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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaaatcaaatacttcaatctctttgcacacagtaagcatttggtgatatttcactacttcctcaggtcatgtaagactgtacctattttccttcccagAACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAG

Basic information

species Zea mays
transcript GRMZM2G157068_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053868_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g03410.1 (Oryza sativa), 3'ss of exon 4
gtagaaatcaaatactt-caatctctttgcacacagtaagcattt-ggtgatatttcactacttcctcaggtcatgtaagactgtacctattttccttcccagAACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAG
||||||||  ||  ||| |||| |||| |||   |||   ||||| |||||||||||| |||||| ||||||||||||||| |||||||||||||||||||||||||||||||||||||| | ||||||||| |||||  ||||||| |||||||||||| ||||||| ||||| || ||||
gtagaaattgaacgctttcaatgtcttggcaattagtgtacattttggtgatatttcattacttc-tcaggtcatgtaagaatgtacctattttccttcccagAACTTCCTTTTCAAATCAACCAAGGAGGACTCACCTTTAAAGGCAACAGATTTTGGTCTGTCAGACTTCATAAAACCAG

upper sequence: GRMZM2G053868_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 6
gtagaaatcaaatacttcaatctctttgcaca--cagtaagcatttggtgatatttcactacttcct-caggtcatgtaagactgtacctattttccttcccagAACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAG
|||  | ||||  || |     | | |||  |    ||  | | |  |   |||   ||||  | ||  |  | || ||  | | |   ||  |    |  ||||| || ||||| ||||| | ||| || ||||||||  ||||||| || ||||||||||||||||||||||| || || |
gtatga-tcaagcacatttgcatatctgccaaatttgtgtgaaatgagatctatactactagatgctatacataatatattaatatttttacctattcttgcagAATTTTCTTTTTAAATCAACCAAAGAAGATTCACCTTTAAAGGCCACTGATTTTGGTTTGTCAGATTTCATAAAACCTG

upper sequence: GRMZM2G053868_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA01G37100.1 (Glycine max), 3'ss of exon 5
gtagaaatcaaatacttcaatctctttgcacacagtaagcatttggtgatatttcactacttcctcaggtcatgtaagactgtacctattttccttcccagAACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAG
|||    |||| | |   |   | | |  || || || | |||||   ||||   ||||           ||| ||| | |       ||   |||  ||||| || |||||||| || | ||| || ||||||||  ||||||| || |||||||||||||| |||||||| || || |
gtatgg-tcaagttcgctagcatatct--acgcaatatggatttg--tatatgctactata---------cat-taaaatt-------ttcctctttgcagAATTTTCTTTTCAAGTCAACCAAAGAAGATTCACCTTTAAAGGCTACCGATTTTGGTTTGTCTGATTTCATAAAACCTG

upper sequence: GRMZM2G053868_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G05440.1 (Glycine max), 3'ss of exon 4
gtagaaatcaaatacttcaatctctttgcaca--cagtaagcatttggtgatatttcactacttcctcaggtcatgtaagactgtacctattttccttcccagAACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAG
|||  | ||||  || |     | | |||  |    ||  | | |  |   |||   ||||  | || |  | ||  |  | |||   ||  |    |  ||||| || ||||| ||||| | ||| || ||||||||  ||||||| |||||||||||||||||||||||||| || || |
gtatga-tcaagcacatttgcatatctgccaaatttgtgtgaactgagatctatactactagatgct-atataatagattaatgtttttacctattcttgcagAATTTTCTTTTTAAATCAATCAAAGAAGATTCACCTTTAAAGGCCACAGATTTTGGTTTGTCAGATTTCATAAAACCTG

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|33096470|gb|CF056464.1|CF056464
EST:     CTGCTGAATGCCATCTGCGTGGTTTAGTTCACCGAGATATGAAGCCTGAG                         AACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGAT
genomic: CTGCTGAATGCCATCTGCGTGGGTTAGTTCACCGAGATATGAAGCCTGAGgtagaaatca ... tccttcccagAACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGAT
EST: gi|149082402|gb|EE171589.2|EE171589
EST:     CTGCTGAATGCCATCTGCGTGGGTTAGTTCACCGAGATATGAAGCCTGAG                         AACTTCCTTTTCAAATCGAACAAAGAGGATTCACCACTAAAG
genomic: CTGCTGAATGCCATCTGCGTGGGTTAGTTCACCGAGATATGAAGCCTGAGgtagaaatca ... tccttcccagAACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAG
EST: gi|211195528|gb|FL100652.1|FL100652
EST:     CTGCTGAATGCCATCTGCGTGGGGTAGTTCACCGAGATATGAAGCCTGAG                         AACTTCCTTTTTCAA-TCGAACA-GGAGGATTCACCACTAA
genomic: CTGCTGAATGCCATCTGCGTGGGTTAGTTCACCGAGATATGAAGCCTGAGgtagaaatca ... tccttcccagAACTTCCTTTT-CAAATCGAACAAGGAGGATTCACCACTAA

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: 43 (upstream exon), 47 (downstream exon)
Score: 35

CTATAGTGAGAAAGATGCTGCAGTGGTAGTCCGCCAAATGCTCAAAGTAGCTGCTGAATGCCATCTGCGTGGGTTAGTTCACCGAGATATGAAGCCTGAGgtagaaatca ... tccttcccagAACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 75

CTATAGTGAGAAAGATGCTGCAGTGGTAGTCCGCCAAATGCTCAAAGTAGCTGCTGAATGCCATCTGCGTGGGTTAGTTCACCGAGATATGAAGCCTGAGgtagaaatca ... tccttcccagAACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 163

CTATAGTGAGAAAGATGCTGCAGTGGTAGTCCGCCAAATGCTCAAAGTAGCTGCTGAATGCCATCTGCGTGGGTTAGTTCACCGAGATATGAAGCCTGAGgtagaaatca ... tccttcccagAACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 92

CTATAGTGAGAAAGATGCTGCAGTGGTAGTCCGCCAAATGCTCAAAGTAGCTGCTGAATGCCATCTGCGTGGGTTAGTTCACCGAGATATGAAGCCTGAGgtagaaatca ... tccttcccagAACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatatttcactacttcctcaggtcatgtaagactgtacctattttccttcccagAACTTCCTTTTCAAATCGAACAAGGAGGATTCACCACTAAAGGCGACAGATTTTGGTTTGTCAGATTTCATTAAGCCAG
                                    tacctattttccttcc  CT-rich tract
                                        tatttt  TA-rich tract