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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacaccacttcgttgtttgcatcaataatattgttttactcaaattgatatatcttttttttacaaaaaatgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAA

Basic information

species Zea mays
transcript GRMZM2G452529_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G452529_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g55360.1 (Oryza sativa), 3'ss of exon 9
-------------------gtatacaccacttcgttgtttgcatcaataatattgttttactcaaattgatatatcttttttttacaaaaaatgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAA
                   |  | | |    |   |  ||| |  |   | | |||  |  |   |||  | |   |   | ||   |     |||||||||||| ||||||||||||||||||||||| ||||||||| ||||||||||||| 
gtaagcagtgcctccttttgcttcctcgggattacttcttgaagtatggaaactgtactgtttttatttctgttgatcactcttttgatgtg-gtagGATTTTGGAGACAGCATACCTGGGCATGGTGGGATTACTGACCGAATGGATTGTCAG

upper sequence: GRMZM2G452529_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA14G02210.1 (Glycine max), 3'ss of exon 7
-----------------------------------gtatacaccacttcgttgtttgcatcaataatattgttttactcaaattgata-tatcttttttttacaaaaaatgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAA
                                   | || || ||  || || ||    ||| |   |   |   |  || |   |||  ||   | | ||  ||  | |  |||| |||||||| || |||||||| ||||||||| |||| ||||||||||| || || 
gtatgttcttgctctttatactagacatttattttgcatccatca--tcctttttccattcactttgaaactcccaaacatagcaatagcattgatctctttgaatgattacagGACTTTGGTGATAGTATACCTGGACATGGTGGATTTACAGACAGAATGGACTGCCAG

upper sequence: GRMZM2G452529_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA10G32660.2 (Glycine max), 3'ss of exon 9
-------------------gtatacaccacttcgttgtttgcatcaataatattgttttactcaaattgatatatctttttt-----ttacaaaaaatgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAA
                   || |     |    | |||  |||   |||||    |||   |||  | || | |   ||  |     || | |    || |||| |||||||| || || || || |||||||||||||| |||||||||||||| || 
gtatgttctcaaaacttatgtttttctaatcaggatgtgagcaaatataat-ccatttaggtcaggtagaaacagacttgctgtgtgtttccatttttgcagGACTTTGGTGATAGTATTCCGGGACATGGTGGAATTACCGACAGAATGGATTGCCAG

upper sequence: GRMZM2G452529_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA02G46440.1 (Glycine max), 3'ss of exon 9
-----------------------------------gtatacaccacttcgttgtttgcatcaataatattgttttactcaaattgatatatcttttttttacaaaaaatgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAA
                                   |||  || |||    ||        |  | | | |     ||  |   |     |||  | | || |||  | |  |||| ||||||||||| |||||||| ||||||||| |||| ||||||||||| || || 
gtctgttcttgctctttatacaagacatttattttgtacccatcaccctttttccattcactttgaaactcccaaacatagcatatagcatcgatctctttcaatgattacagGACTTTGGTGACAGTATACCTGGACATGGTGGATTTACAGACAGAATGGACTGCCAG

upper sequence: GRMZM2G452529_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 9
gtatacacc----acttcgttgtttgca---------tcaataatattgttttactcaaattgatatatctttttt---ttacaaaaaatgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAA
|||| | |     |||||  | |||| |         | |  ||   |  |  | | |  |  | | |   ||  |   || | |    || ||||||||||||| || || || || |||||||||||||| |||||||||||||| || 
gtatgctctcaaaacttctgtttttgtaatcaggaagtgagcaaatataatccatttaggtataaacagacttgctgtgttcccatttttgcagGATTTTGGTGATAGTATTCCAGGACATGGTGGAATTACCGACAGAATGGATTGCCAG

upper sequence: GRMZM2G452529_T02 (Zea mays), 3'ss of exon 9
lower sequence: AT4G26770.1 (Arabidopsis thaliana), 3'ss of exon 8
--gtatacaccacttcgttgtttgcatcaataatattgttttactcaaattgatatatcttttt-tttacaaaaaat--gtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAA
    | |||    |      ||   |    |  |||      |  |||    | |||| |  |  ||||       |    ||||||| || ||||||||||| || ||||| ||| ||||||||||||||||||| |||
gttaacacatttttcaaacattaaaaggttttgtatctacagatccaagaacaaatatttactagtttatgtcgctttgacagGATTTCGGAGACAGCATACCAGGACATGGAGGATTTACTGACAGAATGGATTGCCAA

upper sequence: GRMZM2G452529_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv19s0090g01220.t01 (Vitis vinifera), 3'ss of exon 8
-------------------------------gtatacaccacttcgttgtttgcatcaataatattgttttactcaaattgat-----atatcttttttttacaaaaaatgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAA
                                  || || | |  |   |  || ||  ||        | ||   |||  ||     |||    ||| |   ||    |  |||||||||| || || || ||||| |||||||||||||| ||||||||||||||||| 
gtccacccttgttttaaacacagttgcttaaagttatactaatgtgaaatgagc-tccctatctccacctcacaacaataaattaaaaataaggatttctctgaatttttacagGATTTTGGAGATAGTATTCCTGGACATGGTGGAATTACAGACAGAATGGATTGTCAG

upper sequence: GRMZM2G452529_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv00s0187g00380.t01 (Vitis vinifera), 3'ss of exon 9
----------------------gtatacaccacttcgttgtttgcatcaataatattgtt-ttactcaaattgata------tatcttttttttacaaaaaatgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAA
                       ||   |     |  |  | |||||  | |   |   | ||  | | | || |       ||| | |||||   |     |  |||| ||||| || || || ||||| || |||||||||||||| |||||||||||||| 
gttcactctggttattgttgacttagttaagtgatgctgatatgcatggaaagcttcactgttgttgacactgttggttttttatttctttttccgatttgttacagGACTTTGGCGATAGTATTCCTGGACACGGTGGAATTACTGATAGAATGGATTGTCAG

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|5871566|gb|AW018037.1|AW018037
EST:     CATTTGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTTAAAATTAAG                         GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGAT
genomic: CATTTGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTTAAAATTAAGgtatacacca ... aaaaatgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGAT
EST: gi|60348342|gb|DN215315.1|DN215315
EST:     CATTTGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTTAAAATTAAG                         GATTTTGGTGTCAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGAT
genomic: CATTTGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTTAAAATTAAGgtatacacca ... aaaaatgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGAT
EST: gi|4646646|gb|AI491480.2|AI491480
EST:     TGGCTTCAAAAGGGCTTTTAAAATTAAG                         GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGAT
genomic: TGGCTTCAAGAGGGCTTTTAAAATTAAGgtatacacca ... aaaaatgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGAT
EST: gi|88753935|gb|DY538076.1|DY538076
EST:     CATTTGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTTAAAATTAAG                         GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGAT
genomic: CATTTGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTTAAAATTAAGgtatacacca ... aaaaatgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGAT
EST: gi|6031444|gb|AW076346.1|AW076346
EST:     CATTTGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTTAAAATTAAG                         GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGAT
genomic: CATTTGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTTAAAATTAAGgtatacacca ... aaaaatgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGAT
EST: gi|78021196|gb|DV489583.1|DV489583
EST:     CATTTGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTTAAAATTAAG                         GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGAT
genomic: CATTTGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTTAAAATTAAGgtatacacca ... aaaaatgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGAT
EST: gi|5915325|gb|AW052966.1|AW052966
EST:     CCTTTGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTTAAAATTAAG                         GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGAT
genomic: CATTTGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTTAAAATTAAGgtatacacca ... aaaaatgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGAT
EST: gi|78023335|gb|DV491722.1|DV491722
EST:     CATTTGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTTAAAATTAAG                         GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGAT
genomic: CATTTGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTTAAAATTAAGgtatacacca ... aaaaatgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGAT
EST: gi|166480375|gb|EG306412.1|EG306412
EST:     ATTTGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTTAAAATTAAG                         GATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGAT
genomic: ATTTGGAGGATTTTTTGCGAGTGGCTTCAAGAGGGCTTTTAAAATTAAGgtatacacca ... aaaaatgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaataatattgttttactcaaattgatatatcttttttttacaaaaaatgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAA
                      aattgat  putative branch site (score: 4)
     taatattgttttactc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacaccacttcgttgtttgcatcaataatattgttttactcaaattgatatatcttttttttacaaaaaatgtagGATTTTGGTGACAGCATACCTGGGCATGGTGGAATTACTGACAGAATGGATTGTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA