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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggatgttatgatactgattctgtgttagctatttctgaaaataaggtatatatgctattttgtcagagtaatatttgactgtactttctacatcaacagGTTTACTTCCAGGATTTATCTGGCTCTGAACCAGTGCTGAAACTACGAAGTTCTCCCACATCTCCGATAATTGACCCATTTCTATCTCCAAATGGGAGCA

Basic information

species Zea mays
transcript GRMZM2G174572_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174572_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g18850.1 (Oryza sativa), 3'ss of exon 1
aggatgttatgatactgattc-tgtgttagctatttctgaaaataaggtatatatgctattttgtcagagtaatatttgactgta--ctttctacatcaacagGTTTACTTCCAGGATTTATCTGGCTCTGAACCAGTGCTGAAACTACGAAGTTCTCCCACATCTCCGATAATTGACCCATTTCTATCTCCAAATGGGAGCA
    | || || || |  ||  ||| | || ||    |   ||      |   ||||||  |     ||||   ||   | | ||   ||||||  || | ||||||||||||||||||| |||||  ||||||| || || || || | ||||||  ||||||| || || |||||||||  ||| |||||| |||||||||
---tttttctggtagtttttgatgtttcagataacctttgtaaattttcaaggatgctaaatatcatgagtttcatggaaatatatcttttctatttccatagGTTTACTTCCAGGATTTGTCTGGTGCTGAACCTGTACTCAAGCTGCAAAGTTCAGCCACATCCCCCATCATTGACCCACATCTGTCTCCAGATGGGAGCA
















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|78087367|gb|DV515760.1|DV515760
EST:     ATTCTGGTGAATCCTCACGCGCCGGCATTGTCGTGCCGCTCCCATCCGGG                         GTTTACTTCCAGGATTTATCTGGCTCTGAACCAGTGCTGAAACTACGAAGT
genomic: ATTCTGGTGAATCCTCACGCGCCGGCATTGTCGTGCCGCTCCCATCCGGGgtaactaaaa ... acatcaacagGTTTACTTCCAGGATTTATCTGGCTCTGAACCAGTGCTGAAACTACGAAGT
EST: gi|148948943|gb|EC894362.2|EC894362
EST:     ATTCTGGTGAATCCTCACGCGCCGGCATTGTCGTGCCGCTCCCATCCGGG                         GTT-ACTTCCAGGATTTATCTGGCTCTGACCCAGTGCTGAAACTACGAGGT
genomic: ATTCTGGTGAATCCTCACGCGCCGGCATTGTCGTGCCGCTCCCATCCGGGgtaactaaaa ... acatcaacagGTTTACTTCCAGGATTTATCTGGCTCTGAACCAGTGCTGAAACTACGAAGT
EST: gi|71442825|gb|DR823875.1|DR823875
EST:     ATTCTGGTGAATCCTCACGCGCCGGCATTGTCGTGCCGCTCCCATCCGGG                         GTTTACTTCCAGGATTTATCTGGCTCTGAACCAGTGCTGAAACTACGAAGT
genomic: ATTCTGGTGAATCCTCACGCGCCGGCATTGTCGTGCCGCTCCCATCCGGGgtaactaaaa ... acatcaacagGTTTACTTCCAGGATTTATCTGGCTCTGAACCAGTGCTGAAACTACGAAGT
EST: gi|50327478|gb|CO522604.1|CO522604
EST:     ATTCTGGTGAATCCTCACGCGCCGGCATTGTCGTGCCGCTCCCATCCGGG                         GTTTACTTCCAGGATTTATCTGGCTCTGAACCAGTGCTGAAACTACGAAGT
genomic: ATTCTGGTGAATCCTCACGCGCCGGCATTGTCGTGCCGCTCCCATCCGGGgtaactaaaa ... acatcaacagGTTTACTTCCAGGATTTATCTGGCTCTGAACCAGTGCTGAAACTACGAAGT
EST: gi|149089910|gb|EE179197.2|EE179197
EST:     ATTCTGGTGAATCCTCACGCGCCGGCATTGTCGTGCCGCTCCCATCCGGG                         GTTTACTTCCAGGATTTATCTGGCTCTGAACCAGTGCTGAAACTACGAAGT
genomic: ATTCTGGTGAATCCTCACGCGCCGGCATTGTCGTGCCGCTCCCATCCGGGgtaactaaaa ... acatcaacagGTTTACTTCCAGGATTTATCTGGCTCTGAACCAGTGCTGAAACTACGAAGT
EST: gi|211438015|gb|FL340317.1|FL340317
EST:     ATTCTGGTGAATCCTCACGCGCCGGCATTGTCGTGCCGCTCCCATCCGGG                         GTTTACTTCCAGGATTTATCTGGCTCTGAAC
genomic: ATTCTGGTGAATCCTCACGCGCCGGCATTGTCGTGCCGCTCCCATCCGGGgtaactaaaa ... acatcaacagGTTTACTTCCAGGATTTATCTGGCTCTGAAC
EST: gi|149101321|gb|EE187438.2|EE187438
EST:     ATTCTGGTGAATCCTCACGCGCCGGCATTGTCGTGCCGCTCCCATCCGGG                         GTTTACTTCCAGGATTTATCTGGCTCTGAACCAGTGCTGAAACTACGAAGT
genomic: ATTCTGGTGAATCCTCACGCGCCGGCATTGTCGTGCCGCTCCCATCCGGGgtaactaaaa ... acatcaacagGTTTACTTCCAGGATTTATCTGGCTCTGAACCAGTGCTGAAACTACGAAGT
EST: gi|149074618|gb|EE163025.2|EE163025
EST:     ATTCTGGTGAATCCTCACGCGCCGGCATTGTCGTGCCGCTCCCATCCGGG                         GTTTACTTCCAGGATTTATCTGGCTCTGAACCAGTGCTGAAACTACGAAGT
genomic: ATTCTGGTGAATCCTCACGCGCCGGCATTGTCGTGCCGCTCCCATCCGGGgtaactaaaa ... acatcaacagGTTTACTTCCAGGATTTATCTGGCTCTGAACCAGTGCTGAAACTACGAAGT

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: 44 (upstream exon), 47 (downstream exon)
Score: 56

CGCACGGGAGCGCGGCCTCGGGGTCACCCGCTACGAGTGGCGCTCTCGCCATTCTGGTGAATCCTCACGCGCCGGCATTGTCGTGCCGCTCCCATCCGGGgtaactaaaa ... acatcaacagGTTTACTTCCAGGATTTATCTGGCTCTGAACCAGTGCTGAAACTACGAAGTTCTCCCACATCTCCGATAATTGACCCATTTCTATCTCCAAATGGGAGCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 71

CGCACGGGAGCGCGGCCTCGGGGTCACCCGCTACGAGTGGCGCTCTCGCCATTCTGGTGAATCCTCACGCGCCGGCATTGTCGTGCCGCTCCCATCCGGGgtaactaaaa ... acatcaacagGTTTACTTCCAGGATTTATCTGGCTCTGAACCAGTGCTGAAACTACGAAGTTCTCCCACATCTCCGATAATTGACCCATTTCTATCTCCAAATGGGAGCA


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 38

CGCACGGGAGCGCGGCCTCGGGGTCACCCGCTACGAGTGGCGCTCTCGCCATTCTGGTGAATCCTCACGCGCCGGCATTGTCGTGCCGCTCCCATCCGGGgtaactaaaa ... acatcaacagGTTTACTTCCAGGATTTATCTGGCTCTGAACCAGTGCTGAAACTACGAAGTTCTCCCACATCTCCGATAATTGACCCATTTCTATCTCCAAATGGGAGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

CGCACGGGAGCGCGGCCTCGGGGTCACCCGCTACGAGTGGCGCTCTCGCCATTCTGGTGAATCCTCACGCGCCGGCATTGTCGTGCCGCTCCCATCCGGGgtaactaaaa ... acatcaacagGTTTACTTCCAGGATTTATCTGGCTCTGAACCAGTGCTGAAACTACGAAGTTCTCCCACATCTCCGATAATTGACCCATTTCTATCTCCAAATGGGAGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtatatatgctattttgtcagagtaatatttgactgtactttctacatcaacagGTTTACTTCCAGGATTTATCTGGCTCTGAACCAGTGCTGAAACTACGAAGTTCTCCCACATCTCCGATAATTGACCCATTTCTATCTCCAAATGGGAGCA
                            atttgac  putative branch site (score: 72)
                                       ctttctac  putative PPT
                      agtaatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggatgttatgatactgattctgtgttagctatttctgaaaataaggtatatatgctattttgtcagagtaatatttgactgtactttctacatcaacagGTTTACTTCCAGGATTTATCTGGCTCTGAACCAGTGCTGAAACTACGAAGTTCTCCCACATCTCCGATAATTGACCCATTTCTATCTCCAAATGGGAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - -tgatact
- - - - - - - - gattctg
- - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgctatt