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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgccaaataacaaaatcataaaaaatttcctagcagtgcattttgtcctgttgtgttttgatggtttcttactcctcccattacttttcatatggcagTGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGATAGCTACTGATGCTGATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAA

Basic information

species Oryza sativa
transcript LOC_Os06g05180.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G448913_T01 (Zea mays), 3'ss of exon 6
agtgccaaataacaaaatcataaaaaatttccta-gcagtgcattttgtcctgt-tgtgttttgatggtttcttactcc---tcccattacttt-tcatatggcagTGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGATAGCTACTGATGCTGATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAA
      | |||   |  |  |   |   ||  |  | | | | |         | |    | || |   ||||  |  |   ||   || || | ||||||||||||||||||||||| ||||| || ||||||||| |||| || || ||||||||||| ||||||||||| |||| |||||||||||||||||| |||||||||
------atatacttagttttttgcactctttttctgtatttcgtccaacttcatgtagagtctgttctcttctggcctcagttcttgtttctctctcatatggcagTGTTGCTCATTTTTTGGAATCGAGAGGTATGTTGGAAGAGGCTCTTGAGATAGCCACTGATGCTGACTACAAGTTTGACCTAGCTGTGCAGCTTGGAAAA

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 17
agtgccaaataacaaaatca-taaaaaatttcctagcagtgcattttgtcctgt-tgtgttttgatggtttcttactcc---tcccattacttt-tcatatggcagTGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGATAGCTACTGATGCTGATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAA
      | |||   |  |   |  |   |||    | | | | |         | |    | || |   ||||  |  |   ||   || || | ||||||||||||||||||||||| ||||| || ||||||||| |||| || || ||||||||||| ||||||||||| |||| |||||||||||||||||| |||||||||
------atatacttagttttctgcactctttttctgtatttcgtccaacttcatgtagagtctgttctcttctagcctcagttcttgtttctctctcatatggcagTGTTGCTCATTTTTTGGAATCGAGAGGTATGTTGGAAGAGGCTCTTGAGATAGCCACTGATGCTGACTACAAGTTTGACCTAGCTGTGCAGCTTGGAAAA

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 16
agtgccaaataacaaaatcataaaaaatttcctagcagtgcattttgtcctgttgtgttttga-----tggtttcttactcc----tcccattact-tttcatatggcagTGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGATAGCTACTGATGCTGATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAA
        |||   |  |      |   ||  |    ||| |||||| ||       ||| ||     |  | | |||  |     ||   || || ||||||||||||||||||||||||| ||||| || ||||||||| |||| || || ||||||||||| || |||||||| |||| |||||||||||||||||| |||||||||
------gtatacttagttttctccacccttttt----gtgtattttggccaacatcatttagagtctgtactcttttaacctcggttcttgtttctctttcatatggcagTGTTGCTCATTTTTTGGAATCTAGAGGTATGTTGGAAGAGGCTCTTGAGATAGCCACGGATGCTGACTACAAGTTTGACCTAGCTGTGCAGCTTGGAAAA

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 17
lower sequence: EFJ36319 (Selaginella moellendorffii), 3'ss of exon 12
agtgccaaataacaaaatcataaaaaatttcctagcagtgcattttgtcctgttgtgttttgatggtttcttactcctcccattacttttcatatggcagTGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGATAGCTACTGATGCTGATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAA
                                                   ||    ||  | |||| | | || | || || ||||  |  |    ||||||||| ||||||||||||||| | |||||||||||||| || |||||    || |||||| | |||||  | |||||||| ||||||||||| || |||
---------------------------------------------------gtaaacttgggctggtgtataacac-tctcaatactcctatt----cagTGTTGCCCATTTCTTGGAGTCACGTGGTATGCTGGAGGACGCCCTTGAAGCGGCAACTGATCCGGATTATCGATTTGACCTTGCTGTGCAACTGGGCAAA

upper sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 17
lower sequence: EFJ09529 (Selaginella moellendorffii), 3'ss of exon 12
agtgccaaataacaaaatcataaaaaatttcctagcagtgcattttgtcctgttgtgttttgatggtttcttactcctcccattacttttcatatggcagTGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGATAGCTACTGATGCTGATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAA
                                     ||  | |||| |  ||  |  |||| | || |   ||||     | | || ||||       ||||||| ||||||||||||||| | |||||||||||||| || |||||    || |||||| | |||||  | |||||||| ||||||||||| || |||
-------------------------------------gtaaactttggctggtact--tttgctagtataacactctcaatactcctattca-------gTGTTGCCCATTTCTTGGAGTCACGTGGTATGCTGGAGGACGCCCTTGAAGCGGCAACTGATCCGGATTATCGATTTGACCTTGCTGTGCAACTGGGCAAA

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|58690875|gb|CK079562.1|CK079562
EST:     GAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAA                         TGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGAT
genomic: GAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgct ... catatggcagTGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGAT
EST: gi|2443004|gb|C74775.1|C74775
EST:     GAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAA                         TGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGAT
genomic: GAACGTGCAAATGATATTTTACCATCCATACCAAAGGCGCAATATAATAAgttagttgct ... catatggcagTGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcctgttgtgttttgatggtttcttactcctcccattacttttcatatggcagTGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGATAGCTACTGATGCTGATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAA
                      ttcttac  putative branch site (score: 2)
                     tttcttactcctccca  CT-rich tract
                                    attacttttcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgccaaataacaaaatcataaaaaatttcctagcagtgcattttgtcctgttgtgttttgatggtttcttactcctcccattacttttcatatggcagTGTTGCTCATTTCTTGGAGTCAAGAGGTATGCTGGAGGAAGCACTTGAGATAGCTACTGATGCTGATTACAGGTTTGACCTAGCTGTGCAACTTGGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT