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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtttattttctaatttaattgttatcgagttgttgtacctgccctcacatcaaaatctgagtattgtttgcctaagtaaaccttctcactctgtatatatctcgggcatatttcccaatgggtgtttttgttgatgagcagaggttttggctatctaaactcagaagtcctgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAG

Basic information

species Zea mays
transcript GRMZM2G035150_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035150_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g64219.1 (Oryza sativa), 3'ss of exon 8
gtaatgtttattttctaatttaattgttatcgagttgttgtacctgccctcacatcaaaatctgagtattgtttgcctaagtaaaccttctcactctgtata-tatctcgggcatatttcccaatgggtgtttttgttgatgagcagaggttttggctatctaaactcagaagtcctgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAG
                                                                        |  | | | |   | |  | | | || ||| |   | |  |   |||  |||| | ||| | |  | ||| |     |||     | ||    || | ||  ||       ||||||||||||||||||||||||||||||||||||||||||| |||||||| |||||||
-----------------------------------------------------------------------gtaacttcattgttcttagttagtttgcatagtggattgtac---tttttcaatagatgtgtat-ctaatgtgtttctgttcattttttc----cttaaaaaacc-------cagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCGATATATCCAGAAGGAG

upper sequence: GRMZM2G035150_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g39230.1 (Oryza sativa), 3'ss of exon 15
gtaatgtttattttc--taatttaattgttatcg-agttgttgtacctgccctcacatcaaaatctgagtattgtttgcctaagtaaaccttctcactctgtatatatctcgggcatatttcccaatgggtgtttttgttgatgagcagaggttttggctatctaaactcagaagtcctgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAG
|||   ||| ||||    |||| |||| |||  | | ||  | |||   |       |     ||| ||| |  ||||||||      | | || ||| ||  || ||     |  ||| |    |||  | ||| |||| ||        |||||  ||  | |||| ||||                 |||||| | |||||||||||||||||||||||| | ||  ||||| | |||  ||
gtagcctttttttttggcaattgaatttttactgcaattaatatactaactgcactgt-----tcttagt-tgatttgcctagtaggtcatacttact-tgagtagat-----gtgtatct---gatg--tatttctgtttattttt----gtttt--ctcccaaaacccagAG----------------ATATGCATTAGTTTTTGGGCTGAGGTGCACTACGATTCGGTATATGCAGAAAAAG

upper sequence: GRMZM2G035150_T02 (Zea mays), 3'ss of exon 9
lower sequence: EFJ31563 (Selaginella moellendorffii), 3'ss of exon 7
gtaatgtttattttctaatttaattgttatcgagttgttgtacctgccctcacatcaaaatctgagtattgtttgcctaagtaaaccttctcactctgtatatatctcgggcatatttcccaatgggtgtttttgttgatgagcagaggttttggctatctaaactcagaagtcctgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAG
                                                                                                                                        |    ||      |   |||  ||     | |       | |  |||||| |||| ||| || ||||||||||| ||||||||||||||| | ||||| |||||||
---------------------------------------------------------------------------------------------------------------------------------------gtagcaagtttccttccaggcgctcatcggtaacgctcgttttcttgcagTCATATTCTTAAGCTTTTGGGCTGAAGTGCACTACAACTCCGTGTATCCGGAAGGAG

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|74235678|gb|DT643592.1|DT643592
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|78092883|gb|DV521257.1|DV521257
EST:     AGATACATGTTATATTGAGATTTTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|4804174|gb|AI666040.1|AI666040
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|32808275|gb|CD960509.1|CD960509
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCGGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|76289426|gb|DV028994.1|DV028994
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|71427953|gb|DR809003.1|DR809003
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|113633600|gb|DW792172.1|DW792172
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGC
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGC
EST: gi|32793686|gb|CD945922.1|CD945922
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|86466720|gb|DY233090.1|DY233090
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|71427180|gb|DR808230.1|DR808230
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|50324081|gb|CO519207.1|CO519207
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|50331811|gb|CO526937.1|CO526937
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|78080763|gb|DV509175.1|DV509175
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|24462661|gb|BM660192.1|BM660192
EST:     CTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: CTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
EST: gi|50327716|gb|CO522842.1|CO522842
EST:     AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAG                         TTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG
genomic: AGATACATGTTATATTGAGATTCTTCCTGTTGTTGAGAAATCCAGAAGAGgtaatgttta ... tgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgttgatgagcagaggttttggctatctaaactcagaagtcctgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAG
                           atctaaa  putative branch site (score: 3)
                                          tcctgtt  putative PPT
                          tatctaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtttattttctaatttaattgttatcgagttgttgtacctgccctcacatcaaaatctgagtattgtttgcctaagtaaaccttctcactctgtatatatctcgggcatatttcccaatgggtgtttttgttgatgagcagaggttttggctatctaaactcagaagtcctgttgtgcagTTATATGCTTGAGTTTTTGGGCTGAGGTGCACTACAACTCCATATATCCTGAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG