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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gaggtgagttttttcatcacttaaaaagacatcctatatatctttcaagttagatcatttatggatagagtgctttcatgtcataaccatttcatattttcatgtgttaCAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAA

Basic information

species Zea mays
transcript GRMZM2G141587_T05
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141587_T05 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 6
gaggtgagttttttcatcac-ttaaaaagacatc-ctatatatctttcaagttagatcatttatggatagagtgctttcatgtcataaccatttcatattttcatgtgttaCAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAA
|| ||| ||||||| | | ||||| |||| | |||| || |||||| | || || || | | ||||| ||| || || |||||||||||||| || |||||||||||||||| |||||||||| | ||||||||||| |||||||||||||||||||||||||| |||||||||||
---gtaagtattttcattatatcaaaaatacattgtcacatatgatttg-gttagacccttaattttcaggg-------gtagtataactattcgat--------gtattacagGTCACAACCTTATTTCACTTGGATCGGCAAATGTATTTACTGGGATATCTTGCTAACCAAAGCCGTGTCTATCTTATTGACAAGCAATTTAA

upper sequence: GRMZM2G141587_T05 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 15
gaggtgagttttttcatcac-ttaaaaagacatcctatatatctttcaagttagatcatttatggatagagtgctttcatgtcataaccatttcatattttcatgtgttaCAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAA
|| ||| ||||||| | | ||||| ||| | | |||| || |||||| || || |||| | ||||| ||| || || |||||||||||||| || |||||||||||||||| |||||||||| | ||||||||||| ||||||||||||||||| |||||||| |||||||||||
---gtaagtattttcattatatcaaaaatgcattc-acatatgatttg-gttagactgttaattttcagag-------gtagtataactattcgat--------gtattacagGTCACAACCTTATTTCACTTGGATCGGCAAATGTATTTACTGGGATATCTTGCTAACCAAAGCCGTGTCTACCTTATTGACAAGCAATTTAA

upper sequence: GRMZM2G141587_T05 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA13G43680.1 (Glycine max), 3'ss of exon 15
gaggtgagttttttcatcacttaaaaagacatcctatatatctttcaagttagatcattta--tgga-tagagtgctttcatgtcataaccatttcatattttcatgtgttaCAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAA
| | | ||| | || | | || | | | | | |||| || | || | | | | ||| || || | ||| || |||| || || ||||||| ||||| || || ||||| || || |||||||||||||||||||| ||||| ||| | ||||| || | |||||
-gtattaactcttttcccttctagatttctagtttaaaaaagaattgtgcattcttttttaattgaactacaaggatcatgagacatcttgatgcataatgattatgaatt-tagGTAACTACGATGTTTCATTTGGACCGCCCCATGTACTTGTTGGGATATCTTGCAAACCAAAGTCGTGTTTATTTGATTGACAAAGAGTTTAA

upper sequence: GRMZM2G141587_T05 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 15
gaggtgagttttttcatcacttaaaaagacatcctatatatctttcaagttagatcatttatgga--tagagtgctttcatgtcataaccatttcatattttcatgtgttaCAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAA
| | | | ||||| || | | | | | | | | || || || || | | | ||| || || | ||| || |||| || || ||||||| ||||| || || ||||| || || |||||||||||||||||||| ||||| ||| | ||||| || | |||||
gtattaactcttttcccttctagatttctagtttaaaaaaagaattgtgcattctttttaattgaactacgaggatcatgagacatcttgatacataatgattatgaatt-tagGTAACTACGATGTTTCATTTGGACCGCCCTATGTACTTGTTGGGATATCTTGCAAACCAAAGTCGTGTTTATTTGATTGACAAAGAGTTTAA

upper sequence: GRMZM2G141587_T05 (Zea mays), 3'ss of exon 15
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 15
gaggtgagttttttcatcacttaaaaagacatcctatat-atctttcaagttagatcatttatgga-tagagtgctttcatgtcataaccatttcatattttcatgtgttaCAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAA
| | | || | | | | |||| | || || || | || |||| |||| |||| || || | | || | ||||| || || ||||||||||||| ||||| |||||||| |||||||||||||| | ||||| || || |||||||| || || | |||||
----------------gtataagagagttgattccaggttgtatttctatatatatgatcttcattctaaggtgcagtcat---ataaattgttaatgtgatgat----ttcagGTAACCACCATGTTTCACTTGGACCGGCCTATGTATTTGTTAGGATATCTTGCCAGTCAAAGTCGCGTTTATCTTATAGACAAAGAGTTTAA

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|22489660|gb|BU049570.1|BU049570
EST:     GTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGA                         GAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATAT
genomic: GTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAgaggtgagtt ... tcatgtgttaCAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATAT
EST: gi|18963894|gb|BM660690.1|BM660690
EST:     GTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGA                         GAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATAT
genomic: GTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAgaggtgagtt ... tcatgtgttaCAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATAT
EST: gi|67013287|gb|CO442036.1|CO442036
EST:     GTTTCATCTACAATAATTCTTC-TGGCGTCTTAATTACTGTGTAGGAGGA                         GAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATAT
genomic: GTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAgaggtgagtt ... tcatgtgttaCAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATAT
EST: gi|18384433|gb|BM417632.1|BM417632
EST:     GTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGA                         GAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATAT
genomic: GTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAgaggtgagtt ... tcatgtgttaCAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATAT
EST: gi|211344820|gb|FK991758.1|FK991758
EST:     TTTCATCTACAATAATTCTTCATGGCGGTCTTAATTACTGTGTAGGAGGA                         GAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATAT
genomic: TTTCATCTACAATAATTCTTCATGGCG-TCTTAATTACTGTGTAGGAGGAgaggtgagtt ... tcatgtgttaCAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATAT
EST: gi|18649807|gb|BM498626.1|BM498626
EST:     GTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGA                         GAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATAT
genomic: GTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAgaggtgagtt ... tcatgtgttaCAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATAT
EST: gi|211344819|gb|FK991757.1|FK991757
EST:     GTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGA                         GAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATAT
genomic: GTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAgaggtgagtt ... tcatgtgttaCAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATAT
EST: gi|21809537|gb|BQ667855.1|BQ667855
EST:     GTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTG-GTAGGAGGA                         GAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATAT
genomic: GTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAgaggtgagtt ... tcatgtgttaCAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATAT
EST: gi|89106141|gb|DY576358.1|DY576358
EST:     GTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGA                         GAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATAT
genomic: GTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAgaggtgagtt ... tcatgtgttaCAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATAT
EST: gi|18649903|gb|BM498722.1|BM498722
EST:     GTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGA                         GAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATAT
genomic: GTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAgaggtgagtt ... tcatgtgttaCAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATAT
EST: gi|18384334|gb|BM417533.1|BM417533
EST:     GTTTCATCTACAATAATTCTTCATGGTGTCTTAATTACTGTGTAGGAGGA                         GAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATAT
genomic: GTTTCATCTACAATAATTCTTCATGGCGTCTTAATTACTGTGTAGGAGGAgaggtgagtt ... tcatgtgttaCAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatttatggatagagtgctttcatgtcataaccatttcatattttcatgtgttaCAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAA
                          tcataac  putative branch site (score: 2)
 tattttc  putative PPT
 atttcatattttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaggtgagttttttcatcacttaaaaagacatcctatatatctttcaagttagatcatttatggatagagtgctttcatgtcataaccatttcatattttcatgtgttaCAGGTCACAACTTTGTTTCACTTGGATCGGCCAATGTATTTATTAGGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA