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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgagtgttcgacatgccttttaatcacatcataactatagtatttttttgtgatttgatacttctttggtctaaaatttagttttatgtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAAGCATTCAACAGCGGCAACCTTGCCCTCTACCAAGAACTTTGCAGGGTTC

Basic information

species Zea mays
transcript GRMZM5G868757_T07
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G868757_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g11570.1 (Oryza sativa), 3'ss of exon 3
-gtttgagtgttcgacatgccttttaatcacatcataactatagtatttttttgtgatttgatacttctttggtctaaa--atttagttttatgtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAAGCATTCAACAGCGGCAACCTTGCCCTCTACCAAGAACTTTGCAGGGTTC
 | ||||    | ||   |||  | ||||  || ||| |   | ||| |  |||| ||||| ||| ||| ||    ||    ||||  ||| | || ||||||||||| |||||||||||||| |||||||||||||| ||||||||||||||||||||||||| ||||||||| || |||||||||||||| || ||||| |
ggattgaaatattgaatggcccctaaatc-tat-atatcggca-tatatggttgtcatttggtacatctctgtctgaagttgtttatatttttatatccttagATCAACAGTCTTATTGGAACCAAGGTGGAGTGGGTCTATCATATGTTACAAGCATTCAACACCGGCAACCTAGCTCTCTACCAAGAACTATGTAGGGTCC

upper sequence: GRMZM5G868757_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g32800.1 (Oryza sativa), 3'ss of exon 3
------gtttgagtgttcgacatgccttttaatc-acatcataactatagtatttttttgtgatttgatacttctttggtctaaaatttagttttatgtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAAGCATTCAACAGCGGCAACCTTGCCCTCTACCAAGAACTTTGCAGGGTTC
       ||| | || | ||   |||  | |||| |  |||  | ||||||  |        ||||||||| ||| || ||| ||| |    ||| |  | ||||||||||| ||||| |||||||| |||||||||||||| ||||||||||| |||||||||||||  |||||||| || ||||||||||||||||||| ||| |
ggtgtttttttaatgcttgaatggcccctaaatctatgtcagca-tatagttgtc------aatttgatacatctctgttctgaaactgctattttttaatccttagATCAACAGTCTAATTGGAACCAAGGTGGAGTGGGTCTATCATATGTTGCAAGCATTCAACACTGGCAACCTAGCTCTCTACCAAGAACTTTGCAAGGTCC
















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|149078129|gb|EE166878.2|EE166878
EST:     TGCTGGGTGATAACATTTACAACTTTGGGGAGTTGTTAGCTCACCCGATT                         ATCAATAGTCTTATTGGAACTAAAGTGGAGTGGGTTTATCATATG
genomic: TGCTGGGTGATAACATTTACAACTTTGGGGAGTTGTTAGCTCACCCGATTgtaagtaatt ... gtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATG
EST: gi|194716906|gb|FK934065.1|FK934065
EST:     TGCTGGGTGATAACATTTACAACTTTGGGGAGTTGTTAGCTCACCCGATT                         ATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAA
genomic: TGCTGGGTGATAACATTTACAACTTTGGGGAGTTGTTAGCTCACCCGATTgtaagtaatt ... gtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAA
EST: gi|148930110|gb|EC872431.2|EC872431
EST:     TGCTGGGTGATAACATTTACAACTTTGGGGAGTTGTTAGCTCACCCGATT                         ATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAA
genomic: TGCTGGGTGATAACATTTACAACTTTGGGGAGTTGTTAGCTCACCCGATTgtaagtaatt ... gtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAA
EST: gi|211082970|gb|FL307146.1|FL307146
EST:     TGCTGGGTGATAACATTTACAACTTTGGGGAGTTGTTAGCTCACCCGATT                         ATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAA
genomic: TGCTGGGTGATAACATTTACAACTTTGGGGAGTTGTTAGCTCACCCGATTgtaagtaatt ... gtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAA
EST: gi|28987392|gb|CB351612.1|CB351612
EST:     TGCTGGG-GATAACATTTACAAC-TTGGGGAG-TGTTAGCTCACCCGATT                         ATCAATAGTCTTA-TGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAA
genomic: TGCTGGGTGATAACATTTACAACTTTGGGGAGTTGTTAGCTCACCCGATTgtaagtaatt ... gtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAA
EST: gi|6020572|gb|AW065605.1|AW065605
EST:     TGCTGGGTGATAACATTTACAACTTTGGGGAATTGTTAGCTCACCCGATT                         ATCAATAGTCTTATTGGAACCAAGGTGGAGTGGGTTTATCATATGTTACAA
genomic: TGCTGGGTGATAACATTTACAACTTTGGGGAGTTGTTAGCTCACCCGATTgtaagtaatt ... gtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttgtgatttgatacttctttggtctaaaatttagttttatgtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAAGCATTCAACAGCGGCAACCTTGCCCTCTACCAAGAACTTTGCAGGGTTC
                          gtctaaa  putative branch site (score: 3)
                                              taccctt  putative PPT
                           tctaaaatttagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgagtgttcgacatgccttttaatcacatcataactatagtatttttttgtgatttgatacttctttggtctaaaatttagttttatgtacccttagATCAATAGTCTTATTGGAACTAAGGTGGAGTGGGTTTATCATATGTTACAAGCATTCAACAGCGGCAACCTTGCCCTCTACCAAGAACTTTGCAGGGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC