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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattgtacaagactatttagtcagatgtctacagatttagcctgtcccaaccaaatccccaagaggttcagttgtctgattagatgtttcttggatgcagGAAATAGATATCTGGTCATTTGGATGTTTTTTATTGGAGATGCTTACGCTTCAGATGCCTTACCAGGGACTTTCTGACACTGAAATATATGATCTGATAC

Basic information

species Zea mays
transcript GRMZM2G155312_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155312_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g53250.1 (Oryza sativa), 3'ss of exon 6
cattgta-caagactatttagtcagatgtctacagatttagcctgt--cccaaccaaatccccaagaggtt------cagttgtctgattagatgtttcttggatgcagGAAATAGATATCTGGTCATTTGGATGTTTTTTATTGGAGATGCTTACGCTTCAGATGCCTTACCAGGGACTTTCTGACACTGAAATATATGATCTGATAC
     || ||| | |||      || |  ||     | |||| |||   | || |||  | |||     ||         || | |   || || | | |    |||||||| | ||||||||||||||||| ||||||||||||||||||||||| |||| ||| || |||||||| ||  ||||  | |||||||||||||| ||| 
----atatcaacaatatgctcctaggtacct-----tctagcatgtagtcaaatcaacactccatataattgcttgatgtttatatatatatatatatatatattgcagGAAGTTGATATCTGGTCATTTGGCTGTTTTTTATTGGAGATGCTTACACTTCGGATACCCTACCAGGGCCTACCTGATTCAGAAATATATGATCTCATAA
















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|211106603|gb|FL402533.1|FL402533
EST:     TGGCTCCAGAGGTTGTTAAGGCCATGCATGAAAAACACCACTATGGACTG                         GAAATAGATATCTGGTCATTTGGATGTTTTTTATTGGAGATGCTTACGCTT
genomic: TGGCTCCAGAGGTTGTTAAGGCCATGCATGAAAAACACCACTATGGACTGgtaagaattt ... ttggatgcagGAAATAGATATCTGGTCATTTGGATGTTTTTTATTGGAGATGCTTACGCTT
EST: gi|91052138|gb|EB162556.1|EB162556
EST:     TGGCTCCAGAGGTTGTTAAGGCCATGCATGAAAAACACCACTATGGACTG                         GAAATAGATATCTGGTCATTTGGATGTTTTTTATTGGAGATGCTTACGCTT
genomic: TGGCTCCAGAGGTTGTTAAGGCCATGCATGAAAAACACCACTATGGACTGgtaagaattt ... ttggatgcagGAAATAGATATCTGGTCATTTGGATGTTTTTTATTGGAGATGCTTACGCTT
EST: gi|211454500|gb|FL406359.1|FL406359
EST:     TGGCTCCAGAGGTTGTTAAGGCCATGCATGAAAAACACCACTATGGACTG                         GAAATAGATATCTGGTCATTTGGATGTTTTTTATTGGAGATGCTTACGCTT
genomic: TGGCTCCAGAGGTTGTTAAGGCCATGCATGAAAAACACCACTATGGACTGgtaagaattt ... ttggatgcagGAAATAGATATCTGGTCATTTGGATGTTTTTTATTGGAGATGCTTACGCTT
EST: gi|211521523|gb|FL409909.1|FL409909
EST:     TGGCTCCAGAGGTTGTTAAGGCCATGCATGAAAAACACCACTATGGACTG                         GAAATAGATATCTGGTCATTTGGATGTTTTTTATTGGAGATGCTTACGCTT
genomic: TGGCTCCAGAGGTTGTTAAGGCCATGCATGAAAAACACCACTATGGACTGgtaagaattt ... ttggatgcagGAAATAGATATCTGGTCATTTGGATGTTTTTTATTGGAGATGCTTACGCTT
EST: gi|67010793|gb|CO439542.1|CO439542
EST:     GGCCATGCATGTATAAACACCACTATGGNACTGG                         GAAATACATATCTGGTCATTTGGATGTTTTTTATTGGAGATGCTTACGCT
genomic: GGCCATGCATG-AAAAACACCACTATGG-ACT-Ggtaagaattt ... ttggatgcagGAAATAGATATCTGGTCATTTGGATGTTTTTTATTGGAGATGCTTACGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccaaccaaatccccaagaggttcagttgtctgattagatgtttcttggatgcagGAAATAGATATCTGGTCATTTGGATGTTTTTTATTGGAGATGCTTACGCTTCAGATGCCTTACCAGGGACTTTCTGACACTGAAATATATGATCTGATAC
                            gtctgat  putative branch site (score: 4)
                                       tgtttctt  putative PPT
                                 attagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattgtacaagactatttagtcagatgtctacagatttagcctgtcccaaccaaatccccaagaggttcagttgtctgattagatgtttcttggatgcagGAAATAGATATCTGGTCATTTGGATGTTTTTTATTGGAGATGCTTACGCTTCAGATGCCTTACCAGGGACTTTCTGACACTGAAATATATGATCTGATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - aaccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgtttc