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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataacacatggttgcagttactgctgttagtttcattcattcagtagtgccagctaagtgccctggttatgcatgtttagttgtctacggaacctgttcactgaaatatccacttctgaaagcacttgccattccttccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA

Basic information

species Zea mays
transcript GRMZM2G129987_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G129987_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g10220.1 (Oryza sativa), 3'ss of exon 6
-----------------------------gtataacacatggttgcagttactgctgttagtttcattcattcagt--agtgccagctaagtgccctggttatgcatgtttagttgtctacggaacctgttcactgaaa--tatccacttctgaaagcacttgccattcctt--ccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA
                              | || || ||  |      |||   | |   || | ||  | || |  || ||  || |||||    | |||| |||| | | |         || || ||| ||||||  | || | |  | |||   ||| ||||| | |  ||  |   |||||||||||||||||| || || ||||| |||||| | || ||||| || ||||| || || || ||||| ||||||||||| |||| |||
gtaaatgattatatgctgttgccatataattttatcatataatattgaatacctttttctattccttttctacaatgaagcgctggcaaagtgtttagcttat-catgctaactc--------aatctattccctgaaacttctctaatggttaaactcctttccatttccttcccttttgtagGTGAGCTGAAGTCAACAAAAGCATATGATAAATGGGCCAAGAAGATCTCCGAGATTGAACCTCCCACAAACCCATTAGAGAGAAGAGTGAA
















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:     GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAG                         GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
genomic: GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAGgtataacaca ... ccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
EST: gi|211238012|gb|FL479475.1|FL479475
EST:     GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAG                         GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
genomic: GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAGgtataacaca ... ccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
EST: gi|19436724|gb|BM953134.1|BM953134
EST:     GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAG                         GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGNCTAAAAAGATTTCGG
genomic: GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAGgtataacaca ... ccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
EST: gi|37376764|gb|CF624937.1|CF624937
EST:     GCTTGATCCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAG                         GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
genomic: GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAGgtataacaca ... ccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
EST: gi|149009177|gb|EE041301.2|EE041301
EST:     GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAG                         GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
genomic: GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAGgtataacaca ... ccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
EST: gi|91053239|gb|EB163657.1|EB163657
EST:     GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAG                         GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
genomic: GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAGgtataacaca ... ccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
EST: gi|76011893|gb|DT939063.1|DT939063
EST:     GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAG                         GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
genomic: GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAGgtataacaca ... ccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
EST: gi|71771230|gb|DR969167.1|DR969167
EST:     GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAG                         GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
genomic: GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAGgtataacaca ... ccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
EST: gi|78082398|gb|DV510810.1|DV510810
EST:     GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAG                         GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
genomic: GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAGgtataacaca ... ccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
EST: gi|71320398|gb|DR796949.1|DR796949
EST:     GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAG                         GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
genomic: GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAGgtataacaca ... ccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
EST: gi|71771229|gb|DR969166.1|DR969166
EST:     GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAG                         GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
genomic: GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAGgtataacaca ... ccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
EST: gi|78026730|gb|DV495117.1|DV495117
EST:     GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAG                         GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
genomic: GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAGgtataacaca ... ccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
EST: gi|67022325|gb|CO451074.1|CO451074
EST:     GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAG                         GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
genomic: GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAGgtataacaca ... ccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
EST: gi|91054843|gb|EB165261.1|EB165261
EST:     GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAG                         GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
genomic: GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAGgtataacaca ... ccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
EST: gi|76924244|gb|DV169873.1|DV169873
EST:     GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAG                         GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
genomic: GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAGgtataacaca ... ccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
EST: gi|33098018|gb|CF057978.1|CF057978
EST:     GCTTGATTCCCACCGCTTCAAGGATATAATCGACGGGGCGATTGCTGAAG                         GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
genomic: GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAGgtataacaca ... ccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
EST: gi|60341606|gb|DN208579.1|DN208579
EST:     GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAG                         GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
genomic: GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAGgtataacaca ... ccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
EST: gi|91054842|gb|EB165260.1|EB165260
EST:     GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAG                         GTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG
genomic: GCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAGgtataacaca ... ccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGG

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: 402

GCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAGgtataacaca ... ccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

GCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAGgtataacaca ... ccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 100

GCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAGgtataacaca ... ccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 65

GCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCCCACCGCTTCAAGGATATAATCGATGGGGCGATTGCTGAAGgtataacaca ... ccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgttcactgaaatatccacttctgaaagcacttgccattccttccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA
                                cttgccattccttcc  CT-rich tract
         tgaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataacacatggttgcagttactgctgttagtttcattcattcagtagtgccagctaagtgccctggttatgcatgtttagttgtctacggaacctgttcactgaaatatccacttctgaaagcacttgccattccttccaataccagGTGAGCTGAAGTCAACTAAGGCGTATGAGAAATGGTCTAAAAAGATTTCGGAGATGGAGCCACCAACAAATCCATTAGAGAGGAGAGCGAA

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