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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtctaacctgcgttggttttgcttctcggaatttctatcggcaattcgtagtatctgtgtgaatggtagcatgatatttttcatatcctttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCTGAGGTGAGGGAGCTCGTGGAGAAGGCCTACTCAAGAGCAACGCAGATCA

Basic information

species Oryza sativa
transcript LOC_Os06g51029.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g51029.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G126361_T03 (Zea mays), 3'ss of exon 5
--tgtctaacctgcgttggttttgcttctcggaatttctatcggcaattcgtagtatctgtgtgaatggtagcatgatattt-ttcatatcctttggtt-gcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCTGAGGTGAGGGAGCTCGTGGAGAAGGCCTACTCAAGAGCAACGCAGATCA
      || || |  |   |  |  |      ||| |  |    |||||| ||| | | || ||||  | |   ||| |  | |||| ||  |||      |||||||| ||||||||||||||||| ||||| || |||||||||||||| || ||||||||||| |||||||||||||||||||| ||||||| |||||| |
ctctcttagccagtatgaatagtagtcgcacaaatgttca----caattcctagcaccagtttgaagagcaatctgacaaatattcacattttttcccccacagATGTCAAGCCAGAAGGACTACTCTATGGCAACAGCGGATGTTGTGGACGCCGAGGTGAGGGAACTCGTGGAGAAGGCCTACTCTAGAGCAAGGCAGATAA

upper sequence: LOC_Os06g51029.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G42270.1 (Arabidopsis thaliana), 3'ss of exon 4
tgtctaacctgcgttggttttgcttctcggaatttctatcggcaattcgtagtatctgtgtgaatggtagcatgatatttttcatatcctttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCTGAGGTGAGGGAGCTCGTGGAGAAGGCCTACTCAAGAGCAACGCAGATCA
                    |   | |   ||  || ||   ||  |  |  ||  |   ||  | ||  |       |    | ||  |||| |||||||||||    |||||||| ||||||||||| || |||||||| || ||||| || ||||| |||||||| |||||||| |||   ||||| |   ||||||
-------------------gtaagtatataaaactcgatactcaggttttcataatttattgtgttgtttc-cagctctcaaaacatgttttgtttgcagATGTCATCGCAGAAGGATTACTCGATGGCAACAGCGGATGTGGTTGATGCGGAAGTGAGAGAGCTCGTTGAGAAGGCGTACGTGAGAGCGAAAGAGATCA

upper sequence: LOC_Os06g51029.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv18s0001g00190.t01 (Vitis vinifera), 3'ss of exon 4
-----tgtctaacctgcgttggttttgcttctcggaatttctatcggcaattcgtagtatctgtgtgaatggtagcatgatatttttcatatcctttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCTGAGGTGAGGGAGCTCGTGGAGAAGGCCTACTCAAGAGCAACGCAGATCA
         ||   |  | |  |||||||   |  || |        | || ||    |||    |  |          | ||||||  | |  |    | |||||||||    ||||| ||||| || ||||| || || ||| | |||||||| || ||||||||| | ||||||||||| || |||||||| | ||||||||
gtaggaacatattttaagata-ttttgctctccccaagtgtggagtcccatgcgattcatcacctt--accaagattgaacatttttggtgtt-tcaaatggcagATGTCATCGCAGAAAGACTATTCCATGGCAACTGCAGATATAGTGGATGCGGAAGTGAGGGAGTTGGTGGAGAAGGCATATTCAAGAGCCAAGCAGATCA

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|4715109|gb|AU056226.1|AU056226
EST:     GGCAAGTTNCGATTGGTGGNCCTGGTGGAAATCCTTTCTTGGGCCAGCAG                         ATNTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
genomic: GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
EST: gi|88847224|gb|CI011167.1|CI011167
EST:     GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAG                         ATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
genomic: GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
EST: gi|86864035|gb|CI332945.1|CI332945
EST:     GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAG                         ATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGATGTGGATGCT
genomic: GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
EST: gi|86840045|gb|CI332701.1|CI332701
EST:     GGCAAGTTGCGATTTGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAG                         ATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGTATTTTGTGGATGCT
genomic: GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
EST: gi|38472585|gb|CF956717.1|CF956717
EST:     GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAG                         ATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATTCT
genomic: GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
EST: gi|38476029|gb|CF960162.1|CF960162
EST:     GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAG                         ATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
genomic: GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
EST: gi|86851309|gb|CI312710.1|CI312710
EST:     GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAG                         ATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
genomic: GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
EST: gi|18386233|gb|BM419432.1|BM419432
EST:     GGCAA-TTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAG                         ATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
genomic: GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
EST: gi|58594309|gb|CF992617.1|CF992617
EST:     GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAG                         ATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATTGC
genomic: GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGAT-GC
EST: gi|88989328|gb|CI043827.1|CI043827
EST:     GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAG                         ATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
genomic: GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
EST: gi|38473350|gb|CF957482.1|CF957482
EST:     GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAG                         ATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
genomic: GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
EST: gi|38470910|gb|CF955041.1|CF955041
EST:     GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAG                         ATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
genomic: GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
EST: gi|18386246|gb|BM419445.1|BM419445
EST:     GCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTNTTCTTGGGCCAGCAG                         ATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTTGTGGAT-C
genomic: GCAAGTTGCGATTGGTGGACCTGGTGGAAATCCT-TTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATG-TTGTGGATGC
EST: gi|86861674|gb|CI329487.1|CI329487
EST:     GGCAAGTTGCGATTGGTGGACCTGTTGGAAATCCTTTCTTGGGCCAGCAG                         ATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTTTGGATGGC
genomic: GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGAT-GC
EST: gi|86832871|gb|CI332477.1|CI332477
EST:     GTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGCCCAGCAG                         ATGTCGAGCCAGAAGGACTACTCGATGGCCACCCCCGATGTTTTGGATGCT
genomic: GTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
EST: gi|15847610|gb|BI795900.1|BI795900
EST:     GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCA-CAG                         ATGTCGAGCCAGAAGGACTACTCGATGGCCACC-CGTGATGTTTGTGGATG
genomic: GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCG-GATG-TTGTGGATG
EST: gi|29668700|gb|CB664975.1|CB664975
EST:     GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAG                         ATGTCGAGCCAGAAGGATTACTCGATGGCCACCGCGGATGTTGTGGATGCT
genomic: GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
EST: gi|58657689|gb|CK046369.1|CK046369
EST:     GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAG                         ATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
genomic: GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
EST: gi|89183586|gb|CI046151.1|CI046151
EST:     GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAG                         ATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
genomic: GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
EST: gi|88958856|gb|CI381659.1|CI381659
EST:     GACCTGGTGGAAATCCTTTCTTGGGCCAGCAG                         ATGTCGAGCCAGAAGGACTACTCGAT-GCCACCGCGGATTTTGTGGATGCT
genomic: GACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
EST: gi|86902886|gb|CI312263.1|CI312263
EST:     GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAG                         ATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
genomic: GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
EST: gi|58611024|gb|CK038736.1|CK038736
EST:     GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAG                         ATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATTCT
genomic: GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
EST: gi|88964691|gb|CI070037.1|CI070037
EST:     GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAG                         ATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
genomic: GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
EST: gi|38480033|gb|CF964122.1|CF964122
EST:     GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAG                         ATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
genomic: GGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
EST: gi|87028892|gb|CI349611.1|CI349611
EST:     GTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAG                         ATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT
genomic: GTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCT

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: 73 (upstream exon), 58 (downstream exon)
Score: 100

ACGTGTTGCAAGACAAATGGTTGAAAGATTTGGATTCAGCAAGAAGATCGGGCAAGTTGCGATTGGTGGACCTGGTGGAAATCCTTTCTTGGGCCAGCAGgtaaatcact ... ttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCTGAGGTGAGGGAGCTCGTGGAGAAGGCCTACTCAAGAGCAACGCAGATCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgtagtatctgtgtgaatggtagcatgatatttttcatatcctttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCTGAGGTGAGGGAGCTCGTGGAGAAGGCCTACTCAAGAGCAACGCAGATCA
                                tttttcatatccttt  CT-rich tract
                          atgatatttttcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtctaacctgcgttggttttgcttctcggaatttctatcggcaattcgtagtatctgtgtgaatggtagcatgatatttttcatatcctttggttgcagATGTCGAGCCAGAAGGACTACTCGATGGCCACCGCGGATGTTGTGGATGCTGAGGTGAGGGAGCTCGTGGAGAAGGCCTACTCAAGAGCAACGCAGATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - -cctgcgt
- - - - - - - - - - tgcttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agcatga