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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatagtcactggaaatttctttggaactgtttctgcataaagggtatatttagctattccgtaatccatgtcccttacctagcagtagtaaagttgtgcttcatctactgacattcattcagagatgaacatcatatttaacctgtttggtatttttatatatgcagCTCCCCTGTTGCTTTCATTACATGCTTCGTGACACTATTTGCTTTGGTCATTGCTATAACCAAAGATCTCCCTGATGTTGAAGGAGATCGCAA

Basic information

species Zea mays
transcript GRMZM2G113476_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113476_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g38850.1 (Oryza sativa), 3'ss of exon 5
gtaaa-tagtcactggaaatttctttggaactgtttctgcataaagggtatatttagctattccgtaatccatgtcccttacctagcag--tagtaaa-gttgtgcttcatctactgacattca--ttcagagatgaacatcatatttaac-ctgtttggtatttttatatatgcagCTCCCCTGTTGCTTTCATTACATGCTTCGTGACACTATTTGCTTTGGTCATTGCTATAACCAAAGATCTCCCTGATGTTGAAGGAGATCGCAA
||||| ||||||| ||||| ||||||     || ||   ||  |    |    ||   | ||   || |  || |||  | |||| ||   | ||||| ||| || | |||||  |  ||  ||  ||||||||||| ||| |||| |||  |  | || ||| ||| ||| |||||||| |||||||||||||||||||||||||||||  ||||||||||||||||||||||||||||||||||||| ||||||||||| ||||| ||
gtaaaatagtcaccggaaaattcttta----tgcttaatcagtaccaattagctttatttttagatattagatatcctctgcctatcaaattggtaaaagttctgttacatctcattgcagacagattcagagatgatcattatatctaatgccatatgatatctttctatctgcagCTCGCCTGTTGCTTTCATTACATGCTTCGTGACTTTATTTGCTTTGGTCATTGCTATAACCAAAGATCTCCCAGATGTTGAAGGGGATCGGAA

upper sequence: GRMZM2G113476_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G15720.1 (Glycine max), 3'ss of exon 5
gtaaatagtcactggaaatttctttggaactgtttctgcataaagggtatatttagctattccgtaatccatgtcccttacctagcagtagtaaagttgtgcttcatctactgacattcattcagagatgaacatcatatttaacctgtttggtatttttatatatgcagCTCCCCTGTTGCTTTCATTACATGCTTCGTGACACTATTTGCTTTGGTCATTGCTATAACCAAAGATCTCCCTGATGTTGAAGGAGATCGCAA
                                                       ||| |   ||  |    |    | |   |  | |  |     | |   |  ||   | | |||  ||  ||  | |  || ||||||   ||      | | | | |   |||||||| ||||| | ||| || |||   || || ||| | || ||  |||| ||||||||||| |||||||| |||||||||||||| ||||||||
-------------------------------------------------------gct-tatagtggtgttagcttttcattcaatattttt-----tttaggtgttcggttcatatt--ttgggaacttattat-atatttgttct------tgtatctctgcctgcagCTCTCCTGTGGTTTTTATCACAACATTTGTAACATTTTTCGCACTGGTAATTGCTATAACAAAAGATCTTCCTGATGTTGAAGGTGATCGCAA

upper sequence: GRMZM2G113476_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G26820.1 (Glycine max), 3'ss of exon 5
gtaaatagtcactggaaatttctttggaactgtttctgcataaagggtatatttagctattccgtaatccatgtcccttacctagcagtagtaaagttgtgcttcatctactgacattcattcagagatgaacatcatatttaacctgtttggtatttttatatatgcagCTCCCCTGTTGCTTTCATTACATGCTTCGTGACACTATTTGCTTTGGTCATTGCTATAACCAAAGATCTCCCTGATGTTGAAGGAGATCGCAA
                                                       ||| |   ||  |    |    | | | |  | |  |  ||  ||| |   | |      ||   ||  ||| | |  || ||||||       ||  | | | | |   |||||||| ||||| | ||| || |||   || || ||| | || ||  |||| ||||||||||| |||||||| |||||||||||||||||||||||
-------------------------------------------------------gct-tatagtggtgttagcttttcatccaatatttttttag--gtgttaggttt-----tatattttgggagcttattat-atatttg------ttcatgtatctttgcctgcagCTCTCCTGTGGTTTTTATCACAACATTTGTAACATTTTTCGCACTGGTAATTGCTATAACAAAAGATCTTCCTGATGTTGAAGGAGATCGCAA

upper sequence: GRMZM2G113476_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT3G11945.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaaatagtcactggaaatttctttggaactgtttctgcataaagggtatatttagctattccgtaatccatgtcccttacctagcagtagtaaagttgtgcttcatctactgacattcattcagagatgaacatcatatttaacctgtttggtatttttatatatgcagCTCCCCTGTTGCTTTCATTACATGCTTCGTGACACTATTTGCTTTGGTCATTGCTATAACCAAAGATCTCCCTGATGTTGAAGGAGATCGCAA
                                                                | |  ||       |||  |  |  ||  | |   ||    | || |  | | || |       |  | ||  || | ||| |  ||| |   |   ||| |||||  | ||||| || ||||| ||||  || |||||||| |||||  ||||||||||||| || || || || |||||||||||||||||||| ||
-------------------------------------------------------------aaattagtcaaactttgtactcacaatgagagaggaactgtaggagctccccataatcgt----gagtagatatattactcaactt--ttgat---tcgctatttgcagTGCACCTGTGGCGTTCATCACATCTTTTGTGACACTGTTTGCACTGGTCATTGCTATTACAAAGGACCTTCCTGATGTTGAAGGAGATCGAAA

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|13558184|gb|BG549540.1|BG549540
EST:     GGCGTGTACTATGCTACTAGGGCTGCACTAGGTCTTACATTCCAATGGAG                         CTCCCCTGTTGCTTTCATTACATGCTTCGTGACACTATTTGCTTTGGTCAT
genomic: GGCGTGTACTATGCTACTAGGGCTGCACTAGGTCTTACATTCCAATGGAGgtaaatagtc ... atatatgcagCTCCCCTGTTGCTTTCATTACATGCTTCGTGACACTATTTGCTTTGGTCAT
EST: gi|71445925|gb|DR826975.1|DR826975
EST:     GGCGTGTACTATGCTACTAGGGCTGCACTAGGTCTTACATTCCAATGGAG                         CTCCCCTGTTGCTTTCATTACATGCTT
genomic: GGCGTGTACTATGCTACTAGGGCTGCACTAGGTCTTACATTCCAATGGAGgtaaatagtc ... atatatgcagCTCCCCTGTTGCTTTCATTACATGCTT
EST: gi|148973603|gb|EE024711.2|EE024711
EST:     GGCGTGTACTATGCTACTAGGGCTGCACTAGGTCTTACATTCCAATGGAG                         CTCCCCTGTTGCTTTCATTACATGC
genomic: GGCGTGTACTATGCTACTAGGGCTGCACTAGGTCTTACATTCCAATGGAGgtaaatagtc ... atatatgcagCTCCCCTGTTGCTTTCATTACATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcattcagagatgaacatcatatttaacctgtttggtatttttatatatgcagCTCCCCTGTTGCTTTCATTACATGCTTCGTGACACTATTTGCTTTGGTCATTGCTATAACCAAAGATCTCCCTGATGTTGAAGGAGATCGCAA
                       atttaac  putative branch site (score: 3)
                                        tttttat  putative PPT
                                 tttggtatttttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatagtcactggaaatttctttggaactgtttctgcataaagggtatatttagctattccgtaatccatgtcccttacctagcagtagtaaagttgtgcttcatctactgacattcattcagagatgaacatcatatttaacctgtttggtatttttatatatgcagCTCCCCTGTTGCTTTCATTACATGCTTCGTGACACTATTTGCTTTGGTCATTGCTATAACCAAAGATCTCCCTGATGTTGAAGGAGATCGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC