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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatatttagaataaaaatattccaatgtgatcaccgtgtagacctgttcataacttggaaatgttgtgaaatctctgcagGTGTGGTTGGACATATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACTTGCTCCCAGATATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTA

Basic information

species Zea mays
transcript GRMZM2G010044_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010044_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g03260.3 (Oryza sativa), 3'ss of exon 11
-------gtgatatttagaataaaaatattccaatgtgatcaccgtgtagacctgttcataacttggaaatgttgtgaaatctctgcagGTGTGGTTGGACATATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACTTGCTCCCAGATATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTA
        ||      | |  ||| | || |  |  |||||| | ||| |    | |   |   |   ||||||   |||||| || |||||||| ||||||| |||||| |||||||||||||| | ||||||||||||||||| |||||||||||||||||||||||||| |||||||| || ||||
gtgataaatgcagcaaacagcaaacacatactgaaatgatcatcctgtggtttcgatttaataataagaatgtt---aaatctatgtagGTGTGGATGGACATTTATAGCATCCCTGTACCAGGAGCCGGTGGCAAAACTTGCTCACAGATATTTGAGGAGGCTGGTTGTGATACACCAGCTAGCCCTA

upper sequence: GRMZM2G010044_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA14G40570.1 (Glycine max), 3'ss of exon 13
-----------------------------------------gtgatatttagaataaaaatattccaatgtgatcaccgtgta-gacctgttcataacttggaaatgttg-tgaaatctctgcagGTGTGGTTGGACATATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACTTGCTCCCAGATATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTA
                                          | | | |||  |  |||||  ||    |   |||  ||| | ||    ||   |||||     | ||  |||||| |   ||||| ||| ||||| | ||   ||||||||| || ||||||||||| || || ||||| ||||||||||| || | ||| |||||||||||||| |||||||
gtctgaaaattgtcatatttatatatcttcatatcagttgatttacagttattaagaaaattctcttgggaactcatggtggatgattattttccaacttatctctattaatgaaattt---cagGTTTGGATGGACTTGTACTCCCTCCCTGTCCCTGGATCTGGTGGTAAGACATGCTCACAGATATTTGAAGAAGTTGGGTGTGACACACCAGCTAGTCCTA

upper sequence: GRMZM2G010044_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 13
--------------------------------------gtgatattta---gaataaaaatattccaatgtga--tcaccgtgta-gacctgttcataacttggaaatgttg-tgaaatctctgcagGTGTGGTTGGACATATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACTTGCTCCCAGATATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTA
                                       |||| |      || ||| || ||||   || ||  |||  ||| | ||    ||   |||||     | |   || ||| |   ||||| ||| ||||| ||||   ||| || || || ||||||||||| || || ||||||||||||||||| || ||||| |||||||||||||| |||||| 
ggtctggaaattttcatatttatatatctttatatcagttgatttacgtgtgattaagaaaattctcttgggaaatcatggtggatgataattttccaacttatctctatcaatggaattt---caGGTTTGGATGGACTTATACTCCCTTCCAGTCCCTGGATCTGGTGGTAAGACGTGCTCCCAGATATTTGAAGAAGCTGGGTGTGACACACCAGCTAGTCCT-

upper sequence: GRMZM2G010044_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 3'ss of exon 13
----------------------------gtgatatttagaataaaaatattccaatgtgatcaccgtgtagacc----tgttcataacttggaaatgttg--tgaaatct------ctgcagGTGTGGTTGGACATATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACTTGCTCCCAGATATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTA
                             |||||  |    |   || |||| |      | | | ||   ||     |  |||||| | |   ||  |   | | || |      || ||||| ||| ||||  ||||||| ||||| |||||||||| ||||||||| ||||||||||||||||||||||| ||||||||||| ||||| ||||||||||
gtttgtataatttgttgcactgtaagtgttgatagatttgttgggaagattctag-aaatttatcatgggaactagattaatcataaatggattatagtaattcatatattaaaatcttcagGTCTGGATGGATGTATATAGTCTCCCAGTACCAGGATGTGGTGGCAAGACTTGCTCCCAGATATTTGAGGAAGCTGGTTGTGATACACCTGCAAGTCCTA

upper sequence: GRMZM2G010044_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 3'ss of exon 13
----------------------------------gtgatatttagaataaaaatattccaatgtgatcaccgtgtagacctgttcataacttggaaatgttgtga-aatctctgcagGTGTGGTTGGACATATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACTTGCTCCCAGATATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTA
                                  |  | |||   ||||   || |  ||  |  |  |  || ||  |||   || |  | | || || | ||| ||  |   ||||| ||| ||||| ||||||| ||||| |||||||||| ||||||||| |||||||| |||||||||||||| ||||||||||| ||||| ||||||||||
gtttgtactgtatttttgcttgatggatttgtatggaagattccaaatagggatttgtcataggaaaga--gtttaatcctacgca-atatagtaattgatatgataaaattatcagGTTTGGATGGACGTATATAGTCTCCCGGTACCAGGATGTGGTGGCAAGACTTGCTCTCAGATATTTGAGGAAGCTGGTTGTGATACACCTGCAAGTCCTA

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|7162228|gb|AW519835.1|AW519835
EST:     GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACACAAAAG                         GTGTGGTTGGACATATATAGCCTCCCTGTGCCAGGATCTGGTGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACACAAAAGgtgatattta ... atctctgcagGTGTGGTTGGACATATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT
EST: gi|91051661|gb|EB162079.1|EB162079
EST:     GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACCCAAAAG                         GTGTGGTTGGACATATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACACAAAAGgtgatattta ... atctctgcagGTGTGGTTGGACATATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT
EST: gi|7137997|gb|AW499377.1|AW499377
EST:     GGAAAGAAGGTTAAAGTTCCCCCATTTCTTGTCCCTGCCACACAAAAG                         GTGTGGTTGGACATATATAGCCTCCCTGTGCCAGGATCTGGTGGCAAAACT
genomic: GGAAAGAAGGTTAAAGTTCCCACATTTCTTGTCCCTGCCACACAAAAGgtgatattta ... atctctgcagGTGTGGTTGGACATATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgatcaccgtgtagacctgttcataacttggaaatgttgtgaaatctctgcagGTGTGGTTGGACATATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACTTGCTCCCAGATATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTA
                      tcataac  putative branch site (score: 2)
                                              tctctgc  putative PPT
                     ttcataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatatttagaataaaaatattccaatgtgatcaccgtgtagacctgttcataacttggaaatgttgtgaaatctctgcagGTGTGGTTGGACATATATAGCCTCCCTGTACCAGGATCTGGTGGCAAAACTTGCTCCCAGATATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG