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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCATCACATCATCACTGGTACCATTTTAATGCAGGTTAATGGTCTTATTAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttacctctgcattcgtttgatttttctctacatgtggtaatctgtactagcaatcctgtggtaatgaaattgattttcacgtccttgtcactaaatggtcataatatattgtgttgtag

Basic information

species Oryza sativa
transcript LOC_Os03g16980.4
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g16980.4 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 11
TTGCATCACATCATCACTGGTACCATTTTAATGCAGGTTAATGGTCTTATTAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttacctctgcattcgtttgatttttctctacatgtggtaatctgtactagcaatcctgtggta----atgaaattgattttcacgt----------------ccttgtcactaaatggtcataatatattgtgttgtag
                                    ||| ||||||||||||  |||||||| ||  |||||||||| || ||||| ||||| |||||||||| | |  | |||| |||   || | |||| |    |    || | ||   ||| | | |||||| |     || | ||  ||| ||  |                  |||    ||||||||   |||    | ||| || ||
------------------------------------GTTGATGGTCTTATTAGACTGATGAATGGAAACAACACTGGGCCGATTAACTTGGGGAACCCAGgtaaaatc-catctgaatt---ttaacttttgttactacacagtgagctac-ctacccaacctgtgtttttctattatatgcattctcctggactgagttgggtctcatctttctgctaaatggctgtaac---tggtgctgcag

upper sequence: LOC_Os03g16980.4 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G165357_T01 (Zea mays), 5'ss of exon 11
TTGCATCACATCATCACTGGTACCATTTTAATGCAGGTTAATGGTCTTATTAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttacctctgcattcgtttgatttttctctacatgtggtaatctgtactagcaatcctgtggtaatgaaattgattttcacgtccttg----tcactaaatggtcataatatattgtgttgtag
                                    ||| |||||||||||||||||||||| ||  |||| |||||||| ||||| ||||| |||||||||| ||| |  ||||  ||                           |  |||    || |||||||||||  || |||  |  ||  | |||        |||||||||  |||    |||||  | ||
------------------------------------GTTGATGGTCTTATTAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa-tctgtgtt---------------------------ttcgtatgtacattcctgtggtaaccaagttgggtcccatcttcttcagttcttctaaatggttgtaac---ttgtgccgcag
















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|86852342|gb|CI319277.1|CI319277
EST:     TGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|89186937|gb|CI053340.1|CI053340
EST:     TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|88987937|gb|CI017999.1|CI017999
EST:     TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|86253045|gb|CI057970.1|CI057970
EST:     CTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: CTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|89176626|gb|CI111342.1|CI111342
EST:     TAAGCTGATGAACGGGGACAACACTGGACCCATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|86252444|gb|CI056181.1|CI056181
EST:     TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|38477586|gb|CF961719.1|CF961719
EST:     AAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAAGCCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: AAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAA-CCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|88297272|gb|CI545362.1|CI545362
EST:     TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|33813745|gb|CF332759.1|CF332759
EST:     TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|88981021|gb|CI021148.1|CI021148
EST:     TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|58684041|gb|CK072728.1|CK072728
EST:     TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|8859289|gb|AU096607.1|AU096607
EST:     TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|86257228|gb|CI004046.1|CI004046
EST:     TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|86425774|gb|CI070871.1|CI070871
EST:     TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|89186897|gb|CI053300.1|CI053300
EST:     TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|87034463|gb|CI189087.1|CI189087
EST:     CGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: CGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|86852460|gb|CI320385.1|CI320385
EST:     CCAATTAATGT-GGAAACCCAG                         GTGAATTCACCA-GCTGGAACTTGGCTGAGAATGTGAAGGGAG
genomic: CCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTT-GCTGAGAATGTGAA-GGAG
EST: gi|89194251|gb|CI116688.1|CI116688
EST:     TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|86258634|gb|CI064987.1|CI064987
EST:     ACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: ACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|88839265|gb|CI000737.1|CI000737
EST:     TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|86259156|gb|CI010457.1|CI010457
EST:     GATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: GATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|15853120|gb|BI805916.1|BI805916
EST:     AANCTGATGAACGGGGACAACACTGGACC-ATTAATTGTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: AAGCTGATGAACGGGGACAACACTGGACCAATTAATT-TGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|58607978|gb|CK036011.1|CK036011
EST:     TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|4968619|gb|AU065523.1|AU065523
EST:     CGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: CGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|88841372|gb|CI005452.1|CI005452
EST:     CTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: CTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|94362093|gb|CI052892.1|CI052892
EST:     AATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: AATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|86543097|gb|CI183303.1|CI183303
EST:     CGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: CGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|87018890|gb|CI256775.1|CI256775
EST:     TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|58613250|gb|CK040962.1|CK040962
EST:     CGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: CGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|88837252|gb|CI078612.1|CI078612
EST:     ACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: ACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|33680607|gb|CF308846.1|CF308846
EST:     TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCCGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|86901883|gb|CI298530.1|CI298530
EST:     TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|86254397|gb|CI059124.1|CI059124
EST:     ATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: ATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|87018932|gb|CI256817.1|CI256817
EST:     TAAGCTGATGAACGGGGACTACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|13896507|gb|AU182843.1|AU182843
EST:     GGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: GGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|86250768|gb|CI007631.1|CI007631
EST:     TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|86420903|gb|CI056892.1|CI056892
EST:     GGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: GGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|89174852|gb|CI111050.1|CI111050
EST:     TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttac ... tgtgttgtagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCATCACATCATCACTGGTACCATTTTAATGCAGGTTAATGGTCTTATTAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttacctctgcattcgtttgatttttctctacatgtggtaatctgtactagcaatcctgtggtaatgaaattgattttcacgtccttgtcactaaatggtcataatatattgtgttgtag

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT