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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatatattgagtctgattttgtaaacatcccatcatctatgctgttaaacttcattaatcctctgttattttttgttcctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG

Basic information

species Zea mays
transcript GRMZM2G142984_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G142984_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g38620.1 (Oryza sativa), 3'ss of exon 8
gtaaatatattgagtctgattttgtaaacatcccatca-tctatg-----ctgttaaacttcattaatcctctgttattttttgttcctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
||||| ||| | |||||||||||||| |  | |  | | |||||      |||| || ||| ||| || |  | | ||||      | | |  |||| |||||||| |||||||||||||| ||||| ||||||||||||
gtaaacatactaagtctgattttgtagatgttctctaaatctatattattctgtgaagctttatttattccttttcatttca-acgcatatttgcagTGTTGAAATCCATATTGGTGGTGCAAAGGGACCTCCAGACAGG
















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|211320745|gb|FL468785.1|FL468785
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAA                         GGTTGAAATMCATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAAgtaaatatat ... ctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
EST: gi|17921527|gb|BM259178.1|BM259178
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAA                         GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAAgtaaatatat ... ctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
EST: gi|149107225|gb|EE189109.2|EE189109
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAA                         GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGCCAGG
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAAgtaaatatat ... ctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
EST: gi|32859979|gb|CD999660.1|CD999660
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAA                         GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAAgtaaatatat ... ctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
EST: gi|16926376|gb|BM079444.1|BM079444
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAA                         GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAAgtaaatatat ... ctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
EST: gi|166430660|gb|EG077620.1|EG077620
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAA                         GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGGTGTTC
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAAgtaaatatat ... ctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGGTGTTC
EST: gi|166533363|gb|EG236313.1|EG236313
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAA                         GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGGTGTTC
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAAgtaaatatat ... ctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGGGTGTTC
EST: gi|5070005|gb|AI737970.1|AI737970
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAA                         GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAAgtaaatatat ... ctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
EST: gi|211383190|gb|FL437263.1|FL437263
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAA                         GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAAgtaaatatat ... ctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
EST: gi|67015787|gb|CO444536.1|CO444536
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAA                         GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAAgtaaatatat ... ctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
EST: gi|91867738|gb|EB399776.1|EB399776
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAA                         GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAAgtaaatatat ... ctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
EST: gi|17921853|gb|BM259489.1|BM259489
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAA                         GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAAgtaaatatat ... ctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
EST: gi|60344970|gb|DN211943.1|DN211943
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAA                         GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAAgtaaatatat ... ctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
EST: gi|116819630|gb|EC862778.1|EC862778
EST:     TTATTGGCAGAAAGGGGTCAACGATAATGCCTGTGAAAGAATGTTGCAA                         GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCATACAGG
genomic: TTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAAgtaaatatat ... ctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
EST: gi|91052774|gb|EB163192.1|EB163192
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAA                         GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGCCAGG
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAAgtaaatatat ... ctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
EST: gi|37392421|gb|CF633460.1|CF633460
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAA                         GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAAgtaaatatat ... ctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
EST: gi|111189956|gb|EE288092.1|EE288092
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAA                         GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAAgtaaatatat ... ctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
EST: gi|16918764|gb|BM073885.1|BM073885
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAA                         GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAAgtaaatatat ... ctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
EST: gi|87298726|gb|DY470729.1|DY470729
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAA                         GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAAgtaaatatat ... ctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
EST: gi|110531048|gb|EE035232.1|EE035232
EST:     GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAA                         GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGCCAGG
genomic: GTTATTGGCAGAAAGGGGTCAACGATAATGGCTGTGAAAGAATGTTGCAAgtaaatatat ... ctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
EST: gi|74035099|gb|DT535589.1|DT535589
EST:     GGGTCAACGATAATGGCTGTGAAAGAATGTTGCAA                         GGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
genomic: GGGTCAACGATAATGGCTGTGAAAGAATGTTGCAAgtaaatatat ... ctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catctatgctgttaaacttcattaatcctctgttattttttgttcctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG
                   cattaat  putative branch site (score: 3)
                         tcctctgttatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatatattgagtctgattttgtaaacatcccatcatctatgctgttaaacttcattaatcctctgttattttttgttcctgtgggcagGGTTGAAATACATATTGGTGGTGCTAAGGGGCCTCCAGACAGG

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