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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgctgctctgactcctcgttacttgttgtaagcagtgaaagttaacgtactttgtgaaagattcctgcactgttccttgtggtttcacgttcatgctgcataaacattctgtttcttgatgatctgtagGCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCCCGAGCAACTCGAGCTGCTGCTAGGCAATTTATTCGAGGGGAAACAAGAA

Basic information

species Zea mays
transcript GRMZM2G074530_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074530_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g58880.1 (Oryza sativa), 3'ss of exon 11
gtacgctgctctgactcctcgttacttgttgtaagcagtgaaagttaacgtactttgtgaaagattcctgcactgttccttgtggtttcacgttcatgctgcataaacattctgtttcttgatgatctgtagGCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCCCGAGCAACTCGAGCTGCTGCTAGGCAATTTATTCGAGGGGAAACAAGAA
               |  ||  |  ||  | | |          |  | ||  | | || |       || | |||||  |    |     |||| ||   |   | | || ||   |||| | |||| |||||||||||| ||||| ||||| ||||| || ||||| || |||||||| || |||||| | ||||| ||||| | |||||| || || || |||||||| 
---------------ttttccctcttttcttttatt--------tctatgt-ttctatggata-----tgta-tgttcactagactcaagagttcttgtccctggagc-ttatgagacttg-taatctatagGCCTCTCATCGAGAACAGCAAGGCACCCGGAAAATATGTCAAGCACACACCAGAGCAAGTTGAGCTACTGCTTGCCAATTTGTTTGAAGGAAAACAAGAG
















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|71432760|gb|DR813810.1|DR813810
EST:     GTCGCTGAAATCCTGTTGCCTGCCTCCCGATCATTCATAAAACGTTTTGG                         GCCTCTCATTGAGAATAGCAAAGCCCCTGGGAAATACGTGAAGCCCACTCC
genomic: GTCGCTGAAATCCTGTTGCCTGCCTACCGATCATTCATAAAACGTTTTGGgtacgctgct ... tgatctgtagGCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCC
EST: gi|211149050|gb|FK958467.1|FK958467
EST:     GTCGCTGAAATCCTGTTGCCTGCCTACCGATCATTCATAAAACGTTTTGG                         GCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCC
genomic: GTCGCTGAAATCCTGTTGCCTGCCTACCGATCATTCATAAAACGTTTTGGgtacgctgct ... tgatctgtagGCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCC
EST: gi|32929635|gb|CF034447.1|CF034447
EST:     GTCGCTGAAATCCTGTTGTCTGCCTACCGATCATTCATAAAACGTTTTGG                         GCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCC
genomic: GTCGCTGAAATCCTGTTGCCTGCCTACCGATCATTCATAAAACGTTTTGGgtacgctgct ... tgatctgtagGCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCC
EST: gi|166445227|gb|EG293017.1|EG293017
EST:     CTGAAATCCTGTTGCCCTGCCTACCGATCATTCATAAAACGTTTTGG                         GCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCC
genomic: CTGAAATCCTGTTG-CCTGCCTACCGATCATTCATAAAACGTTTTGGgtacgctgct ... tgatctgtagGCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCC
EST: gi|33092047|gb|CF052041.1|CF052041
EST:     GTCGCTGAAATCCTGTTGCCTGCCTACCGATCATTCATAAAACGTTTTGG                         GCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCC
genomic: GTCGCTGAAATCCTGTTGCCTGCCTACCGATCATTCATAAAACGTTTTGGgtacgctgct ... tgatctgtagGCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCC
EST: gi|5740705|gb|AI948395.1|AI948395
EST:     GTCGCTGAAATCCTGTTGCCTGCCTACCGATCATTCATAAAACGTTTTGG                         GCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCC
genomic: GTCGCTGAAATCCTGTTGCCTGCCTACCGATCATTCATAAAACGTTTTGGgtacgctgct ... tgatctgtagGCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCC
EST: gi|211159123|gb|FL458119.1|FL458119
EST:     GTCGCTGAAATCCTGTTGCCTGCCTACCGATCATTCATAAAACGTTTTGG                         GCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCC
genomic: GTCGCTGAAATCCTGTTGCCTGCCTACCGATCATTCATAAAACGTTTTGGgtacgctgct ... tgatctgtagGCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCC
EST: gi|33093183|gb|CF053177.1|CF053177
EST:     GTCGCTGAAATCCTGTTGCCTGCCTACCGATCATTCATAAAACGTTTTGG                         GCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCC
genomic: GTCGCTGAAATCCTGTTGCCTGCCTACCGATCATTCATAAAACGTTTTGGgtacgctgct ... tgatctgtagGCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCC
EST: gi|211159122|gb|FL458118.1|FL458118
EST:     GTCGCTGAAATCCTGTTGCCTGCCTACCGATCATTCATAAAACGTTTTGG                         GCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCC
genomic: GTCGCTGAAATCCTGTTGCCTGCCTACCGATCATTCATAAAACGTTTTGGgtacgctgct ... tgatctgtagGCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCC
EST: gi|32849856|gb|CD989537.1|CD989537
EST:     GTCGCTGAAATCCTGTTGCCTGCCTACCGATCATTCATAAAACGTTTTGG                         GCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCC
genomic: GTCGCTGAAATCCTGTTGCCTGCCTACCGATCATTCATAAAACGTTTTGGgtacgctgct ... tgatctgtagGCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCC

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: 168

GTGGCTGGTCCGTTCCAGACACTGAGCTGCGCGAGTCACTAAGACTCGCGGTCGCTGAAATCCTGTTGCCTGCCTACCGATCATTCATAAAACGTTTTGGgtacgctgct ... tgatctgtagGCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCCCGAGCAACTCGAGCTGCTGCTAGGCAATTTATTCGAGGGGAAACAAGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 196

GTGGCTGGTCCGTTCCAGACACTGAGCTGCGCGAGTCACTAAGACTCGCGGTCGCTGAAATCCTGTTGCCTGCCTACCGATCATTCATAAAACGTTTTGGgtacgctgct ... tgatctgtagGCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCCCGAGCAACTCGAGCTGCTGCTAGGCAATTTATTCGAGGGGAAACAAGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 328

GTGGCTGGTCCGTTCCAGACACTGAGCTGCGCGAGTCACTAAGACTCGCGGTCGCTGAAATCCTGTTGCCTGCCTACCGATCATTCATAAAACGTTTTGGgtacgctgct ... tgatctgtagGCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCCCGAGCAACTCGAGCTGCTGCTAGGCAATTTATTCGAGGGGAAACAAGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

GTGGCTGGTCCGTTCCAGACACTGAGCTGCGCGAGTCACTAAGACTCGCGGTCGCTGAAATCCTGTTGCCTGCCTACCGATCATTCATAAAACGTTTTGGgtacgctgct ... tgatctgtagGCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCCCGAGCAACTCGAGCTGCTGCTAGGCAATTTATTCGAGGGGAAACAAGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgtggtttcacgttcatgctgcataaacattctgtttcttgatgatctgtagGCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCCCGAGCAACTCGAGCTGCTGCTAGGCAATTTATTCGAGGGGAAACAAGAA
                                       tcttgat  putative branch site (score: 182)
                         ataaacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgctgctctgactcctcgttacttgttgtaagcagtgaaagttaacgtactttgtgaaagattcctgcactgttccttgtggtttcacgttcatgctgcataaacattctgtttcttgatgatctgtagGCCTCTCATTGAGAATAGCAAAGCACCTGGGAAATACGTGAAGCACACTCCCGAGCAACTCGAGCTGCTGCTAGGCAATTTATTCGAGGGGAAACAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT