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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattccttttttgtttagctgtgtaaagcataaactattttcattggatgtggacacagatgttagttatccttcctttcaaatgtcttctatcttgcgtgcagGTATTGAAACTGTAAGAAGGGACAACTGTTTACTGGTAAAGAACCTGGTAACCGAGTGCCTTCATAAAATACTGGTAGACCGTGATGTTCCTGGTGCAGT

Basic information

species Zea mays
transcript GRMZM2G115245_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115245_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g08330.1 (Oryza sativa), 3'ss of exon 22
gtattccttttttgtttagctgtgtaaagcataaactattttcattggatgtggacacagatgttagttatccttc---ctttcaaatgtcttctatcttgcgtgcagGTATTGAAACTGTAAGAAGGGACAACTGTTTACTGGTAAAGAACCTGGTAACCGAGTGCCTTCATAAAATACTGGTAGACCGTGATGTTCCTGGTGCAGT
                                    ||||||| || | | | | |  |||| | |  |  |||||   |||| | |||  |   |  |||| |  |||||||||||| || |||||||||||||||||| | |||||||||||||| || |||||||||||||||||||| || ||| | |||||||||||||||||
-----------------------------------gtattttcttttg-tcttgtcttagatatcatcttaccttcttgctttaacatgattctaactttgcttatagGTATTGAAACAGTGAGAAGGGACAACTGTTTATTAGTAAAGAACCTGGTTACTGAGTGCCTTCATAAAATACTAGTGGACAGAGATGTTCCTGGTGCAGT

upper sequence: GRMZM2G115245_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA06G16110.1 (Glycine max), 3'ss of exon 22
gtattccttttttgtttagctgtgtaaagcataaactattttcattggatgtggacacagatgttagttatccttcctttcaaatgtcttctatcttgcgtgcagGTATTGAAACTGTAAGAAGGGACAACTGTTTACTGGTAAAGAACCTGGTAACCGAGTGCCTTCATAAAATACTGGTAGACCGTGATGTTCCTGGTGCAGT
                               |||||  |  || ||   |     |       || |||    | ||| | |||     | |   ||| |  ||||||||||||| ||  |||| ||||| |||||| |||| || |||||||| | ||| |||||||| |||||| || | ||| | ||  ||||||| |||||
------------------------------gtaaacattactctttacctt----cttgttgctttgttgaagtgcctcttaaactaaatatgcattgag--cagGTATTGAAACAGTTCGAAGAGACAATTGTTTATTGGTCAAAAACCTGGTGAACGATTGCCTTCACAAAATATTGATTGACAGGGACATTCCTGGGGCAGT

upper sequence: GRMZM2G115245_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA04G38800.2 (Glycine max), 3'ss of exon 6
gtattccttttttgtttagctgtgtaaagcataaactattttcattggatgtggacacagatgttagttatccttcctttcaaatgtcttctatcttgcgtgcagGTATTGAAACTGTAAGAAGGGACAACTGTTTACTGGTAAAGAACCTGGTAACCGAGTGCCTTCATAAAATACTGGTAGACCGTGATGTTCCTGGTGCAGT
                               |||||  |  || ||  |  | |   |     || |||    | ||| | |||     | |   ||| |  ||||||||||||| ||  |||| ||||| |||||| ||||||| |||||||| | ||| |||||||| |||||| || | ||| | ||  ||||||| |||||
------------------------------gtaaacattactcttt--accttgttgc-----tttgttgaagtgcctctgaaactaaatttgcattgag--cagGTATTGAAACAGTTCGAAGAGACAATTGTTTATTGGTAAAAAACCTGGTGAACGATTGCCTTCACAAAATATTGATTGACAGGGACATTCCTGGGGCAGT

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|32930209|gb|CF035021.1|CF035021
EST:     GTACTGGACGAATCCTGAGAAATTTGACAAAATGGATGCAAAAG                         GTATTGAAACTGTAAGAAGGGACAACTGTTTACTGGTAAAGAACCTGGTAA
genomic: GTACTGGACGAATCCTGAGAAATTTGACAAAATGGATGCAAAAGgtattccttt ... ttgcgtgcagGTATTGAAACTGTAAGAAGGGACAACTGTTTACTGGTAAAGAACCTGGTAA
EST: gi|32931064|gb|CF035876.1|CF035876
EST:     ACTGNACGAATCTTGAGAAATTTGACAAAATGGATGCAAAAG                         GTATTGAAACTGTAAGAAGGGACAACTGTTTACTGGTAAAGAACCTGGTAA
genomic: ACTGGACGAATCCTGAGAAATTTGACAAAATGGATGCAAAAGgtattccttt ... ttgcgtgcagGTATTGAAACTGTAAGAAGGGACAACTGTTTACTGGTAAAGAACCTGGTAA
EST: gi|94478920|gb|EB707878.1|EB707878
EST:     TGGTTTGTACTGGACGAATCCTGAGAAATTTGACAAAATGGATGCAAAAG                         GTATTGAAACTGTAAGAAGGGACAACTGTTTACTGGTAAAGAACCTGGTAA
genomic: TGGTTTGTACTGGACGAATCCTGAGAAATTTGACAAAATGGATGCAAAAGgtattccttt ... ttgcgtgcagGTATTGAAACTGTAAGAAGGGACAACTGTTTACTGGTAAAGAACCTGGTAA

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: 226

TTTGAGAAGGTCTATTTTCCTTACCTTCTAATCAGCAAGAAGAGATATGCTGGTTTGTACTGGACGAATCCTGAGAAATTTGACAAAATGGATGCAAAAGgtattccttt ... ttgcgtgcagGTATTGAAACTGTAAGAAGGGACAACTGTTTACTGGTAAAGAACCTGGTAACCGAGTGCCTTCATAAAATACTGGTAGACCGTGATGTTCCTGGTGCAGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 32

TTTGAGAAGGTCTATTTTCCTTACCTTCTAATCAGCAAGAAGAGATATGCTGGTTTGTACTGGACGAATCCTGAGAAATTTGACAAAATGGATGCAAAAGgtattccttt ... ttgcgtgcagGTATTGAAACTGTAAGAAGGGACAACTGTTTACTGGTAAAGAACCTGGTAACCGAGTGCCTTCATAAAATACTGGTAGACCGTGATGTTCCTGGTGCAGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 41

TTTGAGAAGGTCTATTTTCCTTACCTTCTAATCAGCAAGAAGAGATATGCTGGTTTGTACTGGACGAATCCTGAGAAATTTGACAAAATGGATGCAAAAGgtattccttt ... ttgcgtgcagGTATTGAAACTGTAAGAAGGGACAACTGTTTACTGGTAAAGAACCTGGTAACCGAGTGCCTTCATAAAATACTGGTAGACCGTGATGTTCCTGGTGCAGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 29

TTTGAGAAGGTCTATTTTCCTTACCTTCTAATCAGCAAGAAGAGATATGCTGGTTTGTACTGGACGAATCCTGAGAAATTTGACAAAATGGATGCAAAAGgtattccttt ... ttgcgtgcagGTATTGAAACTGTAAGAAGGGACAACTGTTTACTGGTAAAGAACCTGGTAACCGAGTGCCTTCATAAAATACTGGTAGACCGTGATGTTCCTGGTGCAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggacacagatgttagttatccttcctttcaaatgtcttctatcttgcgtgcagGTATTGAAACTGTAAGAAGGGACAACTGTTTACTGGTAAAGAACCTGGTAACCGAGTGCCTTCATAAAATACTGGTAGACCGTGATGTTCCTGGTGCAGT
                                    tcttctatctt  CT-rich tract
             ttagttat  TA-rich tract