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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgtattacccacacgactattatacctatttgctgtcatatccctttttttagtatttcttgtgattccttatagacatgaccaatattaatctatttatcatatgctgttggttgcag

Basic information

species Zea mays
transcript GRMZM5G845755_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G845755_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 5'ss of exon 5
GTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgtattacccacacgactat-tatacctatttgctgtcatatcccttttttta-gtatttcttgtgattccttatagacatgaccaatattaatctatttatcatatgctgttggttgcag
|||||||||||| |||||||||||||||||||||||||||||||| |||||| |||||||||||||||| || ||||||||||||||||||||||||||   ||   |||  ||  || |||    |   |||  |||| | | | |  |    |  |   | | |||  | ||   |  | ||    | || || || |||||  |||||
GTACTTCAAGGGACCTGAGCTTCTTGTTGACTTGCAAGATTATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtattaccatgacatttatacattactttttctcatttcatcaattttgtaatgcaactgcctttttctataaaagaattaactggtgctgattcgctaataatgtgttgttgagtgcag

upper sequence: GRMZM5G845755_T02 (Zea mays), 5'ss of exon 5
lower sequence: PP1S63_208V6.1 (Physcomitrella patens), 5'ss of exon 6
GTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgtat--tacccacacg----actattatacctatttgctgtcatatccctttttt---tagtatttct-tgtgattccttatagacatgaccaatattaatctatttatcatatgctgttggttgcag
 ||||||||||| |||||| | || || ||  | ||||||||||| ||||| || || ||||||||  |||| |||||||||||||| ||||||   || || | |     | | | | ||  || |   || || | |  ||||    |  | | | | || ||||  ||              | |   | |  | |  | ||   || ||||||||
ATACTTCAAGGGCCCTGAGTTGCTGGTGGATCTCCAAGATTATGACTACTCCCTTGATATGTGGAGCTTGGGATGCATGTTTGCTGGCATGgtaacgtatcctcgcagtttattttaacactaatctttcgttatttacagttttcccatgatgtgtatctgcgattttttcattctgaagtacttctcgttatgctgaagagattgcgt-ggttgcag

upper sequence: GRMZM5G845755_T02 (Zea mays), 5'ss of exon 5
lower sequence: PP1S230_93V6.1 (Physcomitrella patens), 5'ss of exon 5
GTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgtattacccacacgactattatacctatttgctgtcatatccctttttttagtatttcttgtgattccttatagacatgaccaatattaatctatttatcatatgctgttggttgcag
|||||| ||||| || ||| | ||||| ||  | ||||| || ||||| ||| |||||||||||||| | || |||||||||||||||||||||        | |  |  ||||  |      |  ||| | | ||  |  ||    |  |   ||     |    || |    | |     |    || ||| || |  |  ||| ||
GTACTTTAAGGGCCCAGAGTTACTTGTCGATCTTCAAGACTACGATTATTCTTTGGACATGTGGAGTTTAGGATGCATGTTTGCTGGAATGgtaagga----atgtattctatattttgaattttgcatgtacattcctgaagcccattatcccataatgaaccagcaggttgcaaacctgacaggctaccatttgtt--taattgtag

upper sequence: GRMZM5G845755_T02 (Zea mays), 5'ss of exon 5
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 6
GTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgta---ttacccacacgactattatacctatttgctgtcat-atccctttttttag-tat-ttcttgtgattccttatagacatgaccaatattaatct-atttatcatatgctgt----tggttgcag
||||||||||||||||||||| || |||||  | |||||||||||||||||||| |||||||||||  |||| ||||||||||| || ||||||   |||    || |   | |||  | ||   |  | || ||| |  ||| | | ||  ||  | || ||  |  |  |  |    |   | | |||  || | ||  ||   |    || ||||||
GTACTTCAAGGGTCCTGAGCTGCTGGTTGATCTTCAAGATTATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATGgtaaatttaattccaagttcaatatttcgatggtccttgattatcacagtttgtcgctacgttgatttgctttttggtttagtttttgagcttgattctcgttaaacaggtgaattgaagtgattgcag

upper sequence: GRMZM5G845755_T02 (Zea mays), 5'ss of exon 5
lower sequence: EFJ20478 (Selaginella moellendorffii), 5'ss of exon 5
GTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgtattacccacacgact-attatacctatttgctgtcatatccctttttttagtatttcttgtgattccttatagacatgaccaatattaatctatttatcatatgctgttggttgcag
 |||||||| ||||| ||||| ||||| ||| |||| || || ||||||||||| ||||||||||| || ||||||||||| |||||||||||   |  |    | || || || | || |||||  |    |    ||   ||                                                                  
ATACTTCAAAGGTCCGGAGCTGCTTGTGGACCTGCAGGACTACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATGgtg--agtcttttgtctgatcattcgtacttgctaacgccccaagcttcacag------------------------------------------------------------------

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|31359089|gb|CD443446.1|CD443446
EST:     ATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATG                         ATTTTTCGTAAGGAGCCANNNNNNNACGGTCATGACAACCATGATCAACTT
genomic: ATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgtattaccca ... ttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTT
EST: gi|60354727|gb|DN221700.1|DN221700
EST:     GATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATG                         ATTTTTCGTAAGGAGCCANNNNNNNACGGTCATGACAACCATGATCAACTT
genomic: GATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgtattaccca ... ttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTT
EST: gi|60345260|gb|DN212233.1|DN212233
EST:     ATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATG                         ATTTTTCGTAAGGAGCCANNNNNNNACGGTCATGACAACCATGATCAACTT
genomic: ATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgtattaccca ... ttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTT
EST: gi|60350778|gb|DN217751.1|DN217751
EST:     ATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATG                         ATTTTTCGTAAGGAGCCANNNNNNNACGGTCATGACAACCATGATCAACTT
genomic: ATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgtattaccca ... ttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTT
EST: gi|61117731|gb|DN558692.1|DN558692
EST:     ATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATG                         ATTTTTCGTAAGGAGCCANNNNNNNACGGTCATGACAACCATGATCAACTT
genomic: ATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgtattaccca ... ttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTT
EST: gi|61117730|gb|DN558691.1|DN558691
EST:     ATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATG                         ATTTTTCGTAAGGAGCCANNNNNNNACGGTCATGACAACCATGATCAACTT
genomic: ATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgtattaccca ... ttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTT
EST: gi|61117732|gb|DN558693.1|DN558693
EST:     ATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATG                         ATTTTTCGTAAGGAGCCANNNNNNNACGGTCATGACAACCATGATCAACTT
genomic: ATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgtattaccca ... ttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTT
EST: gi|61117733|gb|DN558694.1|DN558694
EST:     ATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATG                         ATTTTTCGTAAGGAGCCANNNNNNNACGGTCATGACAACCATGATCAACTT
genomic: ATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgtattaccca ... ttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTT

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), 47 (downstream exon)
Score: 368

GTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgtattaccca ... ttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 186

GTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgtattaccca ... ttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203

GTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgtattaccca ... ttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 231

GTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgtattaccca ... ttggttgcagATTTTTCGTAAGGAGCCATTTTTTTACGGTCATGACAACCATGATCAACTTGTTAAGATAGCCAAG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgtattacccacacgactattatacctatttgctgtcatatccctttttttagtatttcttgtgattccttatagacatgaccaatattaatctatttatcatatgctgttggttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA