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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttttcatttactgatatcagaaatataaatttcctttggctcctgttgtgtataaccttgtattttttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTCCCACTCT

Basic information

species Zea mays
transcript GRMZM2G120578_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120578_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g15550.1 (Oryza sativa), 3'ss of exon 4
--------gttcttttcatttactgatatcagaaatataaatttcctttggctcctgttgt-----gtataac------------cttgtattttttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTCCCACTCT
         ||||  |||  || ||| | |  ||||| |||     | | |    | || |     |||| ||            | ||| |||||| | ||||||| ||||||||||| ||||| ||||| |||||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||| || || |
gttctcaacttctcatcacctattgacagccaaaataaaaaaaaaatctagtatttattatactttgtattacagtgttgtgtgacctgttttttttttatgcagTCCTCAACCTATGGAAAAGTTCTTGTCCTTGATGGTATTGTCCAGTTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTTCCGCTTT

upper sequence: GRMZM2G120578_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G13210.3 (Glycine max), 3'ss of exon 4
----gttcttttcatttactgatatcagaaatataaatttcctttggctcctgttgtgtataaccttgtattttttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTCCCACTCT
    | ||| ||||| |  |||| |    | |||||||||    ||      ||  |  ||   ||  |  ||||  | ||||||| ||||  |||||||| || ||||| |||||||| || |||||||||||||| | |||||||||||| |||||||| |||||  |||| || || ||||
gtttggtctcttcatcttatgattt----actataaattttacatgaaa---gtgataaatg--ctaatccttttgttttgcagTCATCAATGTATGGGAATGTGCTTGTACTTGATGGAATAGTTCAATTGACTGAGAGGGATGAATGTGCTTACCAGGAGATGATAGCTCATCTTCCCCTCT

upper sequence: GRMZM2G120578_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G41600.1 (Glycine max), 3'ss of exon 4
gttcttttcatttactgatatcagaaatataaatttcctttggctcctgttgtgtataaccttgtattttttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTCCCACTCT
     |||    |  | || | | || | ||   |  ||||  |       |  || |  ||  |  |||   | ||||||| ||||| ||||||||||| ||||| |||||||| || |||||||||||||| |||||||||||||| |||||||| |||||  |||| || || ||||
----gtttggcctcttcatcttataa-tgtactataactttaacgtgaaagggatagatgctaatcctttcattttgcagTCATCAACTTATGGGAAAGTGCTTGTACTTGATGGAATAGTTCAATTGACTGAGAAGGATGAATGTGCTTACCAGGAGATGATAGCTCATCTTCCCCTCT

upper sequence: GRMZM2G120578_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------------------------gttcttttcatttactgatatcagaaatataaatttcctttggctcctgttgtgta--taaccttgtattttttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTCCCACTCT
                                                |||    |  ||||   || |   |  |     ||| ||||      | ||   ||  |||    |  | |||| | ||||||||||| | ||||| ||||| |||||||||||||| |||||||| ||||  || || ||||||||||| || ||||| |||||| ||||||| || || |
gttctgcattctgaactctaaatactagtgttgttcgaagttgacttagtttccattttttatctatctgtcatgttcttcttttctttcttctatattagctagctaatgcagattcttttatttgcagTCGTCAGCATATGGCAAAGTGCTTGTGCTTGATGGCATTGTTCAGTTGAGCGAGAAAGATGAATGTGCCTATCAGGAGATGATTGCTCACCTTCCCCTTT

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|211320667|gb|FL013191.1|FL013191
EST:     CATATTGTACCAGGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAG                         TCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
genomic: CATATTGTACCAGGGG-AAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
EST: gi|148956445|gb|EC902269.2|EC902269
EST:     ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAG                         TCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
genomic: ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
EST: gi|78117805|gb|DV536192.1|DV536192
EST:     ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAG                         TCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
genomic: ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
EST: gi|148931937|gb|EC875166.2|EC875166
EST:     ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAG                         TCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
genomic: ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
EST: gi|148930370|gb|EE284813.2|EE284813
EST:     ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAG                         TCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
genomic: ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
EST: gi|211322828|gb|FL013194.1|FL013194
EST:     ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAG                         TCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
genomic: ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
EST: gi|149072878|gb|EE161134.2|EE161134
EST:     ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAG                         TCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
genomic: ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
EST: gi|211322835|gb|FL013201.1|FL013201
EST:     CATATTGTACCAGGGGAAATCACCATACCAAGGAAGTCCTGGTCTTTGAG                         TCGTCAACCTATGGGGAAAAGTC-TTGTGNCTTGATGGTATTGTTCAATTG
genomic: CATATTGTACCAGGGGAAATCACCATACCA-GGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGG-AAA-GTCCTTGTG-CTTGATGGTATTGTTCAATTG
EST: gi|211322829|gb|FL013195.1|FL013195
EST:     ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAG                         TCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
genomic: ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
EST: gi|32865849|gb|CF005531.1|CF005531
EST:     ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAG                         TCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
genomic: ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
EST: gi|28188224|gb|CB179834.1|CB179834
EST:     ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAG                         TCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
genomic: ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
EST: gi|148963955|gb|EE015081.2|EE015081
EST:     ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAG                         TCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT
genomic: ACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACT

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), 48 (downstream exon)
Score: 160

GAGAGGCCCATTCCTTGAAAGTGGAGAACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTCCCACTCT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 115

GAGAGGCCCATTCCTTGAAAGTGGAGAACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTCCCACTCT


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 75

GAGAGGCCCATTCCTTGAAAGTGGAGAACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTCCCACTCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 126

GAGAGGCCCATTCCTTGAAAGTGGAGAACATATTGTACCAGGGGAAATCACCATACCAGGAAGTCCTGGTCTTTGAGgttcttttca ... ttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTCCCACTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatataaatttcctttggctcctgttgtgtataaccttgtattttttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTCCCACTCT
                            gtataac  putative branch site (score: 126)
                                       tatttttt  putative PPT
                                    ttgtatttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcttttcatttactgatatcagaaatataaatttcctttggctcctgttgtgtataaccttgtattttttgtgtgcagTCGTCAACCTATGGGAAAGTCCTTGTGCTTGATGGTATTGTTCAATTGACTGATAAGGATGAATGTGCGTACCAGGAAATGATTACTCACCTCCCACTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG