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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacatcttgagtctgacttcgtaaacataccatcctctatgctgttaaacttcattaatcctctctgtttttttggttcctgtgggcagTGTTGAAATCCATATTGGTGGTGCTAAGGGGCCTCCAGACAGG

Basic information

species Zea mays
transcript GRMZM2G081924_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081924_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g38620.1 (Oryza sativa), 3'ss of exon 8
gtaaacatcttgagtctgacttcgtaaacatacc---atcct---ctatgctgttaaacttcattaatcctctctgtttttttggttcctgtgggcagTGTTGAAATCCATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
||||||||  | ||||||| || ||| |  | |    |  ||    ||| |||| || ||| ||| || |  | |    |||     | | |  |||||||||||||||||||||||||||| ||||| ||||||||||||
gtaaacatactaagtctgattttgtagatgttctctaaatctatattattctgtgaagctttatttattcctttt--catttcaacgcatatttgcagTGTTGAAATCCATATTGGTGGTGCAAAGGGACCTCCAGACAGG
















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|19351659|gb|BM896191.1|BM896191
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGT-GTGAAAGAATCTTGCAA                         TGTTGAAATCCATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGTTGTGAAAGAATCTTGCAAgtaaacatct ... ctgtgggcagTGTTGAAATCCATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
EST: gi|113671106|gb|DW821672.1|DW821672
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGTTGTGAAAGAATCTTGCAA                         TGTTGAAATCCATATTGGTGGTGC
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGTTGTGAAAGAATCTTGCAAgtaaacatct ... ctgtgggcagTGTTGAAATCCATATTGGTGGTGC
EST: gi|211331399|gb|FL462812.1|FL462812
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGTTGTGAAAGAATCTTGCAA                         TGTTGAAATCCATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGTTGTGAAAGAATCTTGCAAgtaaacatct ... ctgtgggcagTGTTGAAATCCATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
EST: gi|211412952|gb|FL027552.1|FL027552
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGTTGTGAAAGAATCTTGCAA                         CGTTGAAATCCATATTGGTGGTGCTAAGGGGCCTCCAGATAGG
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGTTGTGAAAGAATCTTGCAAgtaaacatct ... ctgtgggcagTGTTGAAATCCATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
EST: gi|166620247|gb|EG165466.1|EG165466
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGTTGTGAAAGAATCTTGCAA                         CGTTGAAATCC
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGTTGTGAAAGAATCTTGCAAgtaaacatct ... ctgtgggcagTGTTGAAATCC
EST: gi|76292397|gb|DV031965.1|DV031965
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGTTGTGAAAGAATCTTGCAA                         TGTTGAAATCCATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGTTGTGAAAGAATCTTGCAAgtaaacatct ... ctgtgggcagTGTTGAAATCCATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
EST: gi|31358885|gb|CD443242.1|CD443242
EST:     GTTATTGGCAGAAAGGGGTCAACTATAATGGTTGTGAAAGAATCTTGCAA                         CGTTGAAATCCATATTGGTGGTGCTAAGGGGCCTCCAGATAGG
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGTTGTGAAAGAATCTTGCAAgtaaacatct ... ctgtgggcagTGTTGAAATCCATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
EST: gi|60341483|gb|DN208456.1|DN208456
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGTTGTGAAAGAATCTTGCAA                         TGTTGAAATCCATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGTTGTGAAAGAATCTTGCAAgtaaacatct ... ctgtgggcagTGTTGAAATCCATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
EST: gi|113671290|gb|DW822058.1|DW822058
EST:     AAAGAATCTTGCAA                         TGTTGAAATCCATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
genomic: AAAGAATCTTGCAAgtaaacatct ... ctgtgggcagTGTTGAAATCCATATTGGTGGTGCTAAGGGGCCTCCAGACAGG

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: 244

AAGTTGATATCCTATCAGTCTTAGATGTTCCTCATGGGAAAATGGGACGAGTTATTGGCAGAAAGGGGTCAACGATAATGGTTGTGAAAGAATCTTGCAAgtaaacatct ... ctgtgggcagTGTTGAAATCCATATTGGTGGTGCTAAGGGGCCTCCAGACAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 143

AAGTTGATATCCTATCAGTCTTAGATGTTCCTCATGGGAAAATGGGACGAGTTATTGGCAGAAAGGGGTCAACGATAATGGTTGTGAAAGAATCTTGCAAgtaaacatct ... ctgtgggcagTGTTGAAATCCATATTGGTGGTGCTAAGGGGCCTCCAGACAGG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 122

AAGTTGATATCCTATCAGTCTTAGATGTTCCTCATGGGAAAATGGGACGAGTTATTGGCAGAAAGGGGTCAACGATAATGGTTGTGAAAGAATCTTGCAAgtaaacatct ... ctgtgggcagTGTTGAAATCCATATTGGTGGTGCTAAGGGGCCTCCAGACAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

AAGTTGATATCCTATCAGTCTTAGATGTTCCTCATGGGAAAATGGGACGAGTTATTGGCAGAAAGGGGTCAACGATAATGGTTGTGAAAGAATCTTGCAAgtaaacatct ... ctgtgggcagTGTTGAAATCCATATTGGTGGTGCTAAGGGGCCTCCAGACAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctatgctgttaaacttcattaatcctctctgtttttttggttcctgtgggcagTGTTGAAATCCATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
                  cattaat  putative branch site (score: 168)
                        tcctctctgttttttt  CT-rich tract
          ttaaacttcattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacatcttgagtctgacttcgtaaacataccatcctctatgctgttaaacttcattaatcctctctgtttttttggttcctgtgggcagTGTTGAAATCCATATTGGTGGTGCTAAGGGGCCTCCAGACAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG