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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAAAGAACCATCAACCAATATGGTCTTAGCCGATCATGTTACAACGAAGAAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaaaactcaacaccttaaacacataccatgatctatgttacccagatacggggatacggacacgtatacgcgatacggcgacacggggatacg...

Basic information

species Oryza sativa
transcript LOC_Os04g20230.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g20230.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G028730_T02 (Zea mays), 5'ss of exon 3
TAAAAGAACCATCAACCAATATGGTCTTAGCCGATCATGTTACAACGAAGAAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaaaactcaacaccttaaacacataccatgatctatgttacccagatacggggatacggacacgtatacgcgatacggcgacacggggatacg-------
|||||||||| || |||||| | ||| |||| |||||||||||||| ||||||||| || || |||||||||||||||||||||| ||||||||||||||||||||  || | |      |||| |  ||      |||| |||   || | | |     |||   | |   | ||  | |  |      || |  |  |       
TAAAAGAACCTTCTACCAATGTTGTCCTAGCTGATCATGTTACAACAAAGAAATGGGAGAAAATTGTTGATTTCGATGACCACCTTGATGATATTAGCAAgtaagtaaaatattt---ttcttacaagcacttggagatc-atgc--ccgaaaaattataatattaataaaaa-actagttttgtgtgtgcgtgtgtgtgtgttaag

upper sequence: LOC_Os04g20230.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv19s0015g00910.t01 (Vitis vinifera), 5'ss of exon 4
TAAAAGAACCATCAACCAATATGGTCTTAGCCGATCATGTTACAACGAAGAAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaaaactcaacaccttaaacac-ataccatgatctatgttacccagatacggg--gatacggacacgtatacgcgatacggcgacacggggatacg
| || || |||||| ||||| | ||| |    ||| || || |  |  ||||||||||| |  |  | ||||| ||||||||||| ||||| |||||||||||||   ||   ||    | |    | | ||  |  ||  ||| |    ||  |  |    |||||   |     | | |  ||| |               
TCAAGGAGCCATCAGCCAATGTAGTCCTCTTGGATTATATTGCCTCAGAGAAATGGCAGGATATCATAGATTTTGATGACCACCTTGATGACATTAGCAAgtaag---aaccttctgtgcttccctctctatttctagagttatttccttcatttttgatctgatacaatctttcttcctccttacag---------------
















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|86861785|gb|CI329549.1|CI329549
EST:     AAATGGCACCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|700709|gb|D47000.1|D47000
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGACATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|88535687|gb|CI462502.1|CI462502
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|88832118|gb|CI014677.1|CI014677
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|88444207|gb|CI554924.1|CI554924
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|88546887|gb|CI477143.1|CI477143
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|7652121|gb|AU089728.1|AU089728
EST:     AATGGCAGCAAGTTNGTTGATTTCGATGACCACCTCGATGACATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AATGGCAGCAAGTT-GTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|86873136|gb|CI328516.1|CI328516
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|87034371|gb|CI188995.1|CI188995
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|87029911|gb|CI267924.1|CI267924
EST:     AAGTGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|88428035|gb|CI556929.1|CI556929
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|86511407|gb|CI154040.1|CI154040
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|88541094|gb|CI469187.1|CI469187
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|86511306|gb|CI153939.1|CI153939
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|86595452|gb|CI264549.1|CI264549
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|86505090|gb|CI147723.1|CI147723
EST:     AATGGCAGCCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AATGGCAG-CAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|88531548|gb|CI460031.1|CI460031
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGGTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|38470160|gb|CF954291.1|CF954291
EST:     GGCAGCAAGTTGTTGATTTCGATGACCACCTCGATAATATTAGCAA                         AGATTGGTTGAACCCAGAGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: GGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|88322812|gb|CI545518.1|CI545518
EST:     AAATGGCAGCAAGTTGTTGATTTGGATGACCACCTGGATGATATTACCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|88532108|gb|CI461570.1|CI461570
EST:     AAATGGCACCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|88540431|gb|CI469328.1|CI469328
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|88482100|gb|CI419371.1|CI419371
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|88848172|gb|CI086694.1|CI086694
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|87009322|gb|CI313795.1|CI313795
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|163927626|gb|EG713946.1|EG713946
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|88381388|gb|CI528368.1|CI528368
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|88205861|gb|CI205710.1|CI205710
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|86428529|gb|CI075210.1|CI075210
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|88555949|gb|CI486249.1|CI486249
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|88531862|gb|CI458380.1|CI458380
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|86509598|gb|CI152231.1|CI152231
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
EST: gi|87034259|gb|CI188883.1|CI188883
EST:     AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAA                         AGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA
genomic: AAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATA

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: 58 (upstream exon), 36 (downstream exon)
Score: 5

TAAAAGAACCATCAACCAATATGGTCTTAGCCGATCATGTTACAACGAAGAAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaa ... atttttgcagAGATTGGTTGAACCCAGGGCTACTTGCTTGAAATAATTATGTGCTTTGATATTTTTATACTTGTTGGTACCAATATGTTGAGGCTCGTCTCACCAGATTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAAAGAACCATCAACCAATATGGTCTTAGCCGATCATGTTACAACGAAGAAATGGCAGCAAGTTGTTGATTTCGATGACCACCTCGATGATATTAGCAAgtaagttgaaaactcaacaccttaaacacataccatgatctatgttacccagatacggggatacggacacgtatacgcgatacggcgacacggggatacg

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cggcgac