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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGGCAGCAACCAGCAGGAACTTCAAGCAGGCAGCTAAGCTGCTGGGCCTCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAGgtgataaatccactacagttcttttagatctggtaaactgtttcccgctgtttcacttgctcaggggggttcctgtcttcctgatgatgatgaccccccc...

Basic information

species Zea mays
transcript GRMZM2G178415_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178415_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g58040.3 (Oryza sativa), 5'ss of exon 2
ATTGGCAGCAACCAGCAGGAACTTCAAGCAGGCAGCTAAGCTGCTGGGCCTCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAGgtgataaatccactacagttctttt-agatctggtaaactgtttcccgctgtttcacttgctcaggggggttcct------gtcttcctgatgatgatgaccccccc-----------------------------------------------------------------------------
 |||||||| || |||||||||||||||||||| || |||||||||||||| ||||||||||||||||||||||||||||| || |||||||||||||||||||| | || |   ||||| | || ||||||||||| ||||   |    | |||||||||||   | |||| |          |    ||  ||| |||      |                                                                             
GTTGGCAGCGACGAGCAGGAACTTCAAGCAGGCGGCCAAGCTGCTGGGCCTGGACTCCAAGCTGGAGAAGAGCTTGCTCATCCCGTTCAGGGAGATCAAGgtgatgattctagggcagttttcttgagatctggtaacctgtgctctttggcttcacttgctcgaagtggtttcctgatgaacatgagagagaatgttgaaaaattcttgctgtgacggggttcaatggattaaagggctctctttttggtgttgagtgacaagaagtttgtggttgatttcag
















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|148981458|gb|EE027657.2|EE027657
EST:     TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAG                         GTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
genomic: TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAGgtgataaatc ... gtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
EST: gi|86466439|gb|DY232809.1|DY232809
EST:     TCGACTCCAAGCTGGAAAAGAGCTTGCTCATTCCTTTCAGGGAGATCAAG                         GTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
genomic: TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAGgtgataaatc ... gtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
EST: gi|149082772|gb|EE171995.2|EE171995
EST:     TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAG                         GTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
genomic: TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAGgtgataaatc ... gtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
EST: gi|87152935|gb|DY397724.1|DY397724
EST:     TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAG                         GTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
genomic: TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAGgtgataaatc ... gtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
EST: gi|71766899|gb|DR964836.1|DR964836
EST:     TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAG                         GTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
genomic: TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAGgtgataaatc ... gtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
EST: gi|149072180|gb|EE160421.2|EE160421
EST:     TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAG                         GTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
genomic: TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAGgtgataaatc ... gtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
EST: gi|50325462|gb|CO520588.1|CO520588
EST:     TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAG                         GTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
genomic: TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAGgtgataaatc ... gtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
EST: gi|148940231|gb|EC885000.2|EC885000
EST:     TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAG                         GTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
genomic: TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAGgtgataaatc ... gtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
EST: gi|17921570|gb|BM259221.1|BM259221
EST:     TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAG                         GTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
genomic: TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAGgtgataaatc ... gtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
EST: gi|148931517|gb|EC874558.2|EC874558
EST:     TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAG                         GTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
genomic: TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAGgtgataaatc ... gtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
EST: gi|78092010|gb|DV520384.1|DV520384
EST:     TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAG                         GTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
genomic: TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAGgtgataaatc ... gtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
EST: gi|78089717|gb|DV518091.1|DV518091
EST:     TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAG                         GTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
genomic: TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAGgtgataaatc ... gtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
EST: gi|91867926|gb|EB399854.1|EB399854
EST:     TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAG                         GTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
genomic: TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAGgtgataaatc ... gtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
EST: gi|149101283|gb|EE187396.2|EE187396
EST:     TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAG                         GTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
genomic: TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAGgtgataaatc ... gtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
EST: gi|22491555|gb|BU051478.1|BU051478
EST:     GACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTTCCAGGGAGATCAAG                         GTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
genomic: GACTCCAAGCTGGAGAAGAGCTTGCTCATTCCA-TT-CAGGGAGATCAAGgtgataaatc ... gtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
EST: gi|149110227|gb|EE190296.2|EE190296
EST:     TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAG                         GTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
genomic: TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAGgtgataaatc ... gtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
EST: gi|19351039|gb|BM895571.1|BM895571
EST:     TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAG                         GTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA
genomic: TCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAGgtgataaatc ... gtggttgcagGTTGAATGCACAATCCCAAAAGATGATGGAACTTTGGCATCCTATGTTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGGCAGCAACCAGCAGGAACTTCAAGCAGGCAGCTAAGCTGCTGGGCCTCGACTCCAAGCTGGAGAAGAGCTTGCTCATTCCATTCAGGGAGATCAAGgtgataaatccactacagttcttttagatctggtaaactgtttcccgctgtttcacttgctcaggggggttcctgtcttcctgatgatgatgaccccccc

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA