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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgatgacttgtaatcttaaaccagagttctaacagtgaagtgtcagattttagctgctatcacacttgtttattaatcatacttgatcaataattttagGCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG

Basic information

species Zea mays
transcript GRMZM2G145029_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145029_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g34180.1 (Oryza sativa), 3'ss of exon 2
ttgatgacttgtaatcttaaaccagagttctaacagtgaagtgtcagatttt---agctgctatcacacttgtttattaatcatacttgatcaataattttagGCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG
   |      |  || |  ||   ||    || ||  | | ||  | | |||   |      ||   |||  ||| ||| |||       |||  | ||| ||||||||||||||| |||||| |  ||||  ||||||| |||||||| ||||||||||| |||||||||||||||||||||||| |||| |||
-gaactttaaggcatttgcaataggaagagtagcaaagtaatgcaaaactttgttaagcttgattggactaattttttagtcacgtcc--tcataactttcagGCCATCTCATGGAAAAGATAAATTCTGGTCATGTCCTCCACAGAGCGTTCAGTGTTTTTCTTTTCAACTCCAAATATGAATTGTTACTTCAG

upper sequence: GRMZM2G145029_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G38550.1 (Glycine max), 3'ss of exon 2
ttgatgacttgtaatcttaaaccagagttctaacagtgaagtgtcagattttagctgctatcacacttgtttattaatcatact-tgatcaataatttta---gGCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG
    |  | |   |||           ||||     |   |||       |    |||||     || ||| ||| || ||  | || || | |||||||   || ||  | ||||| ||||| |||||||  ||| | ||||| |||||||||||||| ||||| |||||||| || ||||| ||||| || |||
----tatcattatatcaagttttccttttctgttgttattgtgctcttcctctcttgctacagacctggttaatttattattttgtgctccaaaattttattagGTCACTTGATGGAAAAGATTGAAGCTGAGAATTTGCTGCATAGAGCTTTCAGTGTATTCCTGTTCAACTCAAAGTATGAGTTGCTTCTTCAG

upper sequence: GRMZM2G145029_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G47770.1 (Glycine max), 3'ss of exon 2
ttgatgacttgtaatcttaaaccagagttctaacagtgaagtgtcagattttagctgctatcacacttg-tttattaatcatacttgatcaataattttagGCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG-
 |   ||  |  | | ||        ||| | |  |||   |      || |  || |   |    ||  ||||||| |    ||| |  |||  | ||||| ||  | ||||| ||||| |||||||  ||| | ||||| |||||||||||||| ||||| |||||||| || ||||| ||||| || ||| 
ctttagatatcaagttttcgttttctgttgttattgtgc--tcctccgttctgcctacggacctggttaatttattatttgagctttaataattttattaggTCACTTGATGGAAAAGATTGAAGCTGAGAATTTGCTGCATAGAGCTTTCAGTGTATTCCTGTTCAACTCTAAGTATGAGTTGCTTCTTCAGG

upper sequence: GRMZM2G145029_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G16440.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------------------------------ttgatgacttgtaatcttaaaccagagttctaacagtgaagtgtcagattttagctgctatcacacttgtttattaatcatacttgatcaataattt-tagGCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG
                                                         ||||||     || | |   |      | ||   | |  ||||||| | ||| | || |      |  |  ||  | | |  | |  |   | || | |||| ||||| ||||| ||||| |||||||  ||| | || ||||||||||||||||| ||  | ||||||||||| ||||| ||||| || |||
gtaagtgaatttgattctcattccatatataggagaagaatgatggcaaaatcggttttgatgtgacctagt-tgggatttccttgcttctattagagtgtcaaaatttggttgat------ccaggataagactgactcctattttgtgatctgtagGTCATCTGATGGAAAAGATTGAAGCTGAGAATTTACTTCACAGAGCTTTCAGTGTGTTTTTATTCAACTCCAAGTATGAGTTGCTTCTCCAG

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|211100857|gb|FL320689.1|FL320689
EST:     TTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTATAACT                         GCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCA
genomic: TTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTATAACTgtgcgtgatt ... ataattttagGCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCA
EST: gi|211043409|gb|FL322272.1|FL322272
EST:     TTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTATAACT                         GCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCA
genomic: TT-AGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTATAACTgtgcgtgatt ... ataattttagGCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCA
EST: gi|211523188|gb|FL353428.1|FL353428
EST:     TTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTATAACT                         GCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCA
genomic: TTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTATAACTgtgcgtgatt ... ataattttagGCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCA
EST: gi|211514701|gb|FL326221.1|FL326221
EST:     TTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTATAACT                         GCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCA
genomic: TTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTATAACTgtgcgtgatt ... ataattttagGCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCA
EST: gi|148948634|gb|EC898546.2|EC898546
EST:     TTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTATAACT                         GCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCA
genomic: TTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTATAACTgtgcgtgatt ... ataattttagGCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCA
EST: gi|15313313|gb|BI478657.1|BI478657
EST:     TTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTATAACT                         GCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCA
genomic: TTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTATAACTgtgcgtgatt ... ataattttagGCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCA
EST: gi|148930170|gb|EC872550.2|EC872550
EST:     TTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTATAACT                         GCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCA
genomic: TTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTATAACTgtgcgtgatt ... ataattttagGCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCA
EST: gi|211410145|gb|FL360134.1|FL360134
EST:     TTTAGTGGATGAACAAGACAATGTCATCGGCCACGAGTCCAAGTATAACT                         GCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCA
genomic: TTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTATAACTgtgcgtgatt ... ataattttagGCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCA
EST: gi|8318714|gb|BE025279.1|BE025279
EST:     GTCCAAGTATAACT                         GCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCA
genomic: GTCCAAGTATAACTgtgcgtgatt ... ataattttagGCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCA

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: 74

GTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTATAACTgtgcgtgatt ... ataattttagGCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 267

GTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTATAACTgtgcgtgatt ... ataattttagGCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 281

GTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTATAACTgtgcgtgatt ... ataattttagGCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 289

GTGCATTTTAGTGGATGAACAAGACAATGTCATCGGCCATGAGTCCAAGTATAACTgtgcgtgatt ... ataattttagGCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattttagctgctatcacacttgtttattaatcatacttgatcaataattttagGCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG
                        tttattaatcatactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgatgacttgtaatcttaaaccagagttctaacagtgaagtgtcagattttagctgctatcacacttgtttattaatcatacttgatcaataattttagGCCATCTCATGGAGAAGATAGAAGCTGGAAATGTCCTGCACAGAGCTTTCAGTGTTTTCCTTTTCAACTCCAAATATGAATTGCTACTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT