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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcatttgtgcttgtactatgatgttcctgaactcattgttttatttactttaagtacaagaactgtctttttttccttactagttccctgaactttcagATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTGGCTAGGGAACAGTGCGTACCTCTACATATCTGTCGCATTTGCACAGATG

Basic information

species Zea mays
transcript GRMZM2G022793_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022793_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g04110.2 (Oryza sativa), 3'ss of exon 3
ttcatttgtgcttgtactatgatgtt--cctgaactcattgttttatttactttaagtacaagaactgtctttttttccttactagttc-cctgaactttcagATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTGGCTAGGGAACAGTGCGTACCTCTACATATCTGTCGCATTTGCACAGATG
  || | |  ||      ||  || |  | ||   |  |  |  |   |||   || | || ||| ||| ||| |||| |||| ||| |  |||  ||| ||||||||||| ||||||||||||||| |||| |||||||||||||||||| ||||||||||||||||| |||||||| |||||||| |||||||||||||||
aacact-gaactcccggcatattgcttgcttgtgttgttcataatgagtaccagaaatcca-gaattgtatttctttc-ttaccagtacatctgggcttgcagATATATTAGTTCAGTCATTCCAATCGGAGCAATGTTTGCAATGACACTCTGGCTAGGGAACAGTGCTTACCTCTATATATCTGTTGCATTTGCACAGATG

upper sequence: GRMZM2G022793_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G53660.1 (Arabidopsis thaliana), 3'ss of exon 3
ttcatttgtgcttgtactatgatgttcctg-aactcattgttttatttactttaagtacaagaactgtctttttttccttactagttccctgaactttcagATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTGGCTAGGGAACAGTGCGTACCTCTACATATCTGTCGCATTTGCACAGATG
         |   | |  |   |||| ||| ||   |||  |||||||  || |  |  ||  || ||    ||  |   |  |   | ||      |||||||| |||| ||||| |||||||| || | ||||||||||||||| || ||| |||| |||| ||| || ||||||||| |||| |||||| | || |||
---------gtaagaaagaaagtgtttctgtaagcaatttatttattt--ttgagttgtaaataccgt----ttagctaaaacatcactctatgtactcagATATGTTACATCAGTTATTCCAATAGGTGCAATGTTTGCAATGACTCTATGGTTAGGAAACACTGCTTATCTCTACATAACTGTTGCATTTTCCCAAATG

upper sequence: GRMZM2G022793_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G14410.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------ttcatttgtgcttgtactatgatgttcctgaactcattgttttatttactttaagtacaagaactgtctttttttccttactagttccctgaactt--tcagATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTGGCTAGGGAACAGTGCGTACCTCTACATATCTGTCGCATTTGCACAGATG
                 ||| |  |   ||  | | ||  ||    |||   |    |    | | | |   ||| |    | ||  | |  |  || ||  || ||  |  |  |||||||| |||| ||||| |||||||| || | ||||||||||||||| || ||| | || |||| ||| |||||||||||||| || |||||||| ||||||
gtaaggaagaaagagacttcgtaaggaatttgattttggagtagtcgaaaatacccataacataaatatctttactaattttatcaatgtagcagtattaactcactttatgtactcagATATGTTACGTCAGTTATTCCAATAGGTGCAATGTTTGCAATGACCCTCTGGTTGGGAAACACTGCCTACCTCTACATATCAGTTGCATTTGCGCAGATG

upper sequence: GRMZM2G022793_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv15s0046g00460.t01 (Vitis vinifera), 3'ss of exon 3
ttcatttgtgcttgtactatgatgttcctgaactcattgttttatttactttaagtacaagaactgtctttttttccttac-tagtt---ccctgaactttcagATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTGGCTAGGGAACAGTGCGTACCTCTACATATCTGTCGCATTTGCACAGATG
 ||  |    |||| || |||  | |       | ||| | ||   ||||| | |   | |  |  || |||    |  |  || ||      | ||  |||||||||| ||| || || || || ||||| | ||  ||||||||||| |||||||| || |||| ||| ||||| || || ||||| ||||||||||| |||
ctctctctctcttgcac-atgtggatagcatgtttattctattgcatacttgatg---atgttccttcctttagaacaaatataattaaattttcaatgttcagATATACTACATCTGTGATCCCTATTGGTGCAACATTTGCAATGACTCTTTGGCTGGGAAACACTGCTTACCTGTATATTTCTGTTGCATTTGCACAAATG

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|91053683|gb|EB164101.1|EB164101
EST:     ATCATAAAGATTGAGGAGGGAATGACTACAGATAT                         ATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTG
genomic: ATCATAAAGATTGAGGAGGGAATGACTACAGATATgtgagtctca ... gaactttcagATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTG
EST: gi|148949951|gb|EC895462.2|EC895462
EST:     ATCATAAAGATTGAGGAGGGAATGACTACAGATAT                         ATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTG
genomic: ATCATAAAGATTGAGGAGGGAATGACTACAGATATgtgagtctca ... gaactttcagATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTG
EST: gi|148958042|gb|EC904220.2|EC904220
EST:     ATCATAAAGATTGAGGAGGGAATGACTACAGATAT                         ATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTG
genomic: ATCATAAAGATTGAGGAGGGAATGACTACAGATATgtgagtctca ... gaactttcagATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTG
EST: gi|211529569|gb|FL022744.1|FL022744
EST:     ATCATAAAGATTGAGGAGGGAATGACTACAGATAT                         ATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTG
genomic: ATCATAAAGATTGAGGAGGGAATGACTACAGATATgtgagtctca ... gaactttcagATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTG
EST: gi|31351537|gb|CD435894.1|CD435894
EST:     ATCATAAAGATTGAGGAGGGAATGACTACAGATAT                         ATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTG
genomic: ATCATAAAGATTGAGGAGGGAATGACTACAGATATgtgagtctca ... gaactttcagATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTG
EST: gi|211234820|gb|FL436043.1|FL436043
EST:     ATCATAAAGATTGAGGAGGGAATGACTACAGATAT                         ATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTG
genomic: ATCATAAAGATTGAGGAGGGAATGACTACAGATATgtgagtctca ... gaactttcagATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTG
EST: gi|89252538|gb|DY624324.1|DY624324
EST:     ATCATAAAGATTGAGGAGGGAATGACTACAGATAT                         ATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTG
genomic: ATCATAAAGATTGAGGAGGGAATGACTACAGATATgtgagtctca ... gaactttcagATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTG
EST: gi|211529568|gb|FL022743.1|FL022743
EST:     ATCATAAAGATTGAGGAGGGAATGACTACAGATAT                         ATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTG
genomic: ATCATAAAGATTGAGGAGGGAATGACTACAGATATgtgagtctca ... gaactttcagATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTG
EST: gi|30307221|gb|CD001894.1|CD001894
EST:     ATCATAAAGATTGAGGAGGGAATGACTACAGATAT                         ATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTG
genomic: ATCATAAAGATTGAGGAGGGAATGACTACAGATATgtgagtctca ... gaactttcagATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTG

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: 42 (upstream exon), 41 (downstream exon)
Score: 29

ATCATAAAGATTGAGGAGGGAATGACTACAGATATgtgagtctca ... gaactttcagATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTGGCTAGGGAACAGTGCGTACCTCTACATATCTGTCGCATTTGCACAGATG


Block sizes: 35 (upstream exon), 41 (downstream exon)
Score: 35

ATCATAAAGATTGAGGAGGGAATGACTACAGATATgtgagtctca ... gaactttcagATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTGGCTAGGGAACAGTGCGTACCTCTACATATCTGTCGCATTTGCACAGATG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 42

ATCATAAAGATTGAGGAGGGAATGACTACAGATATgtgagtctca ... gaactttcagATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTGGCTAGGGAACAGTGCGTACCTCTACATATCTGTCGCATTTGCACAGATG


Block sizes: 35 (upstream exon), 48 (downstream exon)
Score: 16

ATCATAAAGATTGAGGAGGGAATGACTACAGATATgtgagtctca ... gaactttcagATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTGGCTAGGGAACAGTGCGTACCTCTACATATCTGTCGCATTTGCACAGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactttaagtacaagaactgtctttttttccttactagttccctgaactttcagATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTGGCTAGGGAACAGTGCGTACCTCTACATATCTGTCGCATTTGCACAGATG
                             tccttac  putative branch site (score: 16)
                                       ttccctg  putative PPT
                     tcttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcatttgtgcttgtactatgatgttcctgaactcattgttttatttactttaagtacaagaactgtctttttttccttactagttccctgaactttcagATATATTACTTCAGTCATTCCAATTGGAGGAATGTTTGCAATGACACTTTGGCTAGGGAACAGTGCGTACCTCTACATATCTGTCGCATTTGCACAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
ttcattt
- - - - tgcttgt
- - - - - - - - - -tgatgtt
- - - - - - - - - - - - - cctgaac