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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccctcgcgctgaatcccggttgctcttctctctccctgcctcccgtgctgatggtgcacgctcctgattctgatctagatgttgtggggtgga...

Basic information

species Zea mays
transcript GRMZM2G053764_T04
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053764_T02 (Zea mays), 5'ss of exon 2
lower sequence: AT1G63800.1 (Arabidopsis thaliana), 5'ss of exon 2
GATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaa-tagccc---tcgcgctg-----------aatcccgg----ttgctcttctctctccctgcctcccgtgctgatggtgcacgctcctgattctgatctagatgttgtggggtgga-------------------------------------------------------
||||||||| ||||||||||| |||||| | || ||||| ||||| || ||||| ||||||||||  || ||    || ||||| || | |   |||  | |           ||||   |    ||| |  | | | | | ||       |||||||| ||  |      |  | |  | |  || |       |                                                          
GATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACAgtaagtaactcaattcgtcccgtgaataatttaaatcatagagttttgattctgttttttcttgttcttgctgctgatgatgatcatcatagggttttgtgtcaatttcaacttatcagtatcaacttgttaatttttggtgattttatctctgtgtgtttgtactatggacag

upper sequence: GRMZM2G053764_T02 (Zea mays), 5'ss of exon 2
lower sequence: PP1S37_166V6.1 (Physcomitrella patens), 5'ss of exon 2
GATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccctcgcgctgaatcccggttgctcttctctctccctg-cctcccgtgctgatggtgcacgctcc-tgattctgatctagatgttgtggggtgga-
||||||||| ||||||||||||||||||||||| ||||| |||   |||||||  || || ||  | || |||   || ||||       ||        |     |  ||| | ||| |  | | ||    | |    |  | |  | |   | |  | | |   || | ||  |   |   
GATGATGAGTGACTACAAGGTCGAGATGGTGAATGATGGAATGAGCGAATTCTATGTGGAGTTTCATGGACCGCGTGAGAgtacgttttttcatttc---ttaaattcactcctttctgttgcggaccgtatgcgtaactatttcgagttgtgtaaggccgtttgtgaagctgatgctcgatg

upper sequence: GRMZM2G053764_T02 (Zea mays), 5'ss of exon 2
lower sequence: EFJ34378 (Selaginella moellendorffii), 5'ss of exon 2
GATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccctcgcgctgaatcc--cggttgctcttctctctccctgcctcccgtgctgatggtgcacgctcctgattctgatctagatgttgtggggtgga
||||||||| ||||||||||| |||||||| |||||||||||| | || ||    || || ||| | || ||    || |||||   ||  | | |||    |  |  || ||||| |||| |  ||  |  |||||   ||   | | |  ||  || |||   |||  ||      ||  
GATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATAgtaa-gtcctccacactgccctcttctcttcctcttgtctccctgtggttttcgtgcctctgtgtctctcggcttgtt-tgaaagagagatttcttcttgtt

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|12968800|gb|BG265836.1|BG265836
EST:     GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
EST: gi|5895766|gb|AW037012.1|AW037012
EST:     GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
EST: gi|6022600|gb|AW067412.1|AW067412
EST:     GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
EST: gi|5713918|gb|AI943903.1|AI943903
EST:     GATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: GATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
EST: gi|5895785|gb|AW037031.1|AW037031
EST:     GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
EST: gi|60355446|gb|DN222419.1|DN222419
EST:     GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
EST: gi|5649980|gb|AI920340.1|AI920340
EST:     TCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: TCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
EST: gi|71328419|gb|DR800850.1|DR800850
EST:     GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
EST: gi|87156694|gb|DY401483.1|DY401483
EST:     GGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: GGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
EST: gi|5895786|gb|AW037032.1|AW037032
EST:     GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
EST: gi|5917370|gb|AW054161.1|AW054161
EST:     GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
EST: gi|22715330|gb|BU197707.1|BU197707
EST:     GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
EST: gi|211363205|gb|FL271919.1|FL271919
EST:     GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA                         GTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT
genomic: GAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccc ... aatttggtagGTATCTACCAAGGCGGTGTCTGGAAGGTTAGGGTAGAACTGCCTGATGCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAgtaatagccctcgcgctgaatcccggttgctcttctctctccctgcctcccgtgctgatggtgcacgctcctgattctgatctagatgttgtggggtgga

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