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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTATAGATTCCAAGATTCATCACAACAATCTTATCAACAATATTCTGGCAAAGgttcactttccttttgatttggagttcttaattagttcttagtatataccgtaactgtaatggagtttttgtctggactcgattttccatcctcgtgcag

Basic information

species Zea mays
transcript GRMZM2G108416_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108416_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os03g24460.3 (Oryza sativa), 5'ss of exon 14
AGTATAGATTCCAAGATTCATCACAACAATCTTATCAACAATATTCTGGCAAAGgttcactttccttttgatttgga-----gttcttaattagttcttagtatataccgtaactgtaatggagtttttgtctggactcgattttccatcctc--gtgcag
|| |||||||| ||||| |||||||||||||||||||||||||||||||| ||||| |  | |||||| |||||| |     || ||||  ||  | ||  || ||   |   || || |     || |    | |||   ||    || ||    |||||
AGCATAGATTCAAAGATACATCACAACAATCTTATCAACAATATTCTGGCGAAGgtactttatcctttagatttgtatagctgtccttacatacatttttttaaatggagcc-ctttattaa---ttgtaatagcactaagttgctaatgcttttatgcag

upper sequence: GRMZM2G108416_T01 (Zea mays), 5'ss of exon 14
lower sequence: AT3G05190.1 (Arabidopsis thaliana), 5'ss of exon 14
AGTATAGATTCCAAGATTCATCACAACAATCTTATCAACAATATTCTGGCAAAGgttcactttccttttgatttggagttcttaattagttcttagtatataccgtaactgtaatggagtttttgtctg-gactcgattttccatcctcgtgcag
| | | ||||||||||||||||||||||| ||| |||| || || || |||||||| |   |   ||   | |  |||   | ||  | ||   | | | |    | ||| | |      |||| ||||  | | ||     ||           
AATTTGGATTCCAAGATTCATCACAACAACCTTCTCAATAACATACTAGCAAAGgtac---tgtattcaaaataagagagttcaagaaattgacattgtgttt--ttactatgagattaattttctctgcaaatggaacaaacag----------

upper sequence: GRMZM2G108416_T01 (Zea mays), 5'ss of exon 14
lower sequence: AT5G27410.2 (Arabidopsis thaliana), 5'ss of exon 24
AGTATAGATTCCAAGATTCATCACAACAATCTTATCAACAATATTCTGGCAAAGgttca---ctttccttttgatt---tggagttcttaattagttcttagtatataccgtaactgtaatggagtttttgtctggactcgattttccatcctcgtgcag
| | ||||||||||||||||||||||||| ||  |||| ||||| || |||||||| |    |||| | | | ||    | || | | | || |  | ||| ||   || || | ||| | |  |||||| | |||    ||                  
AATTTAGATTCCAAGATTCATCACAACAACCTCCTCAATAATATACTTGCAAAGgtaccatcctttgcctgtcatcgagttgaatccgtgatcatgtgttattagggac-gtcattgtga-gatgtttttat-tggtaatgacacag-------------

upper sequence: GRMZM2G108416_T01 (Zea mays), 5'ss of exon 14
lower sequence: EFJ34717 (Selaginella moellendorffii), 5'ss of exon 14
AGTATAGATTCCAAGATTCATCACAACAATCTTATCAACAATATTCTGGCAAAGgttcactttccttttgatttggagttctta-attagttcttagtatataccgtaactgtaatggagtttttgtctggactcgattttccatcctcgtgcag
 |  |||||||||||||||| || |||||||| |||||||| || || || |||||    ||| || | ||| |    |||  | |||    | |||  | |  | ||                                               
TGCCTAGATTCCAAGATTCACCATAACAATCTCATCAACAACATACTTGCGAAGgtctgtttttctgt-gatgtccttttcgaagattcacgcatagcgtttttcatag----------------------------------------------

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|60357806|gb|DN224779.1|DN224779
EST:     TAGATTCCAAGATTCATCACAACAATCTTATCAACAATATTCTGGCAAAG                         ATAGAAGGTAATCTTGCCCAGGCTGAGGATGCCATTATGCTAGATAAGGAT
genomic: TAGATTCCAAGATTCATCACAACAATCTTATCAACAATATTCTGGCAAAGgttcactttc ... cctcgtgcagATAGAAGGTAATCTTGCCCAGGCTGAGGATGCCATTATGCTAGATAAGGAT
EST: gi|148969666|gb|EE020531.2|EE020531
EST:     TAGATTCCAAGATTCATCACAACAATCTTATCAACAATATTCTGGCAAAG                         ATAGAAGGTAATCTTGCCCAGGCTGAGGATGCCATTATGCTAGATAAGGAT
genomic: TAGATTCCAAGATTCATCACAACAATCTTATCAACAATATTCTGGCAAAGgttcactttc ... cctcgtgcagATAGAAGGTAATCTTGCCCAGGCTGAGGATGCCATTATGCTAGATAAGGAT
EST: gi|6827209|gb|AW330852.1|AW330852
EST:     TAGATTCCAAGATACATCACAACAATCTTATCAACAATATTCTGGCAAAG                         ATAGAAGGTAATCTTGCCCAGGCTGAGGATGCCATTATGCTAGATAAGGAT
genomic: TAGATTCCAAGATTCATCACAACAATCTTATCAACAATATTCTGGCAAAGgttcactttc ... cctcgtgcagATAGAAGGTAATCTTGCCCAGGCTGAGGATGCCATTATGCTAGATAAGGAT
EST: gi|211381070|gb|FL456665.1|FL456665
EST:     TAGATTCCAAGATTCATCACWACAATCTTATCAACAATATTCTGGCAAAG                         ATAGAAGGTAATCTTGCCCAGGCTGAGGATGCCATTATGCTAGATAAGGAT
genomic: TAGATTCCAAGATTCATCACAACAATCTTATCAACAATATTCTGGCAAAGgttcactttc ... cctcgtgcagATAGAAGGTAATCTTGCCCAGGCTGAGGATGCCATTATGCTAGATAAGGAT
EST: gi|78179722|gb|DV550095.1|DV550095
EST:     TAGATTCCAAGATACATCACAACAATCTTATCAACAATATTCTGGCAAAG                         ATAGAAGGTAATCTTGCCCAGGCTGAGGATGCCATTATGCTAGATAAGGAT
genomic: TAGATTCCAAGATTCATCACAACAATCTTATCAACAATATTCTGGCAAAGgttcactttc ... cctcgtgcagATAGAAGGTAATCTTGCCCAGGCTGAGGATGCCATTATGCTAGATAAGGAT
EST: gi|149084134|gb|EE173537.2|EE173537
EST:     TAGATTCCAAGATTCATCACAACAATCTTATCAACAATATTCTGGCAAAG                         ATAGAAGGTAATCTTGCCCAGGCTGAGGATGCCATTATGCTAGATAAGGAT
genomic: TAGATTCCAAGATTCATCACAACAATCTTATCAACAATATTCTGGCAAAGgttcactttc ... cctcgtgcagATAGAAGGTAATCTTGCCCAGGCTGAGGATGCCATTATGCTAGATAAGGAT
EST: gi|78115926|gb|DV534314.1|DV534314
EST:     TAGATTCCAAGATTCATCACAACAATCTTATCAACAATATTCTGGCAAAG                         ATAGAAGGTAATCTTGCCCAGGCTGAGGATGCCATTATGCTAGATAAGGAT
genomic: TAGATTCCAAGATTCATCACAACAATCTTATCAACAATATTCTGGCAAAGgttcactttc ... cctcgtgcagATAGAAGGTAATCTTGCCCAGGCTGAGGATGCCATTATGCTAGATAAGGAT
EST: gi|12058174|gb|BF733074.1|BF733074
EST:     TAGATTCCAAGATACATCACAACAATCTTATCAACAATATTCTGGCAAAG                         ATAGAAGGTAATCTTGCCCAGGCTGAGGATGCCATTATGCTAGATAAGGAT
genomic: TAGATTCCAAGATTCATCACAACAATCTTATCAACAATATTCTGGCAAAGgttcactttc ... cctcgtgcagATAGAAGGTAATCTTGCCCAGGCTGAGGATGCCATTATGCTAGATAAGGAT

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: 48 (upstream exon), 49 (downstream exon)
Score: 96

AGTATAGATTCCAAGATTCATCACAACAATCTTATCAACAATATTCTGGCAAAGgttcactttc ... cctcgtgcagATAGAAGGTAATCTTGCCCAGGCTGAGGATGCCATTATGCTAGATAAGGATGGCTTTGTATCAGAAACAAACGCAACAAATATT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 113

AGTATAGATTCCAAGATTCATCACAACAATCTTATCAACAATATTCTGGCAAAGgttcactttc ... cctcgtgcagATAGAAGGTAATCTTGCCCAGGCTGAGGATGCCATTATGCTAGATAAGGATGGCTTTGTATCAGAAACAAACGCAACAAATATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 218

AGTATAGATTCCAAGATTCATCACAACAATCTTATCAACAATATTCTGGCAAAGgttcactttc ... cctcgtgcagATAGAAGGTAATCTTGCCCAGGCTGAGGATGCCATTATGCTAGATAAGGATGGCTTTGTATCAGAAACAAACGCAACAAATATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 161

AGTATAGATTCCAAGATTCATCACAACAATCTTATCAACAATATTCTGGCAAAGgttcactttc ... cctcgtgcagATAGAAGGTAATCTTGCCCAGGCTGAGGATGCCATTATGCTAGATAAGGATGGCTTTGTATCAGAAACAAACGCAACAAATATT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTATAGATTCCAAGATTCATCACAACAATCTTATCAACAATATTCTGGCAAAGgttcactttccttttgatttggagttcttaattagttcttagtatataccgtaactgtaatggagtttttgtctggactcgattttccatcctcgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - GCAAAG