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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGACAAAAACCGGATAAGCATGAGCCGACAGCCCCAATATGTTGTGCAGGGAAGGTTTCAGAGGATCAATCAACATCCAgtaatgtttccatctctttttctatcttgttctcatttgctaacattggatcaagtttttgacacgccccctacacag

Basic information

species Zea mays
transcript GRMZM2G412911_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G412911_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g18730.1 (Oryza sativa), 5'ss of exon 10
TCTGACAAAAACCGGATAAGCATGAGCCGACAGCCCCAATATGTTGTGCAGGGAAGGTTTCAGAGGATCAATCAACATCCAgtaatgtttccatctctttttctatcttgttctcatttgctaacattggatcaagtttttgacacgc-cccctacacag
| ||||||||  |||||   ||  |||| || ||||| |||| ||||| | ||||| ||||||||||| |||||||||||||||   |||||||| | | |  ||  ||| |||| || |||||  |||||| ||| || | |  |   |||||| |   
TATGACAAAAGACGGATCGACAACAGCCAACTGCCCCTATATATTGTGGAAGGAAGATTTCAGAGGATTAATCAACATCCAgta-catttccatcgcctctcttacattgctctcgtt-gctaatgttggataaagcttctaatgcatgcccctatag--

upper sequence: GRMZM2G412911_T03 (Zea mays), 5'ss of exon 4
lower sequence: AT4G11720.1 (Arabidopsis thaliana), 5'ss of exon 9
TCTGACAAAAACCGGATAAGCATGAGCCGACAGCCCCAATATGTTGTGCAGGGAAGGTTTCAGAGGATCAATCAACATCCAgtaatgtttccatctctttttctatcttgttct-catttgctaacattgg--atcaagtttttgacacgccccctacacag-----
|| || | |||| | ||   |     || ||  ||   |||||   |  | ||||| ||| |||||||||||||||||||||| |||||      | |  |  | |||   ||   ||  | ||| |||     |    || | |       |  |||||       
TCAGATATAAACAGAATCGACCGACACCAACTTCCTTTATATGGACTTGAAGGAAGATTTGAGAGGATCAATCAACATCCAgttatgttctagcttttactagtttctaaatcaatataagataagattttctgttggcttatcggattatgctttacacgatacag
















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|74243362|gb|DT651276.1|DT651276
EST:     AGCCCCAATATGTTGTGCAGGGAAGGTTTCAGAGGATCAATCAACATCCA                         GATGCAAGTGTTCATTCTTTTTCTATTGGAGTGACAGAAGTTATTAATAGC
genomic: AGCCCCAATATGTTGTGCAGGGAAGGTTTCAGAGGATCAATCAACATCCAgtaatgtttc ... ccctacacagGATGCAAGTGTTCATTCTTTTTCTATTGGAGTGACAGAAGTTATTAATAGC
EST: gi|26457309|gb|CA828892.1|CA828892
EST:     AGCCCCAATATGTTGTGCAGGGAAGGTTTCAGAGGATCAATCAACATCCA                         GATGCAAGTGTTCATTCTTTTTCTATTGGAGTGACAGAAGTTATTAATAGC
genomic: AGCCCCAATATGTTGTGCAGGGAAGGTTTCAGAGGATCAATCAACATCCAgtaatgtttc ... ccctacacagGATGCAAGTGTTCATTCTTTTTCTATTGGAGTGACAGAAGTTATTAATAGC
EST: gi|76915075|gb|DV165808.1|DV165808
EST:     AGCCCCAATATGTTGTGCAGGGAAGGTTTCAGAGGATCAATCAACATCCA                         GATGCAAGTGTTCATTCTTTTTCTATTGGAGTGACAGAAGTTATTAATAGC
genomic: AGCCCCAATATGTTGTGCAGGGAAGGTTTCAGAGGATCAATCAACATCCAgtaatgtttc ... ccctacacagGATGCAAGTGTTCATTCTTTTTCTATTGGAGTGACAGAAGTTATTAATAGC
EST: gi|76936583|gb|DV174787.1|DV174787
EST:     AGCCCCAATATGTTGTGCAGGGAAGGTTTCAGAGGATCAATCAACATCCA                         GATGCAAGTGTTCATTCTTTTTCTATTGGAGTGACAGAAGTTATTAATAGC
genomic: AGCCCCAATATGTTGTGCAGGGAAGGTTTCAGAGGATCAATCAACATCCAgtaatgtttc ... ccctacacagGATGCAAGTGTTCATTCTTTTTCTATTGGAGTGACAGAAGTTATTAATAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGACAAAAACCGGATAAGCATGAGCCGACAGCCCCAATATGTTGTGCAGGGAAGGTTTCAGAGGATCAATCAACATCCAgtaatgtttccatctctttttctatcttgttctcatttgctaacattggatcaagtttttgacacgccccctacacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT