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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagttcaaaaatgaactagcgagcgacaaatattcaagaatggaggtagtaatacatagtatttactgttaaactgttgatgctcacttttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGCATTGAAGAGCACAAACTTGAGCAGCAGTACCCTGTGGATCCACTTCAGA

Basic information

species Zea mays
transcript GRMZM2G160316_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160316_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g07360.1 (Oryza sativa), 3'ss of exon 3
--ttagttcaaaaatgaacta-gcgagcgacaaatattcaagaatggaggtagtaatacatagtatttactgttaaactgttgatgctcacttttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGCATTGAAGAGCACAAACTTGAGCAGCAGTACCCTGTGGATCCACTTCAGA
  ||   |      ||  ||   |       ||  ||    |  || |  |  ||||  || ||  ||   ||  | ||| |||   | ||  |  | |||||||||| ||||||||||| ||| | |||||  ||||| |||  |||||||| || || ||||||||||||||  || | || ||  | || |  |||||||
ttttctcttcttgctggtctgtacattttttaagcatatctgcgtgcat-tcctaattaattgtgattgtagtatatctgatgaa--ttaccatattattcagAATGAAATGAATGAACGAGAGCTGTCTGCCTTGAAAGCTGCTATTAAGTGTATCGAGGAGCACAAACTTGATGAGAAATATCCGATTGACCTGCTTCAGA

upper sequence: GRMZM2G160316_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g07380.1 (Oryza sativa), 3'ss of exon 3
ttagttcaaaaatgaactagcgagcg-acaaatattcaagaatggaggtagtaatacatagtatttactgttaaactgttgatgc-tcacttttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGCATTGAAGAGCACAAACTTGAGCAGCAGTACCCTGTGGATCCACTTCAGA
  | |           || |   | | |    |   ||    || | | | |  ||  |  ||| |  |||   ||   |||||  | |   |    | |||||||| || |||||||| ||||| |||||  ||||| |||| || || || ||||| ||||||||||||||  || | || ||| | || ||||||||||
--attctctcttcttgctggtatgtgcattcttgagcatatctgcatgcattcctaattgttatgttttgtattacatctgatgaattatcatataatgcagAATGAAATTAATGAACGCGAGTTGTCTGCCTTGAAAGCTGTTATCAAATGTATTGAGGAGCACAAACTTGATGAGAAATATCCTATCGACCCACTTCAGA

upper sequence: GRMZM2G160316_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G23740.1 (Glycine max), 3'ss of exon 3
ttagttcaaaaatgaactagcgagcgacaaatattcaagaatggaggtagtaatacata---gtatttactgttaaactgttgatgctcactt-ttgtt--ttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGCATTGAAGAGCACAAACTTGAGCAGCAGTACCCTGTGGATCCACTTCAGA
  || |    | ||| ||   || |     || ||  | |||  |  |  | ||||| |    |||||  | |   | | ||  |  | ||||  | ||   ||||| |||  | ||||| || ||  |   ||| || ||| |||| |||||||| |||||||| |||||||||||  | ||||||||| ||||||| || ||||
--agatgcccagtgatct--tgatc--ttgatgtttgataattaacttgtttatacagatatatattttttctatgaatattcctaattacttgctattgcctcagATTGATGTTAATGATCGAGAACTGATTGCACTTAAAGCTGTAATTAAGTGTATTGAAGATCACAAACTTGATGACCAGTACCCTCTGGATCCTCTCCAGA

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|31557940|gb|CD527152.1|CD527152
EST:     TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAG                         AATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
genomic: TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
EST: gi|211250452|gb|FK978630.1|FK978630
EST:     TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAG                         AATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
genomic: TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
EST: gi|87153317|gb|DY398106.1|DY398106
EST:     TTAAGAAAATGTCACACGCCAGGAATGTCAAAATTTCTCCTGGAGCACAG                         AATGAGATGAATGAACGTGAGTT
genomic: TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTT
EST: gi|29543979|gb|CB604359.1|CB604359
EST:     TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAG                         AATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
genomic: TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
EST: gi|31405937|gb|CD484669.1|CD484669
EST:     TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAG                         AATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
genomic: TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
EST: gi|6020587|gb|AW065620.1|AW065620
EST:     TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAG                         AATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
genomic: TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
EST: gi|31406338|gb|CD485070.1|CD485070
EST:     TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAG                         AATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
genomic: TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
EST: gi|91056387|gb|EB166805.1|EB166805
EST:     TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAG                         AATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
genomic: TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
EST: gi|60354203|gb|DN221176.1|DN221176
EST:     TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAG                         AATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
genomic: TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
EST: gi|8930234|gb|BE224998.1|BE224998
EST:     TTAAGAAAATGTCACACGCCAGGATTGTCAAAACTTCTCCTGGAGCACAG                         AATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
genomic: TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
EST: gi|61118818|gb|DN559779.1|DN559779
EST:     TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAG                         AATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
genomic: TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
EST: gi|76282460|gb|DV022028.1|DV022028
EST:     TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAG                         AATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
genomic: TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
EST: gi|211250451|gb|FK978629.1|FK978629
EST:     TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAG                         AATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
genomic: TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
EST: gi|166450367|gb|EG228309.1|EG228309
EST:     TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAG                         AATGAGATGAATGAACGTGAGTTA
genomic: TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTA
EST: gi|29544335|gb|CB604715.1|CB604715
EST:     TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAG                         AATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
genomic: TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
EST: gi|9733694|gb|BE512446.1|BE512446
EST:     TAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAG                         AATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
genomic: TAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
EST: gi|60400787|gb|DN233594.1|DN233594
EST:     TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAG                         AATGAGATGAATGAACG
genomic: TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACG
EST: gi|60354451|gb|DN221424.1|DN221424
EST:     CAAAACTTCTCCTGGAGCACAG                         AATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
genomic: CAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
EST: gi|60350356|gb|DN217329.1|DN217329
EST:     ACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAG                         AATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
genomic: ACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
EST: gi|17932317|gb|BM269277.1|BM269277
EST:     AGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAG                         AATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
genomic: AGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
EST: gi|60343259|gb|DN210232.1|DN210232
EST:     TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAG                         AATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
genomic: TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
EST: gi|20300669|gb|BQ163612.1|BQ163612
EST:     TTAAGAAAATGTCACACGCCAGGAATGTCAAAATTTCTCCTGGAGC-CAG                         AATGAGATGAATGAACGTGAGTT
genomic: TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTT
EST: gi|22818834|gb|BU498924.1|BU498924
EST:     TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAG                         AATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAA
genomic: TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAA
EST: gi|19436600|gb|BM953010.1|BM953010
EST:     TTAAGAAAATGTCACACGCCAGGAATGTCAAAATTTCTCCTGGAGC-CAG                         AATGAGATGAATGAACGTGAGTT
genomic: T-AAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTT
EST: gi|67018089|gb|CO446838.1|CO446838
EST:     TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAG                         AATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
genomic: TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
EST: gi|8577162|gb|BE129799.1|BE129799
EST:     TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAG                         AATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
genomic: TTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
EST: gi|211256715|gb|FL283526.1|FL283526
EST:     GTCAAAACTTCTCCTGGAGCACAG                         AATGCCTTTATTGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC
genomic: GTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGC

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: 298

TACTGAACAATTTGAACCAGTACACCTTCTTAAAGCATATCTAAGGGATGTTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGCATTGAAGAGCACAAACTTGAGCAGCAGTACCCTGTGGATCCACTTCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

TACTGAACAATTTGAACCAGTACACCTTCTTAAAGCATATCTAAGGGATGTTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGCATTGAAGAGCACAAACTTGAGCAGCAGTACCCTGTGGATCCACTTCAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 108

TACTGAACAATTTGAACCAGTACACCTTCTTAAAGCATATCTAAGGGATGTTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGCATTGAAGAGCACAAACTTGAGCAGCAGTACCCTGTGGATCCACTTCAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 134

TACTGAACAATTTGAACCAGTACACCTTCTTAAAGCATATCTAAGGGATGTTAAGAAAATGTCACACGCCAGGAATGTCAAAACTTCTCCTGGAGCACAGgtacatttgt ... ttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGCATTGAAGAGCACAAACTTGAGCAGCAGTACCCTGTGGATCCACTTCAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtagtaatacatagtatttactgttaaactgttgatgctcacttttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGCATTGAAGAGCACAAACTTGAGCAGCAGTACCCTGTGGATCCACTTCAGA
                                    tgctcac  putative branch site (score: 134)
                                      ctcacttttgttttc  CT-rich tract
     taatacatagtattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagttcaaaaatgaactagcgagcgacaaatattcaagaatggaggtagtaatacatagtatttactgttaaactgttgatgctcacttttgttttcagAATGAGATGAATGAACGTGAGTTATCTGCGCTGAAATCTGTCATTAAGTGCATTGAAGAGCACAAACTTGAGCAGCAGTACCCTGTGGATCCACTTCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - caaaaatg
- - - - - - - - - - - - cgacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgat