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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGATAATGGGAGTCTCTGGTTTTGGGATTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattgatttgcatcatgtatgggctgttattatgtttctttaagtcactaaatcgatcatcttgattgatcttatttccaattatag

Basic information

species Oryza sativa
transcript LOC_Os03g21990.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g21990.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G017089_T01 (Zea mays), 5'ss of exon 15
GGGATAATGGGAGTCTCTGGTTTTGGGATTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattgatttgcatcatgtatgggctgttattatgtttctttaagtcactaaatcgatcatcttgattgatcttatttccaattatag----------
|||||||||| || || ||||||||||| ||||||||||| ||||||||||||||||||||||||||||| || |||||||||| || ||||| |||| | | |  | | || || |        |    ||   ||||   ||   | || | ||   ||  || | ||          
GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTGgtaagttttcatttgaatcacgcaggcaccgataataggagataagcaact-ctgtttcgagtctccacaatg-tttttcctcatatgagaggttcttgaga

upper sequence: LOC_Os03g21990.1 (Oryza sativa), 5'ss of exon 17
lower sequence: Vv05s0077g02310.t01 (Vitis vinifera), 5'ss of exon 16
GGGATAATGGGAGTCTCTGGTTTTGGGATTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattgatttgcatcatgtatgggctgttattatgtttctttaagtcactaaatcgatcatcttgattgatcttatttccaattatag
| || ||||||||| | ||||| ||||||||||||||||| || || ||||| ||||  || || || ||||| ||||||| ||||  | | ||      | | || | ||  |  |||| |  ||   |  |||| |||||  |  ||||||||    |    ||  ||
GCGACAATGGGAGTATGTGGTTCTGGGATTGGAAGAGTGGTCACAATTTTCAGCAAGCCCAAACAATTGTACAGCCTGgtatgtatctaat-gc------tcttggttattgct--gtttgtagaaaggagaaaat-gatcaaat--attgatctatacttttgtttcag
















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|86539397|gb|CI179603.1|CI179603
EST:     TTGGAAGAGTGGCCATGACTTTCAACAAGATCAGACTATAGTACAACCTG                         GATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
genomic: TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
EST: gi|86874182|gb|CI335828.1|CI335828
EST:     ATAACTTTCAACAAGATCAGACTATAGTACAACCTG                         GATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
genomic: ATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
EST: gi|88451871|gb|CI694646.1|CI694646
EST:     TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTG                         GATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
genomic: TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
EST: gi|88996369|gb|CI389080.1|CI389080
EST:     CTTTCAACAAGATCAGACTATAGTACAACCTG                         GATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
genomic: CTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
EST: gi|33653590|gb|CF276204.1|CF276204
EST:     ATAACTTTCAACAAGATCAGACTATAGTACAACCTG                         GATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
genomic: ATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
EST: gi|86843586|gb|CI339619.1|CI339619
EST:     TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTG                         GATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
genomic: TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
EST: gi|88466315|gb|CI529724.1|CI529724
EST:     TCAGACTATAGTACAACCTG                         GATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
genomic: TCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
EST: gi|33691858|gb|CF320097.1|CF320097
EST:     TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTG                         GATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
genomic: TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
EST: gi|86833648|gb|CI337222.1|CI337222
EST:     ACAAGATCAGACTATAGTACAACCTG                         GATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
genomic: ACAAGATCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
EST: gi|86834332|gb|CI344092.1|CI344092
EST:     TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTG                         GATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
genomic: TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
EST: gi|88901914|gb|CI374522.1|CI374522
EST:     TTTCAACAAGATCAGACTATAGTACAACCTG                         GATCATTTGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
genomic: TTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
EST: gi|29643709|gb|CB648716.1|CB648716
EST:     TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTG                         GATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
genomic: TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
EST: gi|86822129|gb|CI357794.1|CI357794
EST:     GAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTG                         GATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
genomic: GAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
EST: gi|29679953|gb|CB676228.1|CB676228
EST:     TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTG                         GATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
genomic: TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
EST: gi|89195126|gb|CI051239.1|CI051239
EST:     TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTG                         GATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
genomic: TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
EST: gi|88852220|gb|CI373988.1|CI373988
EST:     GACTATAGTACAACCTG                         GATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
genomic: GACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
EST: gi|88543819|gb|CI473860.1|CI473860
EST:     AAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTG                         GATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
genomic: AAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
EST: gi|13165136|gb|AU173933.1|AU173933
EST:     AACTTTCAACAAGATCAGACTATAGTACAACCTG                         GATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
genomic: AACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
EST: gi|29633915|gb|CB638924.1|CB638924
EST:     TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTG                         GATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
genomic: TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
EST: gi|88832756|gb|CI369646.1|CI369646
EST:     ATAACTTTCAACAAGATCAGACTATAGTACAACCTG                         GATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
genomic: ATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
EST: gi|29643713|gb|CB648720.1|CB648720
EST:     TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTG                         GATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
genomic: TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
EST: gi|88959830|gb|CI381708.1|CI381708
EST:     TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTG                         GATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATTTTAGTG
genomic: TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
EST: gi|88969983|gb|CI383485.1|CI383485
EST:     TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTG                         GATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
genomic: TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
EST: gi|86421611|gb|CI057600.1|CI057600
EST:     TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTG                         GATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
genomic: TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
EST: gi|89176346|gb|CI043367.1|CI043367
EST:     TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTG                         GATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG
genomic: TTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 69 (upstream exon), 74 (downstream exon)
Score: 19

GGGATAATGGGAGTCTCTGGTTTTGGGATTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattg ... ccaattatagGATCATTGGAGAGTGAGGCATGCATATATGCCCTTTCATACGATGTTAGTGGATCACGGCTGGTGACATGTGAAGCTGACAAGACAATAAAAATGTGGAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGATAATGGGAGTCTCTGGTTTTGGGATTGGAAGAGTGGCCATAACTTTCAACAAGATCAGACTATAGTACAACCTGgtaagtattgatttgcatcatgtatgggctgttattatgtttctttaagtcactaaatcgatcatcttgattgatcttatttccaattatag

- - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA