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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAGCAGTCATGCTACGGAGAAAATTTTATCCAGCTGCTATCAAATATCTGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAGgttagctatgctcaactgtttggtaacattttcttcattttggagtctagccaactactttgtttttctcttgttgaattaatcgatataagttgtagaa...

Basic information

species Zea mays
transcript GRMZM5G809292_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G809292_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os10g32300.1 (Oryza sativa), 5'ss of exon 5
TGGAGCAGTCATGCTACGGAGAAAATTTTATCCAGCTGCTATCAAATATCTGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAGgttagctatgctcaactgtttggtaacattttcttcattttggagtctagccaactactttgtttttctcttgttgaattaatcgatataagttgtagaa---
|||||||||||||||||||||||||||||| || ||||||||||||||||| |||||||||||  | |||||||| || || |||||||||||||| ||||| || ||| ||||||  |    || | |    |  |      ||  |  |  |||   || |  |  |     |  |  ||| |||    |||| | ||   
TGGAGCAGTCATGCTACGGAGAAAATTTTACCCTGCTGCTATCAAATATCTACAGCAAGCAATCCAAAAATGGGATAGGGATGAGCAAGATCTTGCACAGgtcagatatcctcaac-atacaatatcctgaaatctagccaatagaatt-cttactgtcttatcatgtttcatatctacaaattgatgct-gttgcaaaaaga

upper sequence: GRMZM5G809292_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv18s0072g00860.t01 (Vitis vinifera), 5'ss of exon 5
TGGAGCAGTCATGCTACGGAGAAAATTTTATCCAGCTGCTATCAAATATCTGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAGgttagctatgctcaactgtttggtaacattttcttcattttggagtctagcca-actactttgtttttctcttgttgaattaatcgatataagttgtagaa
||||||||| ||| | ||||| |||||||||||||||||||  ||||   |||  || |||||||| ||||||||  |||| || ||||||||||| |||||  ||||  |||       | |  |   |     ||    | |||   |    || | ||     | | | || | | |||||   |     |  ||  |
TGGAGCAGTGATGTTGCGGAGGAAATTTTATCCAGCTGCTACTAAATTCTTGCTTCAGGCAATTGAGAAATGGGATGGAGATGATCAAGATCTTGCCCAGgtatgctagtctcttggaccttgatattctacaaacagacagaagtaatgtgggaccatttgcaaatgcacatgct-acttaatgtgttgccttaatatta
















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|211528640|gb|FL444106.1|FL444106
EST:     TGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAG                         GTCTACAATGCCCTGGGGGTCAGCTACAAGCGAGAGAACAAACTTGACAAG
genomic: TGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAGgttagctatg ... tgttggtaagGTCTACAATGCCCTGGGGGTCAGCTACAAGCGAGAGAACAAACTTGACAAG
EST: gi|71301886|gb|DR787012.1|DR787012
EST:     TGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAG                         GTCTACAATGCCCTGNGGGTCAGCTACAAGCGAGAGAACAAACTTGACAAG
genomic: TGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAGgttagctatg ... tgttggtaagGTCTACAATGCCCTGGGGGTCAGCTACAAGCGAGAGAACAAACTTGACAAG
EST: gi|76281110|gb|DV020678.1|DV020678
EST:     TGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAG                         GTCTACAATGCCCTGGGGGTCAGCTACAAGCGAGAGAACAAACTTGACAAG
genomic: TGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAGgttagctatg ... tgttggtaagGTCTACAATGCCCTGGGGGTCAGCTACAAGCGAGAGAACAAACTTGACAAG
EST: gi|211407779|gb|FL477834.1|FL477834
EST:     TGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAG                         GTCTACAATGCCCTGGGGGTCAGCTACAAGCGAGAGAACAAACTTGACAAG
genomic: TGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAGgttagctatg ... tgttggtaagGTCTACAATGCCCTGGGGGTCAGCTACAAGCGAGAGAACAAACTTGACAAG
EST: gi|32865446|gb|CF005128.1|CF005128
EST:     TGCAGCAAGCAATTGACAAATGGGTCAGAGACGAGCAAGATCTTGCGCAG                         GTCTACAATGCCCTGGGGGTCAGCTACAAGCGAGAGAACAAACTTGCCAAG
genomic: TGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAGgttagctatg ... tgttggtaagGTCTACAATGCCCTGGGGGTCAGCTACAAGCGAGAGAACAAACTTGACAAG
EST: gi|91872953|gb|EB402910.1|EB402910
EST:     TGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAG                         GTCTACAATGCCCTGGGGGTCAGCTACAAGCGAGAGAACAAACTTGACAAG
genomic: TGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAGgttagctatg ... tgttggtaagGTCTACAATGCCCTGGGGGTCAGCTACAAGCGAGAGAACAAACTTGACAAG
EST: gi|71766161|gb|DR964098.1|DR964098
EST:     TGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAG                         GTCTACAATGCCCTGNGGGTCAGCTACAAGCGAGAGAACAAACTTGACAAG
genomic: TGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAGgttagctatg ... tgttggtaagGTCTACAATGCCCTGGGGGTCAGCTACAAGCGAGAGAACAAACTTGACAAG
EST: gi|211491317|gb|FL191819.1|FL191819
EST:     TGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAG                         GTCTACAATGCCCTGGGGGGTCAGCTAC
genomic: TGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAGgttagctatg ... tgttggtaagGTCTACAATGCCCTGGGGG-TCAGCTAC
EST: gi|78087661|gb|DV516054.1|DV516054
EST:     TGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAG                         GTCTACAATGCCCTGNGGGTCAGCTACAAGCGAGAGAACAA-CTTGACAAG
genomic: TGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAGgttagctatg ... tgttggtaagGTCTACAATGCCCTGGGGGTCAGCTACAAGCGAGAGAACAAACTTGACAAG
EST: gi|76916193|gb|DV166281.1|DV166281
EST:     TGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAG                         GTCTACAATGCCCTGGGGGTCAGCTACAAGCGAGAGAACAAACTTGACAAG
genomic: TGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAGgttagctatg ... tgttggtaagGTCTACAATGCCCTGGGGGTCAGCTACAAGCGAGAGAACAAACTTGACAAG
EST: gi|45847367|gb|CN071310.1|CN071310
EST:     TGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAG                         GTCTACAATGCC-TGGGGGTCAGCTACAAGCGAGAGAACAAACTTGACAAG
genomic: TGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAGgttagctatg ... tgttggtaagGTCTACAATGCCCTGGGGGTCAGCTACAAGCGAGAGAACAAACTTGACAAG
EST: gi|211407780|gb|FL477835.1|FL477835
EST:     TGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAG                         GTCTACAATGCCCTGGGGGTCAGCTACAAGCGAGAGAACAAACTTGACAAG
genomic: TGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAGgttagctatg ... tgttggtaagGTCTACAATGCCCTGGGGGTCAGCTACAAGCGAGAGAACAAACTTGACAAG

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGAGCAGTCATGCTACGGAGAAAATTTTATCCAGCTGCTATCAAATATCTGCAGCAAGCAATTGACAAATGGGACAGAGACGAGCAAGATCTTGCGCAGgttagctatgctcaactgtttggtaacattttcttcattttggagtctagccaactactttgtttttctcttgttgaattaatcgatataagttgtagaa

- - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA