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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtacattcttctagactaacatgtttgctcttgttactcgtgttaatactaatatggtcgcagTACCGCAACATGACAACTGTATTGACAAGGGAATACTTGGATGTGAGGCCGGATGGATGGTTGGATTATGCAGCTAAAAGGATCGCACAGCT

Basic information

species Zea mays
transcript GRMZM2G119791_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119791_T07 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g36420.1 (Oryza sativa), 3'ss of exon 4
gttagtacattcttc--------tagactaacatgtttgctcttgt---tact--cgtgttaatactaatatggtcgcagTACCGCAACATGACAACTGTATTGACAAGGGAATACTTGGATGTGAGGCCGGATGGATGGTTGGATTATGCAGCTAAAAGGATCGCACAGCT
||||||||||  ||         |  | || | |||||  |    |   ||||   |||||||| |||||||| |  |||||||| |||||||| ||||| ||||||||||| ||||| |||||| | || ||||| ||||||||||||||||| |||||||| ||||||||
gttagtacatggtttatgaattatgaaatagcgtgtttattagaatatatacttatgtgttaatgctaatatgatgccagTACCGTAACATGACGACTGTGTTGACAAGGGAGTACTTAGATGTGCGACCTGATGGGTGGTTGGATTATGCAGCCAAAAGGATTGCACAGCT

upper sequence: GRMZM2G119791_T07 (Zea mays), 3'ss of exon 4
lower sequence: AT1G08660.1 (Arabidopsis thaliana), 3'ss of exon 4
gttagtacattcttcta-----gactaacatgtttgctcttgttactcgtgttaatactaatat-----ggt--cgcagTACCGCAACATGACAACTGTATTGACAAGGGAATACTTGGATGTGAGGCCGGATGGATGGTTGGATTATGCAGCTAAAAGGATCGCACAGCT
||| || | |  ||||      || ||   | | |  | ||   |||  |   ||| ||||| |     |||   |||||||||||| ||||| || ||||||||||| |||||| | |||||  | || ||||| |||||||| || |||||||  || || |||||| |
gtttgtgcttctttctttctctgattagtttttcttgttttagaacttctcgcaattctaatgtttctgggtaatgcagTACCGCAATATGACTACAGTATTGACAAGAGAATACCTCGATGTACGCCCTGATGGGTGGTTGGACTACGCAGCTATGAGAATTGCACAGTT
















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|148936990|gb|EC881159.2|EC881159
EST:     CTCTAGAATACAAATATGATGTCTGTGAAACTATCCTATTGTGGGAACAG                         TACCGCAACATGACAACTGTATTGACAAGGGAATACTTGGATGTGAGGCCG
genomic: CTCTAGAATACAAATATGATGTCTGTGAAACTATCCTATTGTGGGAACAGgttagtacat ... atggtcgcagTACCGCAACATGACAACTGTATTGACAAGGGAATACTTGGATGTGAGGCCG
EST: gi|78092057|gb|DV520431.1|DV520431
EST:     CTCTAGAATACAAATATGATGTCTGTGAAACTATCCTATTGTGGGAACAG                         TACCGCAACATGACAACTGTATTGACAAGGGAATACTTGGATGTGAGGCCG
genomic: CTCTAGAATACAAATATGATGTCTGTGAAACTATCCTATTGTGGGAACAGgttagtacat ... atggtcgcagTACCGCAACATGACAACTGTATTGACAAGGGAATACTTGGATGTGAGGCCG
EST: gi|211356321|gb|FL081349.1|FL081349
EST:     CTCTAGAATACAAATATGATGTCTGTGAAACTATCCTATTGTGGGAACAG                         TACCGCAACATGA
genomic: CTCTAGAATACAAATATGATGTCTGTGAAACTATCCTATTGTGGGAACAGgttagtacat ... atggtcgcagTACCGCAACATGA
EST: gi|149080539|gb|EE169577.2|EE169577
EST:     CTCTAGAATACAAATATGATGTCTGTGAAACTATCCTATTGTGGGAACAG                         TACCGCAACATGACAACTGTATTGACAAGGGAATACTTGGATGTGAGGCCG
genomic: CTCTAGAATACAAATATGATGTCTGTGAAACTATCCTATTGTGGGAACAGgttagtacat ... atggtcgcagTACCGCAACATGACAACTGTATTGACAAGGGAATACTTGGATGTGAGGCCG
EST: gi|76288008|gb|DV027576.1|DV027576
EST:     CTCTAGAATACAAATATGATGTCTGTGAAACTATCCTATTGTGGGAACAG                         TACCGCAACATGACAACTGTATTGACAAGGGAATACTTGGATGTGAGGCCG
genomic: CTCTAGAATACAAATATGATGTCTGTGAAACTATCCTATTGTGGGAACAGgttagtacat ... atggtcgcagTACCGCAACATGACAACTGTATTGACAAGGGAATACTTGGATGTGAGGCCG
EST: gi|149082841|gb|EE172066.2|EE172066
EST:     CTCTACAATACAAATATGATGTCTGTGAAACTATCCTATTGTGGGAACAG                         TACCGCAACATGACAACTGTATTGACAAGGGAATACTTGAATGTGACGCCG
genomic: CTCTAGAATACAAATATGATGTCTGTGAAACTATCCTATTGTGGGAACAGgttagtacat ... atggtcgcagTACCGCAACATGACAACTGTATTGACAAGGGAATACTTGGATGTGAGGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctagactaacatgtttgctcttgttactcgtgttaatactaatatggtcgcagTACCGCAACATGACAACTGTATTGACAAGGGAATACTTGGATGTGAGGCCGGATGGATGGTTGGATTATGCAGCTAAAAGGATCGCACAGCT
                                      tactaat  putative branch site (score: 1)
                                tgttaatactaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtacattcttctagactaacatgtttgctcttgttactcgtgttaatactaatatggtcgcagTACCGCAACATGACAACTGTATTGACAAGGGAATACTTGGATGTGAGGCCGGATGGATGGTTGGATTATGCAGCTAAAAGGATCGCACAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT