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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagtttttgcctccccatcccctccctccacacagaacgctcacctgtcatttgtttccttttggtgttatacattctactgccatttgcttgtttccaactgattgttgttttgaaccccatggcag

Basic information

species Zea mays
transcript GRMZM2G129987_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G129987_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g10220.1 (Oryza sativa), 5'ss of exon 7
GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagtttttgcctccccatcccctccctccacacagaacgctcacctgtcatttgtttccttttggtgttatacattctactgccatttgcttgtttccaactgattgttgttttgaaccccatggcag
|||||||||||||||| || || ||||| |||||| | || ||||| || ||||| || || || ||||| ||||||||||| |||| |||||||| | |      |  ||| ||      ||   |   |||   ||      |||| | |  |  ||    | |   ||||||| |||||| |    ||   | |  |                     
GTGAGCTGAAGTCAACAAAAGCATATGATAAATGGGCCAAGAAGATCTCCGAGATTGAACCTCCCACAAACCCATTAGAGAGAAGAGTGAAgtaagctctcattctcttatctcc------caagtaatccgccttccgagatgttgtctaccatcagt----tgctcactactgc-atttgcctcaaacctcgtcacag---------------------
















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|78111290|gb|DV529687.1|DV529687
EST:     AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA                         GAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGGCATCTCACAGCG
genomic: AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
EST: gi|211238012|gb|FL479475.1|FL479475
EST:     AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA                         GAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
genomic: AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
EST: gi|71315530|gb|DR794369.1|DR794369
EST:     ACCAACAAATCCATTAGAGAGGAGAGCGAA                         GAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
genomic: ACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
EST: gi|37376764|gb|CF624937.1|CF624937
EST:     AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA                         GAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
genomic: AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
EST: gi|149009177|gb|EE041301.2|EE041301
EST:     AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA                         GAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
genomic: AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
EST: gi|91053239|gb|EB163657.1|EB163657
EST:     AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA                         GAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
genomic: AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
EST: gi|76011893|gb|DT939063.1|DT939063
EST:     AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA                         GAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
genomic: AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
EST: gi|71771230|gb|DR969167.1|DR969167
EST:     AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA                         GAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
genomic: AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
EST: gi|32935871|gb|CF040683.1|CF040683
EST:     AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA                         GAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
genomic: AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
EST: gi|78082398|gb|DV510810.1|DV510810
EST:     AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA                         GAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
genomic: AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
EST: gi|71320398|gb|DR796949.1|DR796949
EST:     AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA                         GAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
genomic: AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
EST: gi|71771229|gb|DR969166.1|DR969166
EST:     AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA                         GAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
genomic: AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
EST: gi|78026730|gb|DV495117.1|DV495117
EST:     AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA                         GAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
genomic: AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
EST: gi|32937133|gb|CF041952.1|CF041952
EST:     AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA                         GAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
genomic: AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
EST: gi|67022325|gb|CO451074.1|CO451074
EST:     AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA                         GAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
genomic: AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
EST: gi|87152358|gb|DY397147.1|DY397147
EST:     AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA                         GAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
genomic: AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
EST: gi|32938024|gb|CF042843.1|CF042843
EST:     GATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA                         GAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
genomic: GATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
EST: gi|91054843|gb|EB165261.1|EB165261
EST:     AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA                         GAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
genomic: AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
EST: gi|32937712|gb|CF042531.1|CF042531
EST:     GATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA                         GAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
genomic: GATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
EST: gi|33098018|gb|CF057978.1|CF057978
EST:     AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA                         GAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
genomic: AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
EST: gi|60341606|gb|DN208579.1|DN208579
EST:     AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA                         GAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
genomic: AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
EST: gi|91054842|gb|EB165260.1|EB165260
EST:     AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA                         GAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG
genomic: AAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCG

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), 48 (downstream exon)
Score: 218

GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCGCAGGGCTGAGCGGAAAAACCAGTTCAACTCCATCCTCTCGAACATCATG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 50

GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCGCAGGGCTGAGCGGAAAAACCAGTTCAACTCCATCCTCTCGAACATCATG


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

GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCGCAGGGCTGAGCGGAAAAACCAGTTCAACTCCATCCTCTCGAACATCATG


Block sizes: 47 (upstream exon), 40 (downstream exon)
Score: 30

GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagttttt ... cccatggcagGAGTAGGAAGAAAAGTGAGGAGAACGATCTGATCCTGGCCATCTCACAGCGCAGGGCTGAGCGGAAAAACCAGTTCAACTCCATCCTCTCGAACATCATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAAgtaagtttttgcctccccatcccctccctccacacagaacgctcacctgtcatttgtttccttttggtgttatacattctactgccatttgcttgtttccaactgattgttgttttgaaccccatggcag

- - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA