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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgcattgagcttctatatggatactttatgtgcttcctagttttgtctaaataataatttgtgcttggattgctctatatagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTTGGTGGTCCTACATGGTATGAGAACCCATACTACATTTCCCCCAATCAG

Basic information

species Zea mays
transcript GRMZM2G168176_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168176_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g37870.1 (Oryza sativa), 3'ss of exon 6
gtaattgcattgagcttctatatggata----ctttatgtgcttcctagttttgtctaaataataatttgtgcttggattgctctatatagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTTGGTGGTCCTACATGGTATGAGAACCCATACTACATTTCCCCCAATCAG
||||  ||    ||||||||| || |||     ||| | || |||| ||||| || | | |     |||| | | | | |   || | ||||||||||| |||||||||||||| ||||||||||||||||| |||||||| ||||| ||||||| ||| ||||| |||| |||  | || |||||||||
gtaaaggcgcatagcttctatttgtataatatttttttatgtttccaagtttagtttcagt-----tttgagatcgaact-tgctgtgtagGTTGGCCCAAGGTTCTGTTTGAACCCAATCAAAATATTTGGCGGTAGTTTCGGTGGCCCTACATTGTACGAGAATCCATTCTATGTGTCTCCCAATCAG

upper sequence: GRMZM2G168176_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G28320.2 (Glycine max), 3'ss of exon 7
gtaattgcattgagcttctatatggatactttatgtgcttcctagttttgtctaaataat--aatttgtgcttggattgctctatatagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTTGGTGGTCCTACATGGTATGAGAACCCATACTACATTTCCCCCAATCAG-
||      ||||   ||   ||| |||   |  | || |  |||  ||| |   | | ||  ||  |||      | | || | | |||||||| ||  | ||||| ||||| ||||| |||||||||||||| |||||||| || || || |  |||||||| ||   |||  | || || |||||| 
gtccgaaaattgttatttgttattgatttatattttgatctctaaatttttaatattcatttaacctgtatgcaaactact-tgtttagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATATGAGAATCCGCTCTATGTGTCACCAAATCAGG

upper sequence: GRMZM2G168176_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G12700.2 (Glycine max), 3'ss of exon 8
-----gtaattgcattgagcttctatatggatacttt-atgtgcttcctagttttgtctaaataataatttgtgcttggattgctctatatagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTTGGTGGTCCTACATGGTATGAGAACCCATACTACATTTCCCCCAATCAG
     | |||||  |   |  | |  ||  ||| ||| || |      |  |    |  |  |||     ||||     | | || | | |||||||| ||  | ||||| ||||| ||||| |||||||||||||| |||||||| || || || |  |||||||| |||| |||  | ||||| ||||||
gtttggaaattggttattggctattgatttatattttgatatatcaattgctaacattcatttaac---ctgtgtgcaaactact-tgtttagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGAAGTTTTGGAGGGCCAACTTTATATGAGAATCCATTCTATGTGTCCCCAAATCAG

upper sequence: GRMZM2G168176_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA18G51310.1 (Glycine max), 3'ss of exon 6
-----gtaattgcattgagcttctatatggatactttatgtgcttcctagttttgtctaaataataatttgtgcttggattgctctatatagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTTGGTGGTCCTACATGGTATGAGAACCCATACTACATTTCCCCCAATCAG
       |||||   |  | |  |  ||  ||| |||   |   ||    | |  |||  ||  |||  ||||  |  | | || | | ||||| |||||  | ||||| ||||| ||||| |||||||||||||| |||||||| || || || |  || ||||| |||  |||  | || || ||||||
gtccgaaaattgttattggttaatg-atttatattttg-atctgtcaatttctaatcttcatt-taacctgtgtgtaaactact-tgtttagGTCGGCCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATACGAGAATCCACTCTATGTGTCACCGAATCAG

upper sequence: GRMZM2G168176_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G28320.1 (Glycine max), 3'ss of exon 7
gtaattgcattgagcttctatatggatactttatgtgcttcctagttttgtctaaataat--aatttgtgcttggattgctctatatagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTTGGTGGTCCTACATGGTATGAGAACCCATACTACATTTCCCCCAATCAG
||      ||||   ||   ||| |||   |  | || |  |||  ||| |   | | ||  ||  |||      | | || | | |||||||| ||  | ||||| ||||| ||||| |||||||||||||| |||||||| || || || |  |||||||| ||   |||  | || || ||||||
gtccgaaaattgttatttgttattgatttatattttgatctctaaatttttaatattcatttaacctgtatgcaaactact-tgtttagGTTGGTCCGCGATTCTGCTTGAACCCAATTAAAATATTTGGTGGCAGTTTTGGAGGCCCAACTTTATATGAGAATCCGCTCTATGTGTCACCAAATCAG

upper sequence: GRMZM2G168176_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv07s0005g04550.t01 (Vitis vinifera), 3'ss of exon 6
gtaattgcattgagcttctatatggatactttatgtgcttcctagttttgtctaaataat---aatttgtgcttgga--ttgctctatatagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTTGGTGGTCCTACATGGTATGAGAACCCATACTACATTTCCCCCAATCAG
    ||| | |||    |  |   |||  | ||     |  |||||| | | ||||||||   |  ||   ||||||  | | | |  ||||||||| || || || ||||||||||| ||||| ||||||||||| || ||||| || || ||||  |||||||| ||||  ||||| || || ||| ||
--gtttgaaatgattcacctttctgat--tatagaacttatctagttgt-tgtaaataattctagcttaatcttggaactggttgttgatagGTTGGTCCAAGATTTTGTTTGAATCCCATCAAGATATTTGGTGGCAGCTTTGGAGGCCCAACATTATATGAGAATCCATTTTACATATCACCGAATGAG

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|148943696|gb|EC888763.2|EC888763
EST:     AGATTGATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAG                         GTTGGCCCCAGGTTCTGTTTGAATC-AATCAA
genomic: AGATTGATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAGgtaattgcat ... ctctatatagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAA
EST: gi|166421475|gb|EG156961.1|EG156961
EST:     ATAAAGTTGATAAAGGTGGTCTGGATAAAATGACACTTATTGAG                         GTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
genomic: ATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAGgtaattgcat ... ctctatatagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
EST: gi|76289777|gb|DV029345.1|DV029345
EST:     AGATTGATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAG                         GTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
genomic: AGATTGATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAGgtaattgcat ... ctctatatagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
EST: gi|60336677|gb|DN203650.1|DN203650
EST:     AGATTGATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAG                         GTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
genomic: AGATTGATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAGgtaattgcat ... ctctatatagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
EST: gi|76283913|gb|DV023481.1|DV023481
EST:     AGATGGATAAAGTTGATAAAGGTGGTATGGAAAAAATGACACTTATTGAG                         GTTGGCCCCAGGTTCTG
genomic: AGATTGATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAGgtaattgcat ... ctctatatagGTTGGCCCCAGGTTCTG
EST: gi|78180563|gb|DV550891.1|DV550891
EST:     AGATTGATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAG                         GTTGGCCCCAGGTTCTGT
genomic: AGATTGATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAGgtaattgcat ... ctctatatagGTTGGCCCCAGGTTCTGT
EST: gi|89249178|gb|DY620964.1|DY620964
EST:     AGATTGATAAAGGTGATAAAGGTGGTATGGATAAAATGACACTTATTGAG                         GTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
genomic: AGATTGATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAGgtaattgcat ... ctctatatagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
EST: gi|32945542|gb|CF050361.1|CF050361
EST:     AGATTGATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAG                         GTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
genomic: AGATTGATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAGgtaattgcat ... ctctatatagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
EST: gi|18659405|gb|BM500320.1|BM500320
EST:     AGATTGATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAG                         GTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
genomic: AGATTGATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAGgtaattgcat ... ctctatatagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
EST: gi|14203242|gb|BG836919.1|BG836919
EST:     AGATTGATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAG                         GTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT
genomic: AGATTGATAAAGTTGATAAAGGTGGTATGGATAAAATGACACTTATTGAGgtaattgcat ... ctctatatagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtgcttcctagttttgtctaaataataatttgtgcttggattgctctatatagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTTGGTGGTCCTACATGGTATGAGAACCCATACTACATTTCCCCCAATCAG
                 gtctaaa  putative branch site (score: 3)
                                          ttgctct  putative PPT
          tagttttgtctaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgcattgagcttctatatggatactttatgtgcttcctagttttgtctaaataataatttgtgcttggattgctctatatagGTTGGCCCCAGGTTCTGTTTGAATCCAATCAAAATATTTGGTGGTAGTTTTGGTGGTCCTACATGGTATGAGAACCCATACTACATTTCCCCCAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG