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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtgatctttgtactatttccttttcctctaatgctatcatatgcctatttattaaccaaaaatttatccgtgacctctactcagGTATCCCTATTCTTCACCGAGACTCCTACTAATCCATTTCTGAGATGCATCGACATTGATCTTGTCTCAAAAATGTGCCATAGCAAGGGAGCATTGCTTT

Basic information

species Oryza sativa
transcript LOC_Os03g25940.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g25940.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G075153_T04 (Zea mays), 3'ss of exon 6
gtgagtgtgatctttgtactatttccttttcctctaatgctatcatatgcctatttattaaccaaaaatttatccgtgacctctactcagGTATCCCTATTCTTCACCGAGACTCCTAC-TAATCCATTTCTGAGATG-CATCGACATT-GATCTTGTCTCAAAAATGTGCCATAGCAAGGGAG--CATTGCTTT----------
                            || |||  ||||  | ||||   |    ||  | |||| || |  || |  |    |     |  |  || |   |   |   |||    | | | | ||   | ||| | |||  || || | |  || |  |   ||      | |||| | ||  |||||||            
---------------------------atttctcagatgcattgatat---tgaacatgtatcaaatatgtg-ccatagc----aagggagcgttgctttgtattgacagtactttcgcgtcacctatcaatcagAAGGCATTAACTTTAGGTGCTGACCTAGTTATTCATTCT-GCAACGAAGTACATTGCTGGACACAATGAT

upper sequence: LOC_Os03g25940.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G075153_T02 (Zea mays), 3'ss of exon 5
gtgagtgtgatctttgtactatttccttttcctctaatg----ctatcatatgcctat-ttattaaccaaaaatttatccgtgacctctactcagGTATCCCTATTCTTCACCGAGACTCCTACTAATCCATTTCTGAGATGCATCGACATTGATCTTGTCTCAAAAATGTGCCATAGCAAGGGAGCATTGCTTT
||||||||| | |   | | ||   |  |   | | ||     |||  |    | ||  ||||||     |  || |||  |    ||   ||||||||| || |||||||| ||||||||||| ||||||||||| |||||||| || ||||| | ||| ||||| |||||||||||||||||||| |||||||
gtgagtgtgttatcatttccatagtccctgattgtgataaaaactaaaaaggacatacattattagatgtagcttaatct-tatggtcatgtcagGTATCTCTTTTCTTCACGGAGACTCCTACAAATCCATTTCTCAGATGCATTGATATTGAACATGTATCAAATATGTGCCATAGCAAGGGAGCGTTGCTTT

upper sequence: LOC_Os03g25940.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G113873_T02 (Zea mays), 3'ss of exon 5
gtgagtgtgatctttgtactatttccttttcctctaatgctat-catatgcctatttattaaccaaa--aatttatccgtgacctctactcagGTATCCCTATTCTTCACCGAGACTCCTACTAATCCATTTCTGAGATGCATCGACATTGATCTTGTCTCAAAAATGTGCCATAGCAAGGGAGCATTGCTTT
||||||||| | |   | | ||| ||  |     |  |   |  ||||     ||  |||  | ||   |   || || |     |   ||||||||| || |||||||| |||||||| || ||||||||||| |||||||| || ||||| | ||| ||||| |||||||||||||||||||| |||||||
gtgagtgtggtatcatttccattgcccctgatcgtggtaaaaaacatacattaatacatttgcaaatgtagcctaaccttatggccatgtcagGTATCTCTTTTCTTCACGGAGACTCCCACAAATCCATTTCTCAGATGCATTGATATTGAACATGTATCAAATATGTGCCATAGCAAGGGAGCGTTGCTTT

upper sequence: LOC_Os03g25940.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA09G37020.3 (Glycine max), 3'ss of exon 5
----------gtgagtgtgatctttgtactatttccttttcctctaatgctatcatatgc--ctatttattaaccaaaaatttatccgtgacctc-----tactcagGTATCCCTATTCTTCACCGAGACTCCTACTAATCCATTTCTGAGATGCATCGACATTGATCTTGTCTCAAAAATGTGCCATAGCAAGGGAGCATTGCTTT
          | ||| ||  |   | | || ||      | |||| ||    | || ||    || |   |   | | | || ||  |  |             ||||| || ||||||||||| ||| ||||||| |||||||| ||||||||  | || ||| | || || ||| |  | ||||| |  |||||  | ||||| |
gttagtgttggagagagtagttggttttcttttatggaattctctgattgatttatttgtagttaatagatggtctagagttaatatggtattatacaatcgtgcagGTGTCTCTATTCTTCACTGAGTCTCCTACCAATCCATTCCTGAGATGTGTTGATATTAAGCTGGTTTCAGAGCTTTGCCACAAGAAGGGGACTTTGCTCT

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|58695584|gb|CK084271.1|CK084271
EST:     TTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGATAATAATAAT                         GTATCCCTATTCTTCACCGAGACTCCTACTAATCCATTTCTGAGATGCATC
genomic: TTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGATAATAATAATgtgagtgtga ... ctctactcagGTATCCCTATTCTTCACCGAGACTCCTACTAATCCATTTCTGAGATGCATC
EST: gi|12622757|gb|AU172970.1|AU172970
EST:     TTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGATAATAATAAT                         GTATCCCTATTCTTCACCGAGACTCCTACTAATCCATTTCTGAGATGCATC
genomic: TTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGATAATAATAATgtgagtgtga ... ctctactcagGTATCCCTATTCTTCACCGAGACTCCTACTAATCCATTTCTGAGATGCATC
EST: gi|38478380|gb|CF962513.1|CF962513
EST:     TTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGATAATAATAAT                         GTATCCCTATTCTTCACCGAGACTCCTACTAATCCATTTCTGAGATGCATC
genomic: TTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGATAATAATAATgtgagtgtga ... ctctactcagGTATCCCTATTCTTCACCGAGACTCCTACTAATCCATTTCTGAGATGCATC
EST: gi|58596991|gb|CK007519.1|CK007519
EST:     TTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGATAATAATAAT                         GTATCCCTATTCTTCACCGAGACTCCTACTAATCCATTTCTGAGATGCATC
genomic: TTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGATAATAATAATgtgagtgtga ... ctctactcagGTATCCCTATTCTTCACCGAGACTCCTACTAATCCATTTCTGAGATGCATC
EST: gi|2311404|gb|C27559.1|C27559
EST:     TTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGATAATAATAAT                         GTATCCCTATTCTTCACCGAGACTCCTACTAATCCATTTCTGAGATGCATC
genomic: TTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGATAATAATAATgtgagtgtga ... ctctactcagGTATCCCTATTCTTCACCGAGACTCCTACTAATCCATTTCTGAGATGCATC
EST: gi|29671055|gb|CB667330.1|CB667330
EST:     TTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGATAATAATAAT                         GTATCCCTATTCTTCACCGAGACTCCTACTAATCCATTTCTGAGATGCATC
genomic: TTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGATAATAATAATgtgagtgtga ... ctctactcagGTATCCCTATTCTTCACCGAGACTCCTACTAATCCATTTCTGAGATGCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgctatcatatgcctatttattaaccaaaaatttatccgtgacctctactcagGTATCCCTATTCTTCACCGAGACTCCTACTAATCCATTTCTGAGATGCATCGACATTGATCTTGTCTCAAAAATGTGCCATAGCAAGGGAGCATTGCTTT
                    tattaac  putative branch site (score: 1)
                                            cctctactc  putative PPT
                tatttattaaccaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgtgatctttgtactatttccttttcctctaatgctatcatatgcctatttattaaccaaaaatttatccgtgacctctactcagGTATCCCTATTCTTCACCGAGACTCCTACTAATCCATTTCTGAGATGCATCGACATTGATCTTGTCTCAAAAATGTGCCATAGCAAGGGAGCATTGCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA