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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGGgtaaatgttcttctgccccgtttcttgaatgccacatcaccctatgcattcacattctaagttatttttatagtgaccatatgtctatgaaatcaatcat...

Basic information

species Zea mays
transcript GRMZM2G082976_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082976_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g63520.1 (Oryza sativa), 5'ss of exon 4
GTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGGgtaaatgttcttctgccccgtttcttg-aatgccacatcaccctatgcattcacattctaagttatttttatagtgaccatatgtctatgaaatcaatcat-
|||||||| ||||||||||||||||| ||||| |||||||||||  ||||  ||||||||||||| ||||| || ||||| ||||||| | || ||     || || | || |   | |||| ||   ||| | | |    | |  | ||| | ||  | |    |  ||   ||      |||| 
GTTTATGTATGGAGCAAGCACAATCCCTTCATTCATATGAGCTTCTTGGGTTTGTTCACCTTTACTGCTGCTTATTTACCTTGGgtaagtatttttagtttcctttccatgtaccacaacatgactacatg-actaatgcac-acttgattctcatcttaagttaacttcctagagcctcttcata

upper sequence: GRMZM2G082976_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv10s0116g00010.t01 (Vitis vinifera), 5'ss of exon 2
GTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGGgtaaatgttcttctgccccgt----ttcttgaatgccacatcaccctatgcattcacattcta-agttatt-tttatagtgaccatatgtctatgaaatcaatcat
|||||||| ||||||||||| |||||||| ||||||||||| ||  ||||||| || ||||| || || || ||| | |||||||| | ||  | ||       |    ||||    |  || |  |  ||||   |  |   | || | ||    ||| |||||  | |       | | |        
GTTTATGTGTGGAGCAAGCAAAATCCTTTTATCCATATGAGTTTCTTGGGCCTCTTTACCTTCACAGCGGCCTACCTTCCATGGgtgagtgagcctcaagtttctattattctaccttttcaaactattctatttctatatgctgtatacttgccatttttagtgttctttcactgttcagaaa------
















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|211475995|gb|FL472681.1|FL472681
EST:     ATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGG                         GTCCTATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTC
genomic: ATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGGgtaaatgttc ... tgaatctcagGTCCTATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTC
EST: gi|37379052|gb|CF626253.1|CF626253
EST:     ATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGG                         GTCATATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTC
genomic: ATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGGgtaaatgttc ... tgaatctcagGTCCTATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTC
EST: gi|42491916|gb|CK700962.1|CK700962
EST:     ATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGG                         GTCCTATTGGGCTTCTCTATCCTGGTGGG
genomic: ATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGGgtaaatgttc ... tgaatctcagGTCCTATTGGGCTTCTCTATCCTGGTGGG
EST: gi|37378913|gb|CF626178.1|CF626178
EST:     ATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGG                         GTCCTATTGGGCTTCTCTAT-CTAGGTGGGAAGCAGCACATGGGTTGATCT
genomic: ATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGGgtaaatgttc ... tgaatctcagGTCCTATTGGGCTTCTCTATCCT-GGTGGGAAGCAGCACATGGGTTGATCT
EST: gi|78543826|gb|DV621324.1|DV621324
EST:     ATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGG                         GTCCTATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTC
genomic: ATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGGgtaaatgttc ... tgaatctcagGTCCTATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTC
EST: gi|88754119|gb|DY538260.1|DY538260
EST:     ATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGG                         GTCCTATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTC
genomic: ATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGGgtaaatgttc ... tgaatctcagGTCCTATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTC
EST: gi|26457330|gb|CA828913.1|CA828913
EST:     ATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGG                         GTCCTATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTC
genomic: ATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGGgtaaatgttc ... tgaatctcagGTCCTATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTC
EST: gi|4573306|gb|AI586865.1|AI586865
EST:     ATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGG                         GTCCTATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTC
genomic: ATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGGgtaaatgttc ... tgaatctcagGTCCTATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTC
EST: gi|31353782|gb|CD438139.1|CD438139
EST:     ATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGG                         GTCCTATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTC
genomic: ATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGGgtaaatgttc ... tgaatctcagGTCCTATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTC

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: 47 (upstream exon), 45 (downstream exon)
Score: 68

GTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGGgtaaatgttc ... tgaatctcagGTCCTATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

GTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGGgtaaatgttc ... tgaatctcagGTCCTATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 99

GTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGGgtaaatgttc ... tgaatctcagGTCCTATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 172

GTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGGgtaaatgttc ... tgaatctcagGTCCTATTGGGCTTCTCTATCCTGGTGGGAAGCAGCACATGGGTTGATCTCTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTATGTCTGGAGCAAGCACAATCCTTTCATCCATATGAGCTTTCTGGGCCTGTTCACCTTTACGGCTGCATACTTACCATGGgtaaatgttcttctgccccgtttcttgaatgccacatcaccctatgcattcacattctaagttatttttatagtgaccatatgtctatgaaatcaatcat

- - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgcccc