatagtgaactgtatat-----gctttatatatgcaac----tgtttcttatactgccatgtttg--cagCTTGTGCTTCGTTTTGCAAACCGCTTATTTTTGCCTCTCTGGAACCGTGATAACATAGCTAACGTACAG
||| ||  ||   ||  || ||      ||||     |||| ||| |     |    |   |||     || | ||| |   ||| | || ||||||||||||||||| |||||  ||||||| ||||||||||| ||||| ||||| || |||
gtagtaaatgattgct-tattggctctcatattgcttgcttcataaacttggcctaatccctctccatttgacttgtattaccagTTAGTACTTCGTTTTGCAAACCGATTATTCATGCCTCTATGGAACCGTGACAACATTGCTAATGTGCAG

upper sequence: GRMZM2G031107_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 6
-------------------------------------------------gtaatatg-tgtgagccatagtgaactgtatat-gctttatatatgcaactgtttc-ttatactgcc-atgtttgcagCTTGTGCTTCGTTTTGCAAACCGCTTATTTTTGCCTCTCTGGAACCGTGATAACATAGCTAACGTACAG
                                                  |||||   |||  | | | ||   |  ||| | |   | | |    |  | | || |||| |  |  |  ||||||| | || |||||||||||||| ||| | |||||||| |||||||||||||| ||||| | ||| ||||||
gtaatacatgtatcataaaaattgtgtctttatttgataaaaaaaaataataataaaatgtttgtctttgtatgccctattttgaaatgtctgctgatttctctccttatgccacttacatttgcagTTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAACCGTGACAACATTGATAATGTACAG

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|111146774|gb|EE258268.1|EE258268
EST:     AACTCTATAGAATTGACCACTATTTAGGAAAAGAGCTTGTCCAAAACTTG                         CTTGTGCTTCGTTTTGCAAACCGCTTATTTTTGCCTCTCTGGAACCGTGAT
genomic: AACTCTATAGAATTGACCACTATTTAGGAAAAGAGCTTGTCCAAAACCTGgtaatatgtg ... atgtttgcagCTTGTGCTTCGTTTTGCAAACCGCTTATTTTTGCCTCTCTGGAACCGTGAT
EST: gi|60672339|gb|DN475101.1|DN475101
EST:     AACTCTATAGAATTGACCACTATTTAGGAAAAGAGCTTGTCCAAAACTTG                         CTTGTGCTTCGTTTTGCAAACCGCTTATTTTTGCCTCTCTGGAACCGTGAT
genomic: AACTCTATAGAATTGACCACTATTTAGGAAAAGAGCTTGTCCAAAACCTGgtaatatgtg ... atgtttgcagCTTGTGCTTCGTTTTGCAAACCGCTTATTTTTGCCTCTCTGGAACCGTGAT
EST: gi|20301108|gb|BQ164051.1|BQ164051
EST:     AACTCTATAGAATTGACCACTATTTAGGAAAAGAGCTTGTCCAAAACTTG                         CTTGTGCTTCGTTTTGCAAACCGCTTATTTTTGCCTCTCTGGAACCGTGAT
genomic: AACTCTATAGAATTGACCACTATTTAGGAAAAGAGCTTGTCCAAAACCTGgtaatatgtg ... atgtttgcagCTTGTGCTTCGTTTTGCAAACCGCTTATTTTTGCCTCTCTGGAACCGTGAT
EST: gi|33103231|gb|CF063191.1|CF063191
EST:     AACTCTATAGAATTGACCACTATTTAGGAAAAGAGCTTGTCCAAAACCTG                         CTTGTGCTTCGTTTTGCAAACCGCTTATTTTTGCCTCTCTGGAACCGTGAT
genomic: AACTCTATAGAATTGACCACTATTTAGGAAAAGAGCTTGTCCAAAACCTGgtaatatgtg ... atgtttgcagCTTGTGCTTCGTTTTGCAAACCGCTTATTTTTGCCTCTCTGGAACCGTGAT

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: 96

CACTGCAGAGGAACTGAGTGCTGAACTTGGGCAGCTGTTTCAAGAAGAACAACTCTATAGAATTGACCACTATTTAGGAAAAGAGCTTGTCCAAAACCTGgtaatatgtg ... atgtttgcagCTTGTGCTTCGTTTTGCAAACCGCTTATTTTTGCCTCTCTGGAACCGTGATAACATAGCTAACGTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 526

CACTGCAGAGGAACTGAGTGCTGAACTTGGGCAGCTGTTTCAAGAAGAACAACTCTATAGAATTGACCACTATTTAGGAAAAGAGCTTGTCCAAAACCTGgtaatatgtg ... atgtttgcagCTTGTGCTTCGTTTTGCAAACCGCTTATTTTTGCCTCTCTGGAACCGTGATAACATAGCTAACGTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 634

CACTGCAGAGGAACTGAGTGCTGAACTTGGGCAGCTGTTTCAAGAAGAACAACTCTATAGAATTGACCACTATTTAGGAAAAGAGCTTGTCCAAAACCTGgtaatatgtg ... atgtttgcagCTTGTGCTTCGTTTTGCAAACCGCTTATTTTTGCCTCTCTGGAACCGTGATAACATAGCTAACGTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 251

CACTGCAGAGGAACTGAGTGCTGAACTTGGGCAGCTGTTTCAAGAAGAACAACTCTATAGAATTGACCACTATTTAGGAAAAGAGCTTGTCCAAAACCTGgtaatatgtg ... atgtttgcagCTTGTGCTTCGTTTTGCAAACCGCTTATTTTTGCCTCTCTGGAACCGTGATAACATAGCTAACGTACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaactgtatatgctttatatatgcaactgtttcttatactgccatgtttgcagCTTGTGCTTCGTTTTGCAAACCGCTTATTTTTGCCTCTCTGGAACCGTGATAACATAGCTAACGTACAG
        tatatgctttatatat  TA-rich tract