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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcgtatcattttccctccccttctgtcctgtgattctgtctttttgttggtatgactgttgttctatgctgacaatggaatggttcgatctactgatagGGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGGACATCGATGCTGTTGGGGAAGTCACCCTGCCCGCACATGGAAAATTACC

Basic information

species Zea mays
transcript GRMZM5G892742_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G892742_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g25210.1 (Oryza sativa), 3'ss of exon 3
-tgcgtatcattttccctccccttctgtcctgtgattctgtctttttgttggtatgactgttgttctatgctgacaatggaatggttcga-tctactgatagGGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGGACATCGATGCTGTTGGGGAAGTCACCCTGCCCGCACATGGAAAATTACC
 |||  || |||| || |    | |  |  | |  | |  |  |||  ||   | ||   |    | || ||    |||||||| ||  | | | |||| |||||||||||||||||||| |||||||| ||||| || ||||| ||| |||| ||||| ||||| |||||||||   ||||| ||||||||||||||||||
ctgcacattatttcccttttgttccatttttttcctgcaatgctttctttcccaagatcata--ccaattcttcacatggaatgattgaaatatgctgacagGGATGTACTGGATGAGGTAGAGATCCGGCAGCTCCTTATTGATCATGTTGGGCATCGGTGCTGCTGGGGAAGTAGGCCTGCTCGCACATGGAAAATTACC

upper sequence: GRMZM5G892742_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G17240.1 (Glycine max), 3'ss of exon 3
tgcgtatcattttccctccccttctgtcctgtgattctgtctttttgttggtatgactgttgttctatgctgacaatgg----aatggttcgatctactgatagGGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGGACATCGATGCTGTTGGGGAAGTCACCCTGCCCGCACATGGAAAATTACC
    |  | |||        |   | |  | ||| | | ||   ||     |   | | || |  |  ||  | |||      ||  |   |||| |    |||| |  |  ||||||| |||||||| ||| || | |||||||| ||| |||| ||||| ||||||||||| ||||  ||||| || |||||||  |||   
---atgccttttgataaaggccattatgatatgaatttctcaagttcaatattccagttttatattg-gcaaataatcttgttaactgggtgatccatgtttagGAAAATCTTGGATGAAGTGGAGATACGAGAGTTGCTCATTGATCATGTTGGTCATCGTTGCTGTTGGGGTAGTCGTCCTGCTCGAACATGGAGGATTCAT
















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|148999746|gb|EE036749.2|EE036749
EST:     GGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAG                         GGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
genomic: GGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAGgtgagttttt ... ctactgatagGGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
EST: gi|26558823|gb|CA831058.1|CA831058
EST:     GGGCCATATCCGTACGGTGGCAGTTACCAACCTTTTGAGAGCGTCGGGAG                         GGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
genomic: GGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAGgtgagttttt ... ctactgatagGGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
EST: gi|71438689|gb|DR819739.1|DR819739
EST:     GGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAG                         GGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
genomic: GGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAGgtgagttttt ... ctactgatagGGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
EST: gi|101401378|gb|EB822366.1|EB822366
EST:     GGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAG                         GGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
genomic: GGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAGgtgagttttt ... ctactgatagGGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
EST: gi|22472922|gb|BU037402.1|BU037402
EST:     GGCCATATCCGTACGNG-GGCAGTTACCAACCTTTTGAGAGCGTCGGGAG                         GGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
genomic: GGCCATATCCGTATG-GTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAGgtgagttttt ... ctactgatagGGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
EST: gi|71438626|gb|DR819676.1|DR819676
EST:     GGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAG                         GGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
genomic: GGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAGgtgagttttt ... ctactgatagGGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
EST: gi|87155688|gb|DY400477.1|DY400477
EST:     GGGCCATATCCGTACGGTGGCAGTTACCAACCTTTTGAGAGCGTCGGGAG                         GGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
genomic: GGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAGgtgagttttt ... ctactgatagGGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
EST: gi|71446190|gb|DR827240.1|DR827240
EST:     GGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAG                         GGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
genomic: GGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAGgtgagttttt ... ctactgatagGGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
EST: gi|71422780|gb|DR805839.1|DR805839
EST:     GGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAG                         GGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
genomic: GGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAGgtgagttttt ... ctactgatagGGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
EST: gi|76285537|gb|DV025105.1|DV025105
EST:     GGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAG                         GGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
genomic: GGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAGgtgagttttt ... ctactgatagGGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
EST: gi|101387480|gb|EB815755.1|EB815755
EST:     GGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAG                         GGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
genomic: GGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAGgtgagttttt ... ctactgatagGGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
EST: gi|71439824|gb|DR820874.1|DR820874
EST:     GGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAG                         GGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
genomic: GGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAGgtgagttttt ... ctactgatagGGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
EST: gi|76014459|gb|DT941629.1|DT941629
EST:     GGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAG                         GGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG
genomic: GGGCCATATCCGTATGGTGGCAGTTACCAACCTTCTGAGAGCGTCGGGAGgtgagttttt ... ctactgatagGGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttggtatgactgttgttctatgctgacaatggaatggttcgatctactgatagGGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGGACATCGATGCTGTTGGGGAAGTCACCCTGCCCGCACATGGAAAATTACC
                      tgctgac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcgtatcattttccctccccttctgtcctgtgattctgtctttttgttggtatgactgttgttctatgctgacaatggaatggttcgatctactgatagGGATGTACTGGATGAGGTGGAGATCCGACAGCTACTCATTGACCATATTGGACATCGATGCTGTTGGGGAAGTCACCCTGCCCGCACATGGAAAATTACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA