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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggttggcttggtagggtttctgatttccttttgttttgtgcgtgtgatgagttggtttgttcgtttggGCTGCAGAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA

Basic information

species Zea mays
transcript GRMZM5G841900_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G841900_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g57070.1 (Oryza sativa), 3'ss of exon 1
-----------gtagggtt---ggcttggtagggtttctgatttccttttgttttgtgcgtgtgatgagttggtttgttcgtttggGCTGCAGAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA
            |||||||   |  ||||| | |  || |||| |  ||    | ||  | ||| |  ||||||| |    ||| |||||||||| ||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| || || 
gtagggttcagctagggttttggatttggtggcgcctcggattcctcttctgatggtctgcgtggttggttggttcg---attttggctgcagAGGTCCACGGTGGAGGTGGTCGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATTGCGCGT
















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|148939988|gb|EC884719.2|EC884719
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACG---A-                         -C--CAGAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGT
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... gttcgtttggGCTGCAGAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGT
EST: gi|50328543|gb|CO523669.1|CO523669
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         GCTGCAGAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGT
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... gttcgtttggGCTGCAGAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGT
EST: gi|211118861|gb|FL110176.1|FL110176
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACG---A-                         -C--CAGAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGT
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... gttcgtttggGCTGCAGAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGT
EST: gi|76012394|gb|DT939564.1|DT939564
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACG---A-                         -C--CAGAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGT
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... gttcgtttggGCTGCAGAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGT
EST: gi|74244670|gb|DT652584.1|DT652584
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACG---A-                         -C--CAGAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGT
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... gttcgtttggGCTGCAGAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGT
EST: gi|71428020|gb|DR809070.1|DR809070
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACG---A-                         -C--CAGAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGT
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... gttcgtttggGCTGCAGAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggtttctgatttccttttgttttgtgcgtgtgatgagttggtttgttcgtttggGCTGCAGAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA
    ttctgat  putative branch site (score: 3)
                                          tttgttc  putative PPT
               ttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagggttggcttggtagggtttctgatttccttttgttttgtgcgtgtgatgagttggtttgttcgtttggGCTGCAGAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT