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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtgcatataccctattctgaatttcttttctgttgactgttgagtttggtgttggatatttttgtgtttgctgcttttattttttgctggcttgccatcagttatatataagtggatttacttctgcctagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGACTTAATGAGACAGGCCCTA

Basic information

species Zea mays
transcript GRMZM2G145704_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145704_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g06190.1 (Oryza sativa), 3'ss of exon 6
gtattgtgcatataccctattctgaatttcttttctgttgactgttgagtttggtgttggatatttttgtgtttgctgcttttattttttgctggcttgccatcagttatatataagtg-gatttacttctgcctagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGACTTAATGAGACAGGCCCTA---------------------------------------
       |  | || |||||   ||   | | ||   || | | |   |||| || |||       | || ||||   | |  || |||| ||   |   |  ||||| ||   |  ||  | | ||| |||   ||||||||||||||||||||||||||||||||||| || |||||||| |||||   |   ||                                        
-------gtgtttaacctata--gaccctatctttcatttatttt--ggtttagtcttg-----cctcgtttttgt--cctacatgttttactatttcatc--cagttttacccacttgcaaataactcctgtacagGTATGCTAGAGAAGATACACACTATCTGTTGTATATGTATGACTTGATGAGGTTGAGACTGCAAAAGGAGTCGACATCTGACAATGATCTTCTTCTAGAG

upper sequence: GRMZM2G145704_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G24130.1 (Glycine max), 3'ss of exon 7
gtattgtgcatataccctattctgaatttcttttctgttgactgttgagtttggtgttggatatttttgtgtttgctgcttttattttttgctggcttgccatcagttatatataagtggatttacttctgcc--tagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGACTTAATGAGACAGGCCCTA---------------------------------------
                                   |||| | | |||  ||| |  |||   |||  || |    |||   |      |  ||   | |  || | |   || ||| |   | |  || ||     || ||||| |||||||||||||||||||||||||| ||||| |||||||||||        ||                                       
---------------------------------cttgttta-tcttggttttagc-ttgatgattactg-gcacactgtcatgggcaat--ctaattagtaattattacaatctaattaactgtttttgtgatgacagATATGCCAGAGAAGATACACACTATCTGTTGTATATATACGACTTAATGAGGATTAAGTTATTTGCCTTGTCTAAGGAGTCTGAAAGTTCTGAGTCTTCA

upper sequence: GRMZM2G145704_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA05G13920.1 (Glycine max), 3'ss of exon 6
gtattgtgcatataccctattctgaatttcttttctgttgactgttgagtttggtgttggatatttttgtgtttgc-tgcttttattttttgctggcttgccatcagttatatataagtggatttacttctgcctagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGACTTAATGAGACAGGCCCTA---------------------------------------
                                     ||     ||||| ||| | || | |   |   |    |  | || | ||      |    || |  | |  |||   | | |   | |  ||      || ||||| |||||||||||||| |||||| | ||||||||||| || |||||    |   ||                                       
----------------------------------aatttattccttgagcttgctattagcttgatagttaccagtatactgtcatggacaccctaattactgtaatctat---tgaattattattttttatgacagATATGCCAGAGAAGATACACATTATCTGCTATACATATATGATTTCATGAGGATTGAGTTATTTTCCATGCTTAAGGAGCCTGAAAGTGTTGACGCTCCA

upper sequence: GRMZM2G145704_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT1G54440.2 (Arabidopsis thaliana), 3'ss of exon 6
gtattgtgcatataccctattctgaatttcttttctgttgactgttgagtttggtgttggatatttttgtgtttgctgcttttattttttgctggcttgccatcagttatatataagtggatttacttctgcctagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGACTTAATGAGACAGGCCCTA
     ||   ||||  || |    | | ||| |  || |  || |||  || | ||        |      |||||   | | ||         ||| |  |  || || | || |     | ||| | |     |  |||| |  | || | ||||| |  ||    |   | ||||   |||  |||   ||   
-----gttagtatattctctgtctagtctctctcatgattgct-ttgcattggttgagttgagctaacacatttgca--tataatggcagATATGCTAG--AGAAGATACACATTATCTTTTGTACATTTATGATGTAATGCGAATGGAGTTGCACACAA--TGGCAAAGGAAGATGAGC-AATCTGACTCTCCT--

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), 41 (downstream exon)
Score: 128

GTATCAAAATGCAGACTGGAGGTCGAGACCACTTCCTGATGAAATGATCAAgtattgtgca ... ttctgcctagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGACTTAATGAGACAGGCCCTA


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 170

GTATCAAAATGCAGACTGGAGGTCGAGACCACTTCCTGATGAAATGATCAAgtattgtgca ... ttctgcctagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGACTTAATGAGACAGGCCCTA


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 206

GTATCAAAATGCAGACTGGAGGTCGAGACCACTTCCTGATGAAATGATCAAgtattgtgca ... ttctgcctagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGACTTAATGAGACAGGCCCTA


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 193

GTATCAAAATGCAGACTGGAGGTCGAGACCACTTCCTGATGAAATGATCAAgtattgtgca ... ttctgcctagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGACTTAATGAGACAGGCCCTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattttttgctggcttgccatcagttatatataagtggatttacttctgcctagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGACTTAATGAGACAGGCCCTA
                                        tttacttct  CT-rich tract
                    atcagttatatataa  TA-rich tract