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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagatgcttgcggcctgtatctgcagcatcgttttctctgtctaatgataacttttttatgaacattttctctgcattcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG

Basic information

species Zea mays
transcript GRMZM2G171745_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171745_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 5
gcaagatgcttgcggcctgtatctgcagcatc---gttttctctgtctaa-tgataacttttttatgaacattttctctgcattcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG
|  |||||||||   | |  |  | ||   |    | ||||  ||| ||  ||  || |  |      | ||| | |||| | |      |||||||||||||| ||||||| |||||||||||||||||||| || || |||||||| || || ||||| ||
gtcagatgcttgtt-cttacaagtacattgttcatggtttcattgtttagctggcaaatgatccccctaaattctgtctgtacttgac--agGTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTG
















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|60346665|gb|DN213638.1|DN213638
EST:     GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|166678942|gb|EG225373.1|EG225373
EST:     GGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACA
genomic: GGGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACA
EST: gi|78118434|gb|DV536820.1|DV536820
EST:     GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|211178524|gb|FK980682.1|FK980682
EST:     GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|211195518|gb|FL100642.1|FL100642
EST:     GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|86472725|gb|DY239095.1|DY239095
EST:     GGTATCGTTAGAGGCAAAGTGAATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|211180926|gb|FK980688.1|FK980688
EST:     GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGA-CATG
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|71427328|gb|DR808378.1|DR808378
EST:     GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|148943925|gb|EC889005.2|EC889005
EST:     GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|148972927|gb|EE023942.2|EE023942
EST:     GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|78112152|gb|DV530548.1|DV530548
EST:     GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|74242379|gb|DT650293.1|DT650293
EST:     GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|149089443|gb|EE178684.2|EE178684
EST:     GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGC
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGC
EST: gi|211178525|gb|FK980683.1|FK980683
EST:     GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|76931006|gb|DV172592.1|DV172592
EST:     GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|78118433|gb|DV536819.1|DV536819
EST:     GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|211180929|gb|FK980691.1|FK980691
EST:     GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|29129753|gb|CB380457.1|CB380457
EST:     GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|76931005|gb|DV172591.1|DV172591
EST:     TTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: TTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|71427327|gb|DR808377.1|DR808377
EST:     GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|78112153|gb|DV530549.1|DV530549
EST:     GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAA-GGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|31352916|gb|CD437273.1|CD437273
EST:     GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|89251568|gb|DY623354.1|DY623354
EST:     AAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: AAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
EST: gi|67021495|gb|CO450244.1|CO450244
EST:     GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAG                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG
genomic: GGTATCGTTAGAGGCAAACTGGATCAGCTGAGAAGGTGCTTTGAGgcaagatgct ... ttcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctctgtctaatgataacttttttatgaacattttctctgcattcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG
              tgataac  putative branch site (score: 2)
                                  ttttctctgcattc  putative PPT
           taatgataactttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagatgcttgcggcctgtatctgcagcatcgttttctctgtctaatgataacttttttatgaacattttctctgcattcattttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC