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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataacatctgtcattatgtgcatttctcatctcctttggtttcttgctctgacaccttcatcatgtcag

Basic information

species Zea mays
transcript GRMZM2G011923_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011923_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g41930.1 (Oryza sativa), 5'ss of exon 4
GCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataacatctgtcattatgtgcatttctcatct-cctttggtttcttgctctgacacc--------ttcatcatgtcag
||| | |||||||| || |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||| || | ||| ||| | |  |||  ||||||||| | | ||||||||| ||| |||| |          |||||  |   ||
GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtaatggttacagctggcgt-gtgtttatttctcatttacttttggtttcatgcactgatattctgctatattcattctactag

upper sequence: GRMZM2G011923_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA16G06100.1 (Glycine max), 5'ss of exon 4
GCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataacatctgtcattatgtgcatttctcatctcctttggtttcttg-ctctgacaccttcatcatgtcag---------------------------
|| || ||||||||||| ||||| || ||||| ||||| ||||||||||| || || ||||| ||||| || || ||||| |||||| |   || ||     ||| ||      |   |   | | |     |||  || | |  |  | |  |   ||                            
GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAGgtagtag-aatatagaatattttgaaatggtgggagaccatgtatgagcttatctgtaaatcaatgaataaaacaatatttttgttccttctcttccttgtag

upper sequence: GRMZM2G011923_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA19G25870.1 (Glycine max), 5'ss of exon 4
GCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactg----ataaca-tctgtcattatgtg---catttctcatctcctttg---gtttcttgctctgacaccttcatcatgtcag-------------
|| || ||||||||||| ||||| || ||||| ||||| ||||||||||| || || ||||| ||||| || || ||||| |||||| |     |||  | | ||  ||  ||     ||| | | | ||  | ||    |   |   |   |||      |  || |               
GCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGGGAATCAAGGTTTCCAGCTCAGgtagtagaatataggactttgaaatggtggagaccatgtatgagcttatctgtaaatcaatgaataaaacaaaaaatttgtgcctcctcttccttgtag

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|22490259|gb|BU050182.1|BU050182
EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTCTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
EST: gi|18655190|gb|BM499995.1|BM499995
EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTCTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
EST: gi|29544431|gb|CB604811.1|CB604811
EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGC
EST: gi|149107938|gb|EE292294.2|EE292294
EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
EST: gi|31351065|gb|CD435422.1|CD435422
EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
EST: gi|31352279|gb|CD436636.1|CD436636
EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
EST: gi|31352997|gb|CD437354.1|CD437354
EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
EST: gi|29544031|gb|CB604411.1|CB604411
EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAG
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAG
EST: gi|87152915|gb|DY397704.1|DY397704
EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTCTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
EST: gi|31351326|gb|CD435683.1|CD435683
EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
EST: gi|148982112|gb|EE028161.2|EE028161
EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
EST: gi|37399688|gb|CF637177.1|CF637177
EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTCTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
EST: gi|60350260|gb|DN217233.1|DN217233
EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
EST: gi|78087740|gb|DV516133.1|DV516133
EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
EST: gi|40303492|gb|CK347879.1|CK347879
EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTCTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
EST: gi|45567374|gb|CK985540.1|CK985540
EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTCTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
EST: gi|60346554|gb|DN213527.1|DN213527
EST:     AAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: AAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
EST: gi|31352510|gb|CD436867.1|CD436867
EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
EST: gi|149082225|gb|EE171408.2|EE171408
EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
EST: gi|60401294|gb|DN234101.1|DN234101
EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTCTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
EST: gi|211413346|gb|FL280968.1|FL280968
EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTCTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
EST: gi|60358053|gb|DN225026.1|DN225026
EST:     CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
EST: gi|29544380|gb|CB604760.1|CB604760
EST:     CATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAG                         GTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC
genomic: CATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataa ... atcatgtcagGTGAGGATCCGCGTTAGGAAGCTGTGCAAGCCGTTGGAAGAGGATTCCTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCCAGTTTTGGTGGGTCTAATATTGATCCCACTGCATGGGAGGATAAGAAGTGTAAAGGTGAATCTAGATTCCCAGCGCAGgtactgataacatctgtcattatgtgcatttctcatctcctttggtttcttgctctgacaccttcatcatgtcag

- - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT