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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTACTGCCCCCATCATCATCTCCCTCGCCAAAGGAATTGAGGCCTCGCTGGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAAgtgaggttcctcgtcctttcgtctagctaactaactaatcattcaattgtgatatttcttaattgaattcaaaccggactctgtttttatttgtggatct...

Basic information

species Zea mays
transcript GRMZM2G090747_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090747_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g58740.1 (Oryza sativa), 5'ss of exon 2
ATTACTGCCCCCATCATCATCTCCCTCGCCAAAGGAATTGAGGCCTCGCTGGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAAgtgaggttcctcgtcctttcgtctagctaactaactaatcattcaattgtgatatttcttaattgaattcaaaccggactctgtt-tttatttgtggatct--------
|||||||||||||||||| |||| || |||||||| || |||||||| |||||||| || |||||||||||||||||||| |||||||||||||||||||||||| |||||   | |||| |    | | || || | ||||      |||  | |  ||  ||||||| ||   |  || |||| ||| ||||||  | |        
ATTACTGCCCCCATCATCCTCTCTCTGGCCAAAGGGATAGAGGCCTCCCTGGATCCCCTGCCACGGATCATAACTCCCACACAGATGATTAGCAATGCAAgtgagattcctttccttttctttacacaatcttacca-tcat------gtg-cactctttgcttgaatt-aacttgttctttgttctttgtttgtgcttatccgtaact
















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|211022600|gb|FL292185.1|FL292185
EST:     TCCACTCCCACGGNATCATA-CTCCCACGCAGATGATTANNGCA-TGCA-                         CTGGAGTTCCATCAGAGAATATT
genomic: TCCACTCCCACGG-ATCATAACTCCCACGCAGATGATTA--GCAATGCAAgtgaggttcc ... tataatgcagCTGGAGTTCCATCAGAGAATATT
EST: gi|71445294|gb|DR826344.1|DR826344
EST:     GGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAA                         CTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTT
genomic: GGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAAgtgaggttcc ... tataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTT
EST: gi|8516489|gb|BE123214.1|BE123214
EST:     GGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAA                         CTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTT
genomic: GGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAAgtgaggttcc ... tataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTT
EST: gi|149111431|gb|EE294934.2|EE294934
EST:     GGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAA                         CTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGC
genomic: GGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAAgtgaggttcc ... tataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGC
EST: gi|148950391|gb|EC895956.2|EC895956
EST:     GGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAA                         CTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTT
genomic: GGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAAgtgaggttcc ... tataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTT
EST: gi|149081257|gb|EE170370.2|EE170370
EST:     GGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAA                         CTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCCTA-TATTGCT
genomic: GGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAAgtgaggttcc ... tataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACC-TAATATTGCT
EST: gi|67026682|gb|CO455431.1|CO455431
EST:     GGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAA                         CTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTT
genomic: GGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAAgtgaggttcc ... tataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTT
EST: gi|5847455|gb|AW000534.1|AW000534
EST:     CTCCCACGCAGATGATTAGCAATGCAA                         CTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTT
genomic: CTCCCACGCAGATGATTAGCAATGCAAgtgaggttcc ... tataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTT
EST: gi|5525703|gb|AI861596.1|AI861596
EST:     GGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAA                         CTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTT
genomic: GGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAAgtgaggttcc ... tataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTT
EST: gi|71320117|gb|DR796812.1|DR796812
EST:     GGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAA                         CTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGA
genomic: GGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAAgtgaggttcc ... tataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGA
EST: gi|91874329|gb|EB404286.1|EB404286
EST:     GGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAA                         CTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTT
genomic: GGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAAgtgaggttcc ... tataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTT
EST: gi|149078504|gb|EE167287.2|EE167287
EST:     GGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAG                         CTGGAGTTCCATCAGAGAATATTCTTTATC
genomic: GGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAAgtgaggttcc ... tataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATC
EST: gi|32804534|gb|CD956770.1|CD956770
EST:     GATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAA                         CTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTT
genomic: GATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAAgtgaggttcc ... tataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTT
EST: gi|7031308|gb|AW461046.1|AW461046
EST:     ATTAGCAATGCAA                         CTGGAGTTCCATCAGAGAATATTCTTTATCTTGNCGGACCTAATATTGCTT
genomic: ATTAGCAATGCAAgtgaggttcc ... tataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTT
EST: gi|71772035|gb|DR969972.1|DR969972
EST:     GGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAA                         CTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTTATATTGCTT
genomic: GGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAAgtgaggttcc ... tataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTT
EST: gi|32804772|gb|CD957008.1|CD957008
EST:     GATCCGCTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAA                         CTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTT
genomic: GATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAAgtgaggttcc ... tataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTT

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: 283

ATTACTGCCCCCATCATCATCTCCCTCGCCAAAGGAATTGAGGCCTCGCTGGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAAgtgaggttcc ... tataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTTCTGAAATTTACAACAAAGAATATGCAAATGCACGTATTTGTGGAGCTGA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 108

ATTACTGCCCCCATCATCATCTCCCTCGCCAAAGGAATTGAGGCCTCGCTGGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAAgtgaggttcc ... tataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTTCTGAAATTTACAACAAAGAATATGCAAATGCACGTATTTGTGGAGCTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 123

ATTACTGCCCCCATCATCATCTCCCTCGCCAAAGGAATTGAGGCCTCGCTGGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAAgtgaggttcc ... tataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTTCTGAAATTTACAACAAAGAATATGCAAATGCACGTATTTGTGGAGCTGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 193

ATTACTGCCCCCATCATCATCTCCCTCGCCAAAGGAATTGAGGCCTCGCTGGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAAgtgaggttcc ... tataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTTCTGAAATTTACAACAAAGAATATGCAAATGCACGTATTTGTGGAGCTGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTACTGCCCCCATCATCATCTCCCTCGCCAAAGGAATTGAGGCCTCGCTGGATCCACTCCCACGGATCATAACTCCCACGCAGATGATTAGCAATGCAAgtgaggttcctcgtcctttcgtctagctaactaactaatcattcaattgtgatatttcttaattgaattcaaaccggactctgtttttatttgtggatct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG