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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcttgtcttgggaacacatgaaaacaacccctttatttttctatttgatgcaaagttaatccagaagctcctcttccgacatgtgccctattattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG

Basic information

species Zea mays
transcript GRMZM2G111510_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111510_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os01g53560.1 (Oryza sativa), 3'ss of exon 12
--ctcttgtcttgggaacacatgaaa-acaaccc-ctttatttttctatttgatgcaaagttaatccagaagctcctcttccgacatgtgccctattattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG
   | |||       || |||  ||| |||| |  || | ||  ||| |||  ||   | |  ||    ||||| | |||  || |  |||| | ||||| ||||||||||||||| |||||||| |||||||||||||| ||||||||||| ||||||| |||||| ||||||
ttttattggtgcaaaaaaacactaaacacaatctgctgttttagtctgttttgtgtgcattatat----aagctgcccttttgataattgccatgttatttcagATCTTTCTATGTTGGTGATGCCGCTGGGAGAGAGAATGATCATAGTGATGCAGATAAAGAATTCGCTAAG
















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:     TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCA                         ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
genomic: TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
EST: gi|32835438|gb|CD975116.1|CD975116
EST:     TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCA                         ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
genomic: TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
EST: gi|211013122|gb|FL458830.1|FL458830
EST:     TGGTTGATGGCTCAGCATTTCAATTYTGGAATCAAAATTGACATGGATCA                         ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
genomic: TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
EST: gi|211130554|gb|FL442100.1|FL442100
EST:     TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCA                         ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
genomic: TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
EST: gi|60359551|gb|DN226524.1|DN226524
EST:     TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCA                         ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
genomic: TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
EST: gi|71432125|gb|DR813175.1|DR813175
EST:     TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCA                         ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
genomic: TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
EST: gi|60341580|gb|DN208553.1|DN208553
EST:     TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCA                         ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
genomic: TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
EST: gi|211443974|gb|FL182596.1|FL182596
EST:     TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCA                         ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
genomic: TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
EST: gi|71759141|gb|DR957078.1|DR957078
EST:     TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCA                         ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
genomic: TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
EST: gi|78088730|gb|DV517123.1|DV517123
EST:     TGGTTGATGGCTCAGCATTTCAATTTTGGAATCAAAATTGACATGGATCA                         ATCTTTTTATGTCGGGGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
genomic: TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
EST: gi|40303060|gb|CK347447.1|CK347447
EST:     TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCA                         ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
genomic: TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
EST: gi|60336621|gb|DN203594.1|DN203594
EST:     TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCA                         ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
genomic: TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
EST: gi|83279155|gb|DV943163.1|DV943163
EST:     TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCA                         ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
genomic: TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
EST: gi|18650379|gb|BM499198.1|BM499198
EST:     TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCA                         ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
genomic: TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
EST: gi|91053260|gb|EB163678.1|EB163678
EST:     TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCA                         ATCTTTTTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
genomic: TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
EST: gi|71316663|gb|DR795006.1|DR795006
EST:     TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCA                         ATCTTTTTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
genomic: TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
EST: gi|60342489|gb|DN209462.1|DN209462
EST:     TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCA                         ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
genomic: TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
EST: gi|32833310|gb|CD972988.1|CD972988
EST:     TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCA                         ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
genomic: TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
EST: gi|60401163|gb|DN233970.1|DN233970
EST:     TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCA                         ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
genomic: TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
EST: gi|37426318|gb|CF650911.1|CF650911
EST:     TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCA                         ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
genomic: TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
EST: gi|60351350|gb|DN218323.1|DN218323
EST:     TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCA                         ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
genomic: TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
EST: gi|33092918|gb|CF052912.1|CF052912
EST:     TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCA                         ATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC
genomic: TGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGC

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: 261

GAAAAGGTATTCCAGATGATCCATACCGCAAACCAAATCCTGGAATGTGGTGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 45

GAAAAGGTATTCCAGATGATCCATACCGCAAACCAAATCCTGGAATGTGGTGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 77

GAAAAGGTATTCCAGATGATCCATACCGCAAACCAAATCCTGGAATGTGGTGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 58

GAAAAGGTATTCCAGATGATCCATACCGCAAACCAAATCCTGGAATGTGGTGGTTGATGGCTCAGCATTTCAATTCTGGAATCAAAATTGACATGGATCAgtaatcacct ... attattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatgcaaagttaatccagaagctcctcttccgacatgtgccctattattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG
         agttaat  putative branch site (score: 58)
                                         ccctatt  putative PPT
                                            tattattaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcttgtcttgggaacacatgaaaacaacccctttatttttctatttgatgcaaagttaatccagaagctcctcttccgacatgtgccctattattacagATCTTTCTATGTCGGTGATGCTGCTGGGAGAGAGAACGATCATAGTGACGCAGATATAGAATTTGCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - acacatg
- - - - - - - - - - -aaaacaa
- - - - - - - - - - - - - - - - - - - - - - tttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtgc