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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCgtaagtttacagtgaacatatattttgtactggatcctggcactttgtcaatgtcacaggaattagctcttccctcttgcatacaccatgtgttacacaattagactgatgtcaccaaatatactgttaatgcag

Basic information

species Zea mays
transcript GRMZM2G069765_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069765_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 5'ss of exon 7
CATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCgtaagtttacagtgaacatatattttgtactggatcctggcactttgtcaatgtcacaggaattagctcttccctcttgcatacaccatgtgttacacaattagactgatgtcaccaaatatactgttaatgcag
|||| |||||||| ||||| |||||| | ||||| ||||||||||||||||||  |||||| |||||||| ||||||| ||     | | |||      |||   ||  ||  | |||   | | |   || |  ||  | |   ||  ||  |      | ||||||   ||| || |||         || |||  | |||||||
CATACACCAAAGCTCTTGAGGATGCTTTAGCTGTCCTTGACAAAATTGCAATGCATGTTGACGTGAATGACCgtaagtatatgtcaagcttat------tac-aaatattgcaaattt--tagt-ttggagaatctatgtatcgtcttctgtgtt-----tttgttac-tgatttgagtga--------gatgtaccat-aatgcag

upper sequence: GRMZM2G069765_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA16G33380.1 (Glycine max), 5'ss of exon 8
CATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCgtaagtttacagtgaacatatattttgtactggatcctggcactttgtcaatgtcacaggaattagctcttccctcttgcatacaccatgtgttacacaattagactgatgtcaccaaatatactgttaatgcag
||||| |||||||  | || |||||||||||||| |||||||||||||||||| || |  |||   | ||||||||||||          |||      | |||| |  | | || || |   | | | |  ||||    ||| |  |    |      |     | |||| |    ||||       ||  |              
CATATGCCAAAGCTTTGGAGGATGCTATTGCTGTTCTTGACAAAATTGCAATGCCTATCAATGCTCAGGATCgtaagttt----------tat------tgctggtt--tagtaccttattg-tattaaaaaaatt----cttgctcccaataataggaagaaagttcacagtcg--ctgacaatttaaagcaagac----------

upper sequence: GRMZM2G069765_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA09G28650.1 (Glycine max), 5'ss of exon 8
CATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCgtaagttt-acagtgaacata----tattttgtactggatcctggcactttgtcaatgtcacaggaattagct--cttccctcttgcatacaccatgtgttacacaattagactgatgtcaccaaatatactgttaatgcag
|||||| ||||||  | || |||||||||||||| |||||||||||||||||| || ||||||   | |||||||||||| |  |      ||      ||||||  |  |   |  |    |  |||| | |    ||  |  |  |   | | ||| |   |   || ||                                          
CATATAACAAAGCTTTGGAGGATGCTATTGCTGTCCTTGACAAAATTGCAATGCCTATTGATGCTCAGGATCgtaagttttattgctggtttagtacctttttgtgttaaaaattt-cttcctcccaatattaggaaaaaaaatttacactcattttgaagcaagactgagtc-----------------------------------------

upper sequence: GRMZM2G069765_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA20G35760.1 (Glycine max), 5'ss of exon 5
CATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCgtaagttt-acagtgaacatatattttgtactggatcctggcactttgtcaatgtcacaggaattagctcttccctcttgcatacaccatgtgttacacaattagactgatgtcaccaaatatactgttaatgcag
| |||  ||||||  | || ||||| |||||||| |||||||||||||| ||| | |||||||  |||||||||||||||    |  |       |||| |  |   || |  || ||| |    ||    |    || |   ||| | |   || |   |||  || || ||                                   
CTTATGACAAAGCTTTGGAGGATGCCATTGCTGTCCTTGACAAAATTGCTATGCCCGTTGATGCCAATGATCgtaagttttgttgctatttctctttttctttttattcttctcattttttaggagtgcaggagggtaaca--tccttttcttattccttatgatttgcagaaa----------------------------------

upper sequence: GRMZM2G069765_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv07s0130g00410.t01 (Vitis vinifera), 5'ss of exon 7
CATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCgtaagtttacagtgaacatatattttgtactggatcctggcactttgtcaatgtcacaggaattagctcttccctcttgcatacaccatgtgttacacaattagactgatgtcaccaaatatactgttaatgcag
|||| |  ||||| || || |||||||||||||| |||||||||||||||||| |  | |||||||| || ||| ||||    |   |||| |  | | | ||  || |  |   |  ||   || ||    ||||  |   ||  ||   || |||| |      ||| ||  | |                              
CATACAATAAAGCTCTGGAGGATGCTATTGCTGTGCTTGACAAAATTGCAATGTCCATAGATGTGAAGGACCgtgagttcctggactacatttcctctcttctacattc-agtgttacgtt--tgacatgctaatttccctctctttcacacacacac-acacaa-acataagcaca------------------------------

upper sequence: GRMZM2G069765_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv17s0000g08170.t01 (Vitis vinifera), 5'ss of exon 7
CATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCgtaagtttacagtgaacatatattttgtactggatcctggcactttgtcaatgtcacaggaattagctcttccctcttgcatacaccatgtgttacacaattagactgatgtcaccaaatatactgttaatgcag
| ||||  ||||| ||||| ||||||||||| || |||||||| ||||||    |||||||||||||||| |||||| ||    | |  |||| ||   | ||   |    ||||||  |     | |   || |||    ||| || |    |      |    |    |||||||   |                          
CTTATAATAAAGCTCTTGAGGATGCTATTGCGGTGCTTGACAAGATTGCAGCCCCTGTTGATGTGAATGACCgtaagctt----ttacaatat-ttcccttcttattttatgcacttcttt----ttatttgagttaaaatttctctttgtagtgtttatttacctgggtaattagaaata--------------------------

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|149105498|gb|EE291023.2|EE291023
EST:     TGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATC                         GTGGGGCAATGCTAGGCCTTGTGAAGAGCTCCATTGGTACGAAATTCACTG
genomic: TGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCgtaagtttac ... gttaatgcagGTGGGGCAATGCTAGGCCTTGTGAAGAGCTCCATTGGTACGAAATTCACTG
EST: gi|211229383|gb|FL136771.1|FL136771
EST:     GCTATTGCTGTACTTGACAAA-TTGNCA-TGGCTGTTGATGTGAATGATC                         GTGGGG-AATGCTAGGCCTTGTGAAGAGCTCCATTGGTACGAAAT-CACTG
genomic: GCTATTGCTGTACTTGACAAAATTG-CAATGGCTGTTGATGTGAATGATCgtaagtttac ... gttaatgcagGTGGGGCAATGCTAGGCCTTGTGAAGAGCTCCATTGGTACGAAATTCACTG
EST: gi|76014861|gb|DT942031.1|DT942031
EST:     TGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATC                         GTGGGGCAATGCTAGGCCTTGTGAAGAGCTCCATTGGTACGAAATTCACTG
genomic: TGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCgtaagtttac ... gttaatgcagGTGGGGCAATGCTAGGCCTTGTGAAGAGCTCCATTGGTACGAAATTCACTG
EST: gi|211229381|gb|FL136769.1|FL136769
EST:     GCTATTGCTGTACTTGACAAAAT-GCAATGGGTGGTGATGGTGA-TGATC                         GTGGGGCAATGCTAGG
genomic: GCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATG-TGAATGATCgtaagtttac ... gttaatgcagGTGGGGCAATGCTAGG
EST: gi|211229385|gb|FL136773.1|FL136773
EST:     TGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATC                         GTGGGGGCA-TGCTAGGCCTTGTGAAGAGCT
genomic: TGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCgtaagtttac ... gttaatgcagGTGGGG-CAATGCTAGGCCTTGTGAAGAGCT
EST: gi|211229394|gb|FL136782.1|FL136782
EST:     TGCTATTGCTGTACTTGACAAAAATGCAATGGCTGTTGATGTGAATGATC                         GTGGGGCAATGCTAGGCCCTTGTGAAGAGCTCCAT-GGNTACGAAAATCAC
genomic: TGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCgtaagtttac ... gttaatgcagGTGGGGCAATGCTAGGCC-TTGTGAAGAGCTCCATTGG-TACGAAATTCAC
EST: gi|211229386|gb|FL136774.1|FL136774
EST:     TGCTATTGCTGTACTTGACAAAAATGCAATGGCTGTTGATGTGAATGATC                         GTGGGGCAATGCTAGGCCCTTGTGAAGAGCTCCAT-GGNTACGAAAATCAC
genomic: TGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCgtaagtttac ... gttaatgcagGTGGGGCAATGCTAGGCC-TTGTGAAGAGCTCCATTGG-TACGAAATTCAC
EST: gi|31354522|gb|CD438879.1|CD438879
EST:     TGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATC                         GTGGGGCAATGCT
genomic: TGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCgtaagtttac ... gttaatgcagGTGGGGCAATGCT
EST: gi|22491149|gb|BU051072.1|BU051072
EST:     TGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATC                         GTGGGGCAATGCTAGGCCT
genomic: TGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCgtaagtttac ... gttaatgcagGTGGGGCAATGCTAGGCCT
EST: gi|87153647|gb|DY398436.1|DY398436
EST:     TGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATC                         GTGGGGCAATGCTAGGCCTTGTGAAGAGCTCCATTGGTACGAAATTCACTG
genomic: TGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCgtaagtttac ... gttaatgcagGTGGGGCAATGCTAGGCCTTGTGAAGAGCTCCATTGGTACGAAATTCACTG
EST: gi|211231450|gb|FL136786.1|FL136786
EST:     CTATTGCTGTACTTGACAAAAT-GCA-TGGGGCTGT-GATGTGAATGATC                         GTGGGGCAATGCTAGGCCTTGT
genomic: CTATTGCTGTACTTGACAAAATTGCAATGG--CTGTTGATGTGAATGATCgtaagtttac ... gttaatgcagGTGGGGCAATGCTAGGCCTTGT
EST: gi|149084479|gb|EE173941.2|EE173941
EST:     GCTATTGCTGTACTTTGACAAA-TTGCAATGGCTGTTGATGTGAATGATC                         GTGGGGCAATGCTAGGCCTTGTGAAGAGCTC-ATTGGTACGAAATT
genomic: GCTATTGCTGTACTT-GACAAAATTGCAATGGCTGTTGATGTGAATGATCgtaagtttac ... gttaatgcagGTGGGGCAATGCTAGGCCTTGTGAAGAGCTCCATTGGTACGAAATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATATACCAAAGCGCTTGATGATGCTATTGCTGTACTTGACAAAATTGCAATGGCTGTTGATGTGAATGATCgtaagtttacagtgaacatatattttgtactggatcctggcactttgtcaatgtcacaggaattagctcttccctcttgcatacaccatgtgttacacaattagactgatgtcaccaaatatactgttaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT