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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaatcttgtttgcctgtagtaatcagcaagcttttttctccattggattcaaacaaattggaaggcctcttgcgctatagttgtaattcagag...

Basic information

species Zea mays
transcript GRMZM2G111510_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111510_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os01g53560.1 (Oryza sativa), 5'ss of exon 13
ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaatcttgtttgcctgtagtaatcagcaagcttttttctccattggattcaa---acaaattgga-aggcctcttgcg--ctatagttgtaattcagag
|||||||||||| |||||||| |||||||||||||| ||||||||||| ||||||| |||||| ||||||||||         ||    |||  || | ||    | | ||| | | |   |    |||   |||| ||  | | |  | ||  |  |  |||  |  |||     
ATCTTTCTATGTTGGTGATGCCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAGgtattggtggagctgcc--ccttgagcagtccatgaacatttatttgcccagttcacaatagacaatttcaacatgaattttagggtccttagcaggtattg----
















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|6563667|gb|AW231394.1|AW231394
EST:     CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG                         GCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
genomic: CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
EST: gi|32835438|gb|CD975116.1|CD975116
EST:     CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG                         GCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACCTCGG
genomic: CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGG
EST: gi|211013122|gb|FL458830.1|FL458830
EST:     CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG                         GCCATCGGTYTCAAGTTCCAWGTTCCCRAGGAGWACTTCGGTTTYTAATTA
genomic: CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
EST: gi|211130554|gb|FL442100.1|FL442100
EST:     CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG                         GCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
genomic: CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
EST: gi|60359551|gb|DN226524.1|DN226524
EST:     CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG                         GCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
genomic: CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
EST: gi|71432125|gb|DR813175.1|DR813175
EST:     CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG                         GCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
genomic: CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
EST: gi|60341580|gb|DN208553.1|DN208553
EST:     CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG                         GCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
genomic: CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
EST: gi|211443974|gb|FL182596.1|FL182596
EST:     CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG                         GCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTT
genomic: CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTT
EST: gi|71759141|gb|DR957078.1|DR957078
EST:     CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG                         GCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
genomic: CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
EST: gi|78088730|gb|DV517123.1|DV517123
EST:     CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG                         GCCATCGGTTTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTTTAATTT
genomic: CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
EST: gi|40303060|gb|CK347447.1|CK347447
EST:     CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG                         GCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
genomic: CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
EST: gi|60336621|gb|DN203594.1|DN203594
EST:     CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG                         GCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
genomic: CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
EST: gi|83279155|gb|DV943163.1|DV943163
EST:     CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG                         GCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
genomic: CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
EST: gi|18650379|gb|BM499198.1|BM499198
EST:     CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG                         GCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
genomic: CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
EST: gi|91053260|gb|EB163678.1|EB163678
EST:     CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG                         GCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTTTAATTA
genomic: CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
EST: gi|71316663|gb|DR795006.1|DR795006
EST:     CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG                         GCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTTTAATTA
genomic: CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
EST: gi|60342489|gb|DN209462.1|DN209462
EST:     CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG                         GCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
genomic: CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
EST: gi|32833310|gb|CD972988.1|CD972988
EST:     CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG                         GCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGT
genomic: CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGT
EST: gi|60401163|gb|DN233970.1|DN233970
EST:     CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG                         GCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
genomic: CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
EST: gi|37426318|gb|CF650911.1|CF650911
EST:     CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG                         GCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
genomic: CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
EST: gi|60351350|gb|DN218323.1|DN218323
EST:     CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG                         GCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
genomic: CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTA
EST: gi|33092918|gb|CF052912.1|CF052912
EST:     CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG                         GCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGT
genomic: CTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGT

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), 47 (downstream exon)
Score: 215

ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTACCTGTGACCAGCTAGTAAGATGGTTACACTACGTCGTTTAGTGTTTGGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 44

ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTACCTGTGACCAGCTAGTAAGATGGTTACACTACGTCGTTTAGTGTTTGGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 58

ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTACCTGTGACCAGCTAGTAAGATGGTTACACTACGTCGTTTAGTGTTTGGA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 27

ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaa ... cctgttatagGCCATCGGTCTCAAGTTCCATGTTCCCGAGGAGTACTTCGGTTTCTAATTACCTGTGACCAGCTAGTAAGATGGTTACACTACGTCGTTTAGTGTTTGGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAGgtatgaaaaatcttgtttgcctgtagtaatcagcaagcttttttctccattggattcaaacaaattggaaggcctcttgcgctatagttgtaattcagag

- - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaacaaa