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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattcaaagttgttgatatgtggtggtagccatttattgtgcttatatgccctatggttgaatggtgtgcttcatttatctgacttgtctctttcactagGTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACTTCAGTGCTGGCAGCTAAAGCTTACAAATACAAAGCAGAATCACTTGTTA

Basic information

species Zea mays
transcript GRMZM5G825226_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825226_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g56230.5 (Oryza sativa), 3'ss of exon 1
gattcaaagttgttgatatgtggtggtagccatttattgtgcttatatgccctatggttgaatggtgtgcttcatttatctgacttgtctctttcactagGTTCAGTAGGTTGTTGAGTCTAG--ATACCAGATGATGGACCTGTCCACGACTTCAGTGCTGGCAGCTAAAGCTTACAAATACAAAGCAGAATCACTTGTTA--------
 ||||  |||| |     ||| ||  | |||||||||||| |||  |  | |||   |  |  | ||    |    | ||  ||||| ||| | |  |   ||||  ||||    ||||| ||  ||| ||||||||||| |||||||||||||||||  |||| ||||| || ||||| |||| |||||||||||||||||        
-attcttagttttc----tgtagtactggccatttattgttcttg-actctctaatttccatggctgaatctacaatgtcctacttgactcatccctt---ttcatcagGTCAG-GAGTCAAGGTATATCAGATGATGGATCTGTCCACGACTTCAGTAGTGGCTGCTAAGGCCTACAAGTACAGAGCAGAATCACTTGTTAAGGACTAC

upper sequence: GRMZM5G825226_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g56230.1 (Oryza sativa), 3'ss of exon 1
gattcaaagttgttgatatgtggtggtagccatttattgtgcttatatgccctatggttgaatggtgtgcttcatttatctgacttgtctctttcactagGTTCAGTAGGTTGTTGAGTCTAG--ATACCAGATGATGGACCTGTCCACGACTTCAGTGCTGGCAGCTAAAGCTTACAAATACAAAGCAGAATCACTTGTTA-------------
          |  |  | ||| ||  | |||||||||||| |||  |  | |||   |  |  | ||    |    | ||  ||||| ||| | |  |   ||||  ||||    ||||| ||  ||| ||||||||||| |||||||||||||||||  |||| ||||| || ||||| |||| |||||||||||||||||             
----------tagttttctgtagtactggccatttattgttcttg-actctctaatttccatggctgaatctacaatgtcctacttgactcatccctt---ttcatcaggtcag-
















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|149069941|gb|EE158341.2|EE158341
EST:     TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAG                         GTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
genomic: TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAGgtaactaatg ... ctttcactagGTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
EST: gi|26455029|gb|CA826612.1|CA826612
EST:     TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAG                         GTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
genomic: TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAGgtaactaatg ... ctttcactagGTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
EST: gi|148934690|gb|EC878738.2|EC878738
EST:     TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAG                         GTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
genomic: TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAGgtaactaatg ... ctttcactagGTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
EST: gi|71771875|gb|DR969812.1|DR969812
EST:     TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAG                         GTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
genomic: TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAGgtaactaatg ... ctttcactagGTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
EST: gi|76925225|gb|DV170328.1|DV170328
EST:     TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAG                         GTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
genomic: TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAGgtaactaatg ... ctttcactagGTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
EST: gi|21330525|gb|BQ485906.1|BQ485906
EST:     TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAG                         GTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
genomic: TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAGgtaactaatg ... ctttcactagGTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
EST: gi|78082331|gb|DV510743.1|DV510743
EST:     TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAG                         GTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
genomic: TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAGgtaactaatg ... ctttcactagGTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
EST: gi|78112273|gb|DV530667.1|DV530667
EST:     TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAG                         GTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
genomic: TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAGgtaactaatg ... ctttcactagGTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
EST: gi|74237536|gb|DT645450.1|DT645450
EST:     TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAG                         GTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
genomic: TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAGgtaactaatg ... ctttcactagGTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
EST: gi|149078049|gb|EE166790.2|EE166790
EST:     TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAG                         GTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
genomic: TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAGgtaactaatg ... ctttcactagGTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
EST: gi|76918369|gb|DV167265.1|DV167265
EST:     TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAG                         GTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
genomic: TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAGgtaactaatg ... ctttcactagGTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
EST: gi|28566726|gb|CB278374.1|CB278374
EST:     TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAG                         GTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
genomic: TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAGgtaactaatg ... ctttcactagGTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
EST: gi|87154553|gb|DY399342.1|DY399342
EST:     TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAG                         GTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT
genomic: TCGCGCCCCTCCTTCCTGCCTGCCGTAACCGCGCCGTGCAACTGTGCAAGgtaactaatg ... ctttcactagGTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgccctatggttgaatggtgtgcttcatttatctgacttgtctctttcactagGTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACTTCAGTGCTGGCAGCTAAAGCTTACAAATACAAAGCAGAATCACTTGTTA
                                atctgac  putative branch site (score: 3)
                                      cttgtctctttcact  CT-rich tract
                         ttcatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattcaaagttgttgatatgtggtggtagccatttattgtgcttatatgccctatggttgaatggtgtgcttcatttatctgacttgtctctttcactagGTTCAGTAGGTTGTTGAGTCTAGATACCAGATGATGGACCTGTCCACGACTTCAGTGCTGGCAGCTAAAGCTTACAAATACAAAGCAGAATCACTTGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - tgttgat
- - - - - - - - - tgtggtg
- - - - - - - - - - - - -gtagcca
- - - - - - - - - - - - - - - - - - -tgtgctt
- - - - - - - - - - - - - - - - - - - - - - - -tgcccta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgaatg