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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAGgtacatatacatcattgttgataacttgcatgcattaaaaattctcttatttcaatgatcatcaatatatctagggatgcctatcaactttacataaaaa...

Basic information

species Oryza sativa
transcript LOC_Os12g01140.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01140.5 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G001457_T02 (Zea mays), 5'ss of exon 16
GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAGgtacatatacatcattgttgataacttgcatgcattaaaaattctcttatttcaatg-atcatcaatatatctagggatgcctatcaactttacataaaaa
|||||||||||| ||||||||    ||||| ||||||||||||||||||||||   ||| ||  |  |  |  || | |   |   || | || || | |   | |  ||  |  |  |||   |  |    ||  ||      |  ||  
GTTCTATGCTGCAGAAGTGGTCACAGCACTTGAATACCTACATTGCCAAGgtagtcatatat-gtcatatactacctccggtctcgaatatttgtcgtttgctagttcatgtttgaactataacgtaacaaataaaaaaaacggacgaagt
















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|66913937|gb|CX100785.1|CX100785
EST:     GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG                         GTATAATATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATG
genomic: GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAGgtacatatac ... ttgtcttcagGTATAATATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATG
EST: gi|29623925|gb|CB628936.1|CB628936
EST:     GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG                         GTATAATATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATG
genomic: GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAGgtacatatac ... ttgtcttcagGTATAATATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATG
EST: gi|86908120|gb|CI300633.1|CI300633
EST:     GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG                         GTATAATATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATG
genomic: GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAGgtacatatac ... ttgtcttcagGTATAATATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATG
EST: gi|29622723|gb|CB627734.1|CB627734
EST:     GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG                         GTATAATATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATG
genomic: GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAGgtacatatac ... ttgtcttcagGTATAATATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATG
EST: gi|29672018|gb|CB668293.1|CB668293
EST:     GTTCTATGCTGCCGAAGTGGTTGTTGCACTAAAATACCTACATTGCCAAG                         GTATAATATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATG
genomic: GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAGgtacatatac ... ttgtcttcagGTATAATATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATG
EST: gi|87007902|gb|CI296880.1|CI296880
EST:     GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG                         GTATAATATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATG
genomic: GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAGgtacatatac ... ttgtcttcagGTATAATATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATG
EST: gi|27334351|gb|CA882802.1|CA882802
EST:     GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG                         GTATAATATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATG
genomic: GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAGgtacatatac ... ttgtcttcagGTATAATATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATG
EST: gi|58695041|gb|CK083728.1|CK083728
EST:     GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG                         GTATAATATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATG
genomic: GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAGgtacatatac ... ttgtcttcagGTATAATATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATG
EST: gi|29623926|gb|CB628937.1|CB628937
EST:     CGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG                         GTATAATATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATG
genomic: CGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAGgtacatatac ... ttgtcttcagGTATAATATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATG
EST: gi|29641400|gb|CB646407.1|CB646407
EST:     GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG                         GTATAATATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATG
genomic: GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAGgtacatatac ... ttgtcttcagGTATAATATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATG
EST: gi|33680724|gb|CF308963.1|CF308963
EST:     GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAG                         GTATAATATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATG
genomic: GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAGgtacatatac ... ttgtcttcagGTATAATATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATG

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: 50 (upstream exon), 62 (downstream exon)
Score: 41

GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAGgtacatatac ... ttgtcttcagGTATAATATACCGAGACTTAAAACCAGAGAATATCTTACTTCATAGAGATGGGCACATCTCCCTTACAGACTTCGATTTGTCTTGTCTAACATCTTGCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCTATGCTGCCGAAGTGGTTGTTGCACTAGAATACCTACATTGCCAAGgtacatatacatcattgttgataacttgcatgcattaaaaattctcttatttcaatgatcatcaatatatctagggatgcctatcaactttacataaaaa

- -  ATGCTG
- - - TGCTGC