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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCAGAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgctcagaaatactgggcataatatggtttcaagaattgcaattcatttgcttttgtgaaaacactcaatggcaattggccatgctctgaaatt...

Basic information

species Zea mays
transcript GRMZM5G841900_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G841900_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g57070.1 (Oryza sativa), 5'ss of exon 2
GCTGCAGAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgctcagaaatactgggcat-aatatggttt-caagaattgc-aattcatttgcttttgtgaaaacactcaatggcaattggccatgctctgaaatt
       || ||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| || || |||||||           |    | |   | ||  |     ||  ||  || |  || |||| |      | || |  | | | || |    | | |||    
-------AGGTCCACGGTGGAGGTGGTCGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATTGCGCGTgtaagatctatctctgagcaaaccgttggtttgactcgtgtgacctgtgaaattgttagcttattgttgtataccctgttg-attttgtgtggatgtgacg--
















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:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|50328543|gb|CO523669.1|CO523669
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|211118861|gb|FL110176.1|FL110176
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|76012394|gb|DT939564.1|DT939564
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|32796285|gb|CD948521.1|CD948521
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|74244670|gb|DT652584.1|DT652584
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|71428020|gb|DR809070.1|DR809070
EST:     ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: ACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
EST: gi|6827420|gb|AW331063.1|AW331063
EST:     GCCGGGAAGCGTCGTCATCGCCCGA                         GTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC
genomic: GCCGGGAAGCGTCGTCATCGCCCGAgtaagatgct ... acttttgcagGTAACAAAGGTTATGGCTAGAATGGCCTCTGCAGATATCATGTGTGTTGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCAGAGATCCACGGTGGAGGTGGTGGGGCACAAGGCCCATGGAGCTGTGCCGCAGCCGGGAAGCGTCGTCATCGCCCGAgtaagatgctcagaaatactgggcataatatggtttcaagaattgcaattcatttgcttttgtgaaaacactcaatggcaattggccatgctctgaaatt

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