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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_T04
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|211102908|gb|FK962289.1|FK962289
EST:     TCACCGGGCGCCGCCGCATCGTGCCGSCCKCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211118860|gb|FL110175.1|FL110175
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211102904|gb|FK962285.1|FK962285
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211118861|gb|FL110176.1|FL110176
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211118854|gb|FL110169.1|FL110169
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCNCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|76012394|gb|DT939564.1|DT939564
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211118858|gb|FL110173.1|FL110173
EST:     TCACCGGGCGCCG-CGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211102910|gb|FK962291.1|FK962291
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211118856|gb|FL110171.1|FL110171
EST:     TCACCGGGCGCCGCCGCAYCGTGCCGCCCGCACCTGCCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211118859|gb|FL110174.1|FL110174
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211102909|gb|FK962290.1|FK962290
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGASGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211102911|gb|FK962292.1|FK962292
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGSACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|148939988|gb|EC884719.2|EC884719
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|74244670|gb|DT652584.1|DT652584
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|50328543|gb|CO523669.1|CO523669
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGGCTGCAG                   
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACG---A--C--CAGgtagggttgg ... tggg
EST: gi|211102902|gb|FK962283.1|FK962283
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|71428020|gb|DR809070.1|DR809070
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
EST: gi|211102903|gb|FK962284.1|FK962284
EST:     CACCGGGCGCCGSCGCATCGTGCCGCCMGCACCTGGCTCCGACGAACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCACA
genomic: CACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGA-CCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCA
EST: gi|211118857|gb|FL110172.1|FL110172
EST:     TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAG                         AGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG
genomic: TCACCGGGCGCCGCCGCATCGTGCCGCCCGCACCTGGCTCCGACGACCAGgtagggttgg ... tgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatttccttttgttttgtgcgtgtgatgagttggtttgttcgtttgggctgcagAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA
 ttctgat  putative branch site (score: 3)
                                       ttcgttt  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