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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtatgacaaccctttatttttcctctttcaataataaaaatcttgtccaaaccatcaatttcctactgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAATCACTGATGTACCTGTGGCGCTTGACGGGGAATAAAACATACCAAGATT

Basic information

species Zea mays
transcript GRMZM2G130889_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130889_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 12
gtagtatgacaaccctttatttttcctctttcaataataaaaatcttgtcca------aaccatcaat--ttcctactgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAATCACTGATGTACCTGTGGCGCTTGACGGGGAATAAAACATACCAAGATT
|||| | | || | |||  ||| | |||| | |||||| |    ||  ||||      | |  | |||  |  || || | | ||||| |||   |||||||| || ||||| ||| ||||||| |||||||| |||||||| |||||| |||||||  | |||||||| |||||||||||||| |
gtagcaaggcagctcttattttattctctat-aataatcacgtactattccatcatttatctctaaatgatagcttcttaatttagGATATGAACGTGGGCACATCATGGAATATCCTGAGACCTGAGACTGTCGAATCACTTATGTACTTGTGGCGTCTTACGGGGAACAAAACATACCAAGACT

upper sequence: GRMZM2G130889_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 12
gtagtatgacaaccctttatttttcctctttcaataataaaaatcttgtccaaaccatcaatttcc-tac-tgactat--agGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAATCACTGATGTACCTGTGGCGCTTGACGGGGAATAAAACATACCAAGATT
   ||||| ||      | | |||         ||  |  |  |  ||    |   ||   ||    ||| |||  ||  |||||||| |||| || ||||||||||||||||||||||| || ||||| ||||||||| | ||||| ||||| || || || || || ||||| ||||| |
---gtatgtcatttgcctgtctttttcaaacacattgtttattttatgcgttatttattgtttagtatacatgatgattcagGACATGAGTGTTGGAACGTCGTGGAACATCTTGAGACCAGAAACTGTCGAATCACTGTTTTACCTCTGGCGGTTAACTGGAAACAAGACATATCAAGAGT

upper sequence: GRMZM2G130889_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 12
gtagtatgacaaccctttatttttcctctttcaa--taataaa--aatcttgtccaaaccatcaatttcctactgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAATCACTGATGTACCTGTGGCGCTTGACGGGGAATAAAACATACCAAGATT
|| |  | |  ||  |||     ||   ||  |   || |       |  ||||  | |||| ||   | |  |   |  |||||||| |||| ||||| || |||||||| || ||||| || || |||||||||||| | ||||| ||||| || || ||||| || ||||| ||||| |
gttg-gtaaatactttttgcgcatctgtttgtatgttagttggttggttatgtcgtatccat-aagcacatgattgtttcagGACATGAGTGTTGGCACATCTTGGAACATTTTAAGACCAGAAACCGTTGAATCACTGTTTTACCTCTGGCGATTAACTGGGAACAAGACATATCAAGAGT

upper sequence: GRMZM2G130889_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv09s0054g00370.t01 (Vitis vinifera), 3'ss of exon 12
gtagtatgacaaccctttatttttcctctttcaataataaaaatcttgtcca--aacca--tcaatttcctactga-----ctatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAATCACTGATGTACCTGTGGCGCTTGACGGGGAATAAAACATACCAAGATT
           |   ||| | ||| || |||  ||| ||   || |  |  |    |||     | ||||  || |      || |||| ||| ||||||| || || |||||||| ||||| || ||||| |||||||||||| | ||||| ||||| || || || || || ||||||||||| |
--------gttagtttttctcttttctttttatatactagttatttcttttactgcccaatcttacttccatctaaaacatttacagGATATGAGTGTGGGTACATCATGGAACATATTGAGGCCCGAGACGGTTGAATCACTGTTTTACCTCTGGCGTTTAACTGGCAACAAGACATACCAAGAGT

upper sequence: GRMZM2G130889_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv09s0054g00230.t01 (Vitis vinifera), 3'ss of exon 7
gtagtatgacaaccctttatttttcctctttcaataataaaaatcttgtccaaaccatca----atttcctactga-----ctatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAATCACTGATGTACCTGTGGCGCTTGACGGGGAATAAAACATACCAAGATT
           |   ||| | ||| || |||  ||| ||   || |  |  |   |   |    ||||||  || |      || |||| ||| ||||||| || || |||||||| ||||| || ||||| |||||||||||| | ||||| ||||| || || || |  || ||||||||||| |
--------gttagtttttctcttttctttttatatactagttatttcttttactgctcaatctcatttccatctaaaacatttacagGATATGAGTGTGGGTACATCATGGAACATATTGAGGCCCGAGACAGTTGAATCACTGTTTTACCTCTGGCGTTTAACTGGCAGCAAGACATACCAAGAGT

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|67028781|gb|CO457530.1|CO457530
EST:     CCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAG                         GACATGGGTGTGGGCACATCGTGGAACATCTTGAGACCGGAGACTGTTGAA
genomic: CCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAGgtagtatgac ... ctgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAA
EST: gi|60349712|gb|DN216685.1|DN216685
EST:     CCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAG                         GGAC-TGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGA
genomic: CCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAGgtagtatgac ... ctgactatagG-ACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGA
EST: gi|211104642|gb|FL379460.1|FL379460
EST:     CCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAG                         GACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAA
genomic: CCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAGgtagtatgac ... ctgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAA
EST: gi|13125955|gb|BG316630.1|BG316630
EST:     CCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAG                         GACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAA
genomic: CCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAGgtagtatgac ... ctgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAA
EST: gi|32849483|gb|CD989164.1|CD989164
EST:     CACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCACTACTGGACAG                         GACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAA
genomic: CACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCA-TACTGGACAGgtagtatgac ... ctgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAA
EST: gi|60291876|gb|DN190115.1|DN190115
EST:     TTTTTCCATACTGGACAG                         GACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAA
genomic: TTTTTCCATACTGGACAGgtagtatgac ... ctgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAA
EST: gi|32941898|gb|CF046717.1|CF046717
EST:     CCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAG                         GACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAA
genomic: CCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAGgtagtatgac ... ctgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAA

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: 48 (upstream exon), 49 (downstream exon)
Score: 107

CTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAGgtagtatgac ... ctgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAATCACTGATGTACCTGTGGCGCTTGACGGGGAATAAAACATACCAAGATT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 171

CTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAGgtagtatgac ... ctgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAATCACTGATGTACCTGTGGCGCTTGACGGGGAATAAAACATACCAAGATT


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

CTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAGgtagtatgac ... ctgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAATCACTGATGTACCTGTGGCGCTTGACGGGGAATAAAACATACCAAGATT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 121

CTTGCTAGGACCTGCTATAATTTCTACCAAACCACTCCCACGAAGTTGGCTGGAGAAAATTATTTTTTCCATACTGGACAGgtagtatgac ... ctgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAATCACTGATGTACCTGTGGCGCTTGACGGGGAATAAAACATACCAAGATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctctttcaataataaaaatcttgtccaaaccatcaatttcctactgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAATCACTGATGTACCTGTGGCGCTTGACGGGGAATAAAACATACCAAGATT
                                           tactgac  putative branch site (score: 121)
                                      tttcctact  CT-rich tract
     tttcaataataaaaat  TA-rich tract