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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccagccttctagacatatgaatcttttgttgtgttcagcgtttttcccgtatggagcttaccttttttccttacagaatgtttgctcgaaattttgcagTGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTTTCTGACTCCTGTAAATCCAATTGAAGAAGTGGAAGGAGCTACTAAAGCG

Basic information

species Zea mays
transcript GRMZM2G120578_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120578_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g15550.2 (Oryza sativa), 3'ss of exon 9
--gccagccttctagacatatgaatcttttgttgtgttcagcgtttttcc----cgtatggagcttaccttttttccttacagaatgtttgctcgaaattttgcagTGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTTTCTGACTCCTGTAAATCCAATTGAAGAAGTGGAAGGAGCTACTAAAGCG
     |  |  |||||   |||  | |   || ||  | |  |  || ||     || ||||| | ||  ||||  | ||||   | ||   | | |  |||||||||| ||||||||||||||| |||| ||||| || || ||||| |||||||| |||||||||| ||||||||||||| || | ||||||||||   |||| 
gcataaatcgcctagatg-atgtttttcaagtggtaattactggcttgccgcaatgtttggagttcac--ttttaacatacatt-tattcctttgca--tttgcagTGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTTCCTGACTCCTGCAAATCCAATTGAAAAACTAGAAGGAGCTATGGAAGCA

upper sequence: GRMZM2G120578_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g15550.3 (Oryza sativa), 3'ss of exon 9
----------------------------------------------------------------------------------------gccagccttctagacatatgaatcttttgttgtgttcagcgtttttcc----cgtatggagcttaccttttttccttacagaatgtttgctcgaaattttgcagTGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTTTCTGACTCCTGTAAATCCAATTGAAGAAGTGGAAGGAGCTACTAAAGCG
                                                                                           |  |  |||||   |||  | |   || ||  | |  |  || ||     || ||||| | ||  ||||  | ||||   | ||   | | |  |||||||||| ||||||||||||||| |||| ||||| || || ||||| |||||||| |||||||||| ||||||||||||| || | ||||||||||   |||| 
gttagacagttggttgcgattctttttattgtgtattaagctcattgctccactgttttaatatggtgaaagtgaagcattaagctgcataaatcgcctagatg-atgtttttcaagtggtaattactggcttgccgcaatgtttggagttcac--ttttaacatacatt-tattcctttgca--tttgcagTGGTGTGATTGGGTTTCTGCTATGTGCCAAAGAAGGTCCACCAGTCAACTTCCTGACTCCTGCAAATCCAATTGAAAAACTAGAAGGAGCTATGGAAGCA
















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|148928250|gb|EE284812.2|EE284812
EST:     TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT
genomic: TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAGgttcttcata ... aattttgcagTGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT
EST: gi|37380776|gb|CF627223.1|CF627223
EST:     GCTATGCATGGGCTAGTGT-CCTACATACCCGAG                         TGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT
genomic: GCTATGCATGGGCTAGTGTCCCAACATACCCGAGgttcttcata ... aattttgcagTGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT
EST: gi|32919151|gb|CF023963.1|CF023963
EST:     TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCGACATACCCGAG                         TGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCA
genomic: TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAGgttcttcata ... aattttgcagTGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCA
EST: gi|6448423|gb|AW181189.1|AW181189
EST:     TTCAAGGGTTCTGTCCCCTATGCATGGGCTAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCNCCGGTCAACTT
genomic: TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAGgttcttcata ... aattttgcagTGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT
EST: gi|32866078|gb|CF005760.1|CF005760
EST:     TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT
genomic: TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAGgttcttcata ... aattttgcagTGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT
EST: gi|211227788|gb|FL398706.1|FL398706
EST:     TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT
genomic: TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAGgttcttcata ... aattttgcagTGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT
EST: gi|78117804|gb|DV536191.1|DV536191
EST:     TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT
genomic: TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAGgttcttcata ... aattttgcagTGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT
EST: gi|4804277|gb|AI666143.1|AI666143
EST:     TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT
genomic: TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAGgttcttcata ... aattttgcagTGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT
EST: gi|78024870|gb|DV493257.1|DV493257
EST:     TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT
genomic: TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAGgttcttcata ... aattttgcagTGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT
EST: gi|12968943|gb|BG265784.1|BG265784
EST:     TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT
genomic: TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAGgttcttcata ... aattttgcagTGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT
EST: gi|110496613|gb|EE015080.1|EE015080
EST:     TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT
genomic: TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAGgttcttcata ... aattttgcagTGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT
EST: gi|89247054|gb|DY618840.1|DY618840
EST:     TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT
genomic: TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAGgttcttcata ... aattttgcagTGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT
EST: gi|37382012|gb|CF627919.1|CF627919
EST:     TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT
genomic: TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAGgttcttcata ... aattttgcagTGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT
EST: gi|211042510|gb|FL401130.1|FL401130
EST:     TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAG                         TGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT
genomic: TTCAAGGGTTCTGTCCGCTATGCATGGGCTAGTGTCCCAACATACCCGAGgttcttcata ... aattttgcagTGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcccgtatggagcttaccttttttccttacagaatgtttgctcgaaattttgcagTGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTTTCTGACTCCTGTAAATCCAATTGAAGAAGTGGAAGGAGCTACTAAAGCG
                       tccttac  putative branch site (score: 2)
                                            aaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gccagccttctagacatatgaatcttttgttgtgttcagcgtttttcccgtatggagcttaccttttttccttacagaatgtttgctcgaaattttgcagTGGGGTGATTGGGTTTCTGTTATGCGCCAAGGATGGCCCACCGGTCAACTTTCTGACTCCTGTAAATCCAATTGAAGAAGTGGAAGGAGCTACTAAAGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT