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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGAAGCGTAATACAGAGCATGACCCCCCTTATTGGAGAGGTGCCATTTGGATAAACATGAACTACATGGTTCTTTCGGCACTACATCACTATGCACATAgtaagctctttaattgcctagtttataccctttgcaaacccttctgctggcataatgatatagcattctgctttcctgtag

Basic information

species Zea mays
transcript GRMZM2G071675_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G071675_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g69210.1 (Oryza sativa), 5'ss of exon 20
ATGAAGCGTAATACAGAGCATGACCCCCCTTATTGGAGAGGTGCCATTTGGATAAACATGAACTACATGGTTCTTTCGGCACTACATCACTATGCACATAgtaagctctttaat-----------------tgcctagtttataccctt-tgcaaacccttctgctggcataatgat---atagcattctgctttcctgtag
|||||||| || || |||||||| ||||| ||||||||||||||||||||||||||||||||||||||| ||||||| | |||||| |||||||||||| |||| |||| |||                  |    || || ||||||| || |||   | ||| | |||  |||||   ||| |||| | ||   ||| ||
ATGAAGCGCAACACTGAGCATGATCCCCCATATTGGAGAGGTGCCATTTGGATAAACATGAACTACATGATTCTTTCAGGACTACACCACTATGCACATGgtaaactctataacagatgctgctaaacaactattcagcttttacccttctgtaaattttactgtttgcacgatgatctaataacattgttctgctctgaag

upper sequence: GRMZM2G071675_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G10870.2 (Glycine max), 5'ss of exon 22
ATGAAGCGTAATACAGAGCATGACCCCCCTTATTGGAGAGGTGCCATTTGGATAAACATGAACTACATGGTTCTTTCGGCACTACATCACTATGCACATAgtaagctctttaattgcctagtttataccc-tttgcaaacccttctgctggcataatg---------atatagcattctgcttt----cctgtag
|||||||  || |||||||||||||| || || ||||||||| |  |||||||||||||||| ||||   ||| ||| ||||| || || ||  |  |  ||||  | |  | | ||| ||  || |    | ||||||   | |  ||    | ||          |  ||   || || |||    | |||||
ATGAAGCACAACACAGAGCATGACCCTCCATACTGGAGAGGTCCTGTTTGGATAAACATGAATTACAGAATTCCTTCCGCACTCCACCATTACTCCAAAGgtaa--tatggactggccaaggctaaaaatatctgcaaatattcccactatatttataccctcctgaaactaaatttttggtttaaatcttgtag

upper sequence: GRMZM2G071675_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT1G67490.2 (Arabidopsis thaliana), 5'ss of exon 19
ATGAAGCGTAATACAGAGCATGACCCCCCTTATTGGAGAGGTGCCATTTGGATAAACATGAACTACATGGTTCTTTCGGCACTACATCACTATGCACATAgtaa------gctctttaattgcctagt----ttataccct-ttgcaa-acccttctgctggcataatgatata-gcattctgctttcc-tgtag--------------
||||| ||||| || ||||||||  | || || ||||||||| | || ||||| ||||||||||||||| |||||||  | ||  | || ||  |     ||||       | ||  | |||   |        | | | |  | ||| |||  |  | |  | || |   ||| |||||| | || || |||                
ATGAAACGTAACACTGAGCATGATGCACCATACTGGAGAGGTCCTATATGGATGAACATGAACTACATGATTCTTTCTTCTCTTTACCATTACTCTATAGgtaattttctaccctccacttggtcaaaagcgccacatcatactacaagacctctacgttttcttactatcatatgcattcggtttaccatgtgtcaaaattcctgcag

upper sequence: GRMZM2G071675_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv01s0010g03300.t01 (Vitis vinifera), 5'ss of exon 20
ATGAAGCGTAATACAGAGCATGACCCCCCTTATTGGAGAGGTGCCATTTGGATAAACATGAACTACATGGTTCTTTCGGCACTACATCACTATGCACATAgtaagctcttt---aattgcctagtttataccctttgcaaacccttctgctggcataatgata--tagcattctgctttcctgtag---------------------------------------------------------
||||| ||||| |||||||||||||| ||||| ||||||||| | |||||||| |||||||| |||| | ||||||| ||||| || || ||| | ||  ||||  | | |    |    |      | || |     |||| ||  | |||  ||  | |    |     | ||  |  ||  |                                                          
ATGAAACGTAACACAGAGCATGACCCACCTTACTGGAGAGGTCCAATTTGGATGAACATGAATTACAGGATTCTTTCTGCACTCCACCATTATTCCCAAGgtaatatttatctggaaaaacagacaaaaacacacaagaaactctcttactgaaattttcaagcttgaagatttgaatatctccatttgcatttacactttttttcctgatgcttgcgggtggttttggttgaattcctgcag

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|32908966|gb|CF013779.1|CF013779
EST:     GATAAACATGAACTACATGGTTCTTTCGGCACTACATCACTATGCACATA                         AGGATGGTCCATATAGCGGCAGGGCAAAGGAATTGTATGACAAGCTAAGAT
genomic: GATAAACATGAACTACATGGTTCTTTCGGCACTACATCACTATGCACATAgtaagctctt ... tttcctgtagAGGATGGTCCATATAGCGGCAGGGCAAAGGAATTGTATGACAAGCTAAGAT
EST: gi|4887313|gb|AI677412.1|AI677412
EST:     GATAACCATGAACTACATGGTTCTTTCGGCACTACATCACTATGCACATA                         AGGATGGTCCATATAGCGGCAGGGCAAAGGAATTGTATGACAAGCTAAGAT
genomic: GATAAACATGAACTACATGGTTCTTTCGGCACTACATCACTATGCACATAgtaagctctt ... tttcctgtagAGGATGGTCCATATAGCGGCAGGGCAAAGGAATTGTATGACAAGCTAAGAT
EST: gi|7844296|gb|AW787518.1|AW787518
EST:     GATAAACATGAACTACATGGTTCTTTCGGCACTACATCACTATGCACATA                         AGGATGGTCCATATAGCGGCAGGGCAAAGGAATTGTATGACAAGCTAAGAT
genomic: GATAAACATGAACTACATGGTTCTTTCGGCACTACATCACTATGCACATAgtaagctctt ... tttcctgtagAGGATGGTCCATATAGCGGCAGGGCAAAGGAATTGTATGACAAGCTAAGAT
EST: gi|89247235|gb|DY619021.1|DY619021
EST:     GGCACTACATCACTATGCACATA                         AGGATGGTCCATATAGCGGCAGGGCAAAGGAATTGTATGACAAGCTAAGAT
genomic: GGCACTACATCACTATGCACATAgtaagctctt ... tttcctgtagAGGATGGTCCATATAGCGGCAGGGCAAAGGAATTGTATGACAAGCTAAGAT
EST: gi|87152875|gb|DY397664.1|DY397664
EST:     GATAAACATGAACTACATGGTTCTTTCGGCACTACATCACTATGCACATA                         AGGATGGTCCATATAGCGGCAGGGCAAAGGAATTGTATGACAAGCTAAGAT
genomic: GATAAACATGAACTACATGGTTCTTTCGGCACTACATCACTATGCACATAgtaagctctt ... tttcctgtagAGGATGGTCCATATAGCGGCAGGGCAAAGGAATTGTATGACAAGCTAAGAT

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: 177

ATGAAGCGTAATACAGAGCATGACCCCCCTTATTGGAGAGGTGCCATTTGGATAAACATGAACTACATGGTTCTTTCGGCACTACATCACTATGCACATAgtaagctctt ... tttcctgtagAGGATGGTCCATATAGCGGCAGGGCAAAGGAATTGTATGACAAGCTAAGATCAAACCTTATCCG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 98

ATGAAGCGTAATACAGAGCATGACCCCCCTTATTGGAGAGGTGCCATTTGGATAAACATGAACTACATGGTTCTTTCGGCACTACATCACTATGCACATAgtaagctctt ... tttcctgtagAGGATGGTCCATATAGCGGCAGGGCAAAGGAATTGTATGACAAGCTAAGATCAAACCTTATCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

ATGAAGCGTAATACAGAGCATGACCCCCCTTATTGGAGAGGTGCCATTTGGATAAACATGAACTACATGGTTCTTTCGGCACTACATCACTATGCACATAgtaagctctt ... tttcctgtagAGGATGGTCCATATAGCGGCAGGGCAAAGGAATTGTATGACAAGCTAAGATCAAACCTTATCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 92

ATGAAGCGTAATACAGAGCATGACCCCCCTTATTGGAGAGGTGCCATTTGGATAAACATGAACTACATGGTTCTTTCGGCACTACATCACTATGCACATAgtaagctctt ... tttcctgtagAGGATGGTCCATATAGCGGCAGGGCAAAGGAATTGTATGACAAGCTAAGATCAAACCTTATCCG