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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgccttctgtttagatttattattatttttcagtgttcatataatggcagctactgtattaaatagtgttgccgaaccatgtttcttacttgatggcagAAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCG

Basic information

species Zea mays
transcript GRMZM2G171745_T05
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171745_T05 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g30840.2 (Oryza sativa), 3'ss of exon 7
ctgccttctgtttagatttattattatttttcagtgttcatataatggcagctactgtattaaatagtgttgccgaaccatgtttcttacttgatggcagAAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCG---------
          |||||  |||  | |  |||| ||| |||||||| |   |  || || |          |||||| ||||||||||||||||||||||||||||| |||||||||||||||||||||| |||||||||||||||||||| |||||||||||| |||||||||||||||||||||||||||||||| ||||         
---------ttttagtatta--aatgcttttaagtattcatatagtattaaatagtgga---------attgccggaccatgtttcttacttgatggcagaagttgaacaatttaagcagGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAG

upper sequence: GRMZM2G171745_T05 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g30840.3 (Oryza sativa), 3'ss of exon 7
ctgccttctgtttagatttattattatttttcagtgttcatataatggcagctactgtattaaatagtg---ttgccgaaccatgtttcttacttgatggcagAAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCG
 || | | ||||    | |  | ||| | || | || |  ||      ||  ||  |||||||||||||   |||||| ||||||||||||||||||||||||||||| |||||||||||||||||||||| |||||||||||||||||||| |||||||||||| |||||||||||||||||||||||||||||||| ||||
-tgtcatgtgttccattctgattttagtattaaatgcttttaagtattca--tatagtattaaatagtggaattgccggaccatgtttcttacttgatggcagAAGTTGAACAATTTAAGCAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCG

upper sequence: GRMZM2G171745_T05 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g30840.1 (Oryza sativa), 3'ss of exon 7
ctgccttctgtttagatttattattatttttcagtgttcatataatggcagctactgtattaaatagtgttgccgaaccatgtttcttacttgatggcagAAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCG---------
        || ||  | |  | | |  |||| ||| |||||||| |   |  || || |          |||||| ||||||||||||||||||||||||||||| |||||||||||||||||||||| |||||||||||||||||||| |||||||||||| |||||||||||||||||||||||||||||||| ||||         
--------tgattttagtattaaatgcttttaagtattcatatagtattaaatagtgga---------attgccggaccatgtttcttacttgatggcagaagttgaacaatttaagCAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAG

upper sequence: GRMZM2G171745_T05 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 7
ctgccttctgtttagatttattattatttttcagtgttcatataatggcagctactgtattaaatagtg---ttgccgaaccatgtttcttacttgatggcagAAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCG---
    | | ||||    | |  | ||| | || | || |  ||      ||  ||  |||||||||||||   |||||| ||||||||||||||||||||||||||||| |||||||||||||||||||||| |||||||||||||||||||| |||||||||||| |||||||||||||||||||||||||||||||| ||||   
----catgtgttccattctgattttagtattaaatgcttttaagtattca--tatagtattaaatagtggaattgccggaccatgtttcttacttgatggcagaagTTGAACAATTTAAGCAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACC

upper sequence: GRMZM2G171745_T05 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G25690.2 (Glycine max), 3'ss of exon 7
ctgccttctgtttagatttattattatttttcagtgttcatataatggcagctact---gtattaaatagtgttgccgaaccatgtttcttacttgatggcagAAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCG
     |  | |  |  | | | | || || |        |  |    || | |  |   |  |  ||||   | | |||    | || |||||||  |||||||||||| ||| | ||||||||| ||||| |||||  | |||||||| ||| |   |||||||||||| ||| | ||||||| |||||| || ||   |||
---gataatataaaagtatctgactaattatacacacatagttgcctgctgttctttatgcttggaatatattggtcgacgtgtcttacttacttcgtggcagAAGTTACACACTGTAAGCAGGCCGACATCGACTTCAGAGGGCATGAGGAGATCTGCTCTGAATCTGGTGGAGTGATGGATTATGAAGAAGATCGAAGCCG

upper sequence: GRMZM2G171745_T05 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G25690.1 (Glycine max), 3'ss of exon 7
ctgccttctgtttagatttattattatttttcagtgttcatataatggcagctactgtattaaatagtgttgccgaaccatgtttcttacttgatggcagAAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCG---------
                    | |||||       |  |    |  ||     || ||  |  ||||   | | |||    | || |||||||  |||||||||||| ||| | ||||||||| ||||| |||||  | |||||||| ||| |   |||||||||||| ||| | ||||||| |||||| || ||   |||         
-------------------ctaattatacacacatagttgcctgctgttcttta-tgcttggaatatattggtcgacgtgtcttacttacttcgtggcagaagttacacactgtaagcagGCCGACATCGACTTCAGAGGGCATGAGGAGATCTGCTCTGAATCTGGTGGAGTGATGGATTATGAAGAAGATCGAAGCCGACCAAAGAG

upper sequence: GRMZM2G171745_T05 (Zea mays), 3'ss of exon 6
lower sequence: Vv15s0021g01580.t01 (Vitis vinifera), 3'ss of exon 7
ctgccttctgtttagatttattattatttttcagtgttcatataatggcagctactgtattaaatagtgttgccgaaccatgtttcttacttgatggcagAAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCG---------
                    ||   || |       |  | | |   |    |    |  |      |||||    |   | || ||||| |  |||||||||||| ||| | ||||||||| ||||||||||| || ||||| || ||| |   ||||||| |||| ||| | ||||| |  || || || ||   |||         
--------------------ttgaaatgtgcagacatataaaaatgagttattcaaatgctgggatatgttggtcgattgtcttacttacgttgtggcagaagttacacactgtaagcagGCCGACATTGACTTCCGAGGGCACGAGGAGATCTACTCTGAACCTGGTGGAGTGATGGACTACGAGGAAGATCGAAGCCGACCCAAGAG

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|37419216|gb|CF647286.1|CF647286
EST:     CCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCNNNNNNNTCAATCAAG                         AAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGT
genomic: CCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCC-AAAAAATCAATCAAGgtgagctgga ... ttgatggcagAAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGT
EST: gi|149027222|gb|EE046433.2|EE046433
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         AAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGT
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... ttgatggcagAAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGT
EST: gi|60398630|gb|DN231446.1|DN231446
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         AAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGT
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... ttgatggcagAAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGT
EST: gi|78109059|gb|DV527476.1|DV527476
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         AAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGT
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... ttgatggcagAAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGT
EST: gi|113702753|gb|EE680257.1|EE680257
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         AAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGT
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... ttgatggcagAAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGT
EST: gi|211477594|gb|FL101253.1|FL101253
EST:     ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAG                         AAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGT
genomic: ACCAGAAAGAATTTGAAGACAGAGTGGAAGAGGCCAAAAAATCAATCAAGgtgagctgga ... ttgatggcagAAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcagctactgtattaaatagtgttgccgaaccatgtttcttacttgatggcagAAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCG
                                     tttcttactt  CT-rich tract
       tactgtattaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgccttctgtttagatttattattatttttcagtgttcatataatggcagctactgtattaaatagtgttgccgaaccatgtttcttacttgatggcagAAGTTAAACAATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA