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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggaagatcaaaattctctatcttaaactgggctaaacgaagctgccaaagttactgattccagctttgcctttctgttctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC

Basic information

species Zea mays
transcript GRMZM5G818887_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G818887_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g10290.2 (Oryza sativa), 3'ss of exon 4
gtagggaagatcaaaattctctatcttaaactgggctaaacgaagctgccaaagtt----------actgattccagctttgcctttctgttctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC
||| | |||      || || |  |||  |   || |||   | |||   || |||          ||||||||||||||||||||  |  ||| |||  ||||| | ||| |||| ||||| ||| |||||||||| || |||||||||||||| |||| ||| || |||||||| |||||||| ||
gtaagaaaggctgtgatccttt--cttcgatgtggttaaggaaggctcataatgttcatagtcattactgattccagctttgccttcgtcatcttattttagGCTACCGCTCAACCTTCATATTTTGTCGCAGAAGAGCCTGAAGATGACAACATCCTTCGTACTAGGACATATGACGTTAGCATCAC

upper sequence: GRMZM5G818887_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g41110.1 (Oryza sativa), 3'ss of exon 4
gtagggaagatcaaaattctctatcttaaactgggctaaacgaagctgccaaagtt----------actgattccagctttgcctttctgttctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC
||| | ||||     || ||  |||||  |   || |||   | |||   || |||          || |||||||||||||||||  |  ||| |||  ||||| | ||| |||| ||||| ||| |||||||||| || |||||||||||||| |||| ||| || |||||||| |||||||| ||
gtaagaaagactgtgatcct--atcttcgatgtggttaagaaaggctcataatgttcatagtcattaccgattccagctttgccttcgtcatcttattttaggctaccgctcaaccttcatattttgtcgcagAAGAGCCTGAAGATGACAACATCCTTCGTACTAGGACATATGACGTTAGCATCAC
















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|211435031|gb|FL327502.1|FL327502
EST:     AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTG                         GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
genomic: AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
EST: gi|148960724|gb|EE011368.2|EE011368
EST:     AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTG                         GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
genomic: AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
EST: gi|32809166|gb|CD961400.1|CD961400
EST:     AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTG                         GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
genomic: AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
EST: gi|32804145|gb|CD956381.1|CD956381
EST:     AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTG                         GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
genomic: AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
EST: gi|71313247|gb|DR793147.1|DR793147
EST:     AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTG                         GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
genomic: AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
EST: gi|78091451|gb|DV519825.1|DV519825
EST:     AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTG                         GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
genomic: AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
EST: gi|149045355|gb|EE047779.2|EE047779
EST:     AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTG                         GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
genomic: AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
EST: gi|76013821|gb|DT940991.1|DT940991
EST:     AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTG                         GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
genomic: AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
EST: gi|60342765|gb|DN209738.1|DN209738
EST:     AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTG                         GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
genomic: AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
EST: gi|76013820|gb|DT940990.1|DT940990
EST:     AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTG                         GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
genomic: AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
EST: gi|71313249|gb|DR793148.1|DR793148
EST:     AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTG                         GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
genomic: AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
EST: gi|60341702|gb|DN208675.1|DN208675
EST:     AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTG                         GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
genomic: AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
EST: gi|78091450|gb|DV519824.1|DV519824
EST:     AGGGGATAATTTG                         GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
genomic: AGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
EST: gi|211389689|gb|FL031640.1|FL031640
EST:     AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTG                         GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
genomic: AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
EST: gi|32826943|gb|CD966621.1|CD966621
EST:     AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTG                         GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
genomic: AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
EST: gi|110482572|gb|EE011367.1|EE011367
EST:     CATGGATACTTATGAAGACACAGGGGATAATTTG                         GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
genomic: CATGGATACTTATGAAGACACAGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
EST: gi|60393918|gb|DN226788.1|DN226788
EST:     AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTG                         GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
genomic: AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
EST: gi|87156323|gb|DY401112.1|DY401112
EST:     AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTG                         GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
genomic: AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
EST: gi|78113031|gb|DV531425.1|DV531425
EST:     AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTG                         GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
genomic: AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
EST: gi|76016276|gb|DT943446.1|DT943446
EST:     AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTG                         GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
genomic: AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
EST: gi|76016277|gb|DT943447.1|DT943447
EST:     AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTG                         GCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC
genomic: AGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAAC

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), 49 (downstream exon)
Score: 133

TGGAATAAAGTCTATCCCCTCTTACTTTAGCGGTGGCAAGGATGAAGAGGAGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 236

TGGAATAAAGTCTATCCCCTCTTACTTTAGCGGTGGCAAGGATGAAGAGGAGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 282

TGGAATAAAGTCTATCCCCTCTTACTTTAGCGGTGGCAAGGATGAAGAGGAGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 181

TGGAATAAAGTCTATCCCCTCTTACTTTAGCGGTGGCAAGGATGAAGAGGAGGAAGATATACCTGACATGGATACTTATGAAGACACAGGGGATAATTTGgtagggaaga ... ctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacgaagctgccaaagttactgattccagctttgcctttctgttctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC
                                           ttctaat  putative branch site (score: 181)
                              ctttgcctttctgttc  CT-rich tract
                                           ttctaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagggaagatcaaaattctctatcttaaactgggctaaacgaagctgccaaagttactgattccagctttgcctttctgttctaattgcagGCTGCTGCTGAACCATCATACTTTATCGCAGAAGAACCAGAAGATGACAACATTCTTCATACCAGAACATATGATGTTAGCATAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG