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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgcttaggaaaatataaatttcttgcatatcctttgtattacatcaggagattagcacgcgtgtagatctggcacattttcagaaagttcaaaatcgtgttcttttatttgggagatgctgaaatctgaattatttatgggttacatggggataatttgttctgacattttttctcatgctgatcagGCGTTGTTCCGTAAGATTGCGGCTGCACTTCCTGGAATGGAGACCCTCTCATCAGCAAAGCAGGAAGACATGGTTGATGTGAACTTGAAGTCAAGCAACG

Basic information

species Oryza sativa
transcript LOC_Os07g31370.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G075719_T02 (Zea mays), 3'ss of exon 5
gtgtgcttaggaaaatataaatttcttgcatatcctttgtattacatcaggagattagcacgcgtgtagatctggcacattttcagaaagttcaaaatcgtgttcttttatttgggagatgctgaaatctgaat-tatttatgggttacatggggataatttgttctgacattttttctcatgctgatcagGCGTTGTTCCGTAAGATTGCGGCTGCACTTCCTGGAATGGAGACCCTCTCATCAGCAAAGCAGGAAGACATGGTTGATGTGAACTTGAAGTCAAGCAACG
                                                                             | |||||  |  |     ||     ||  ||| | ||          |  |||| || | |||||  || | |      |  || ||| || || |      | || ||| |||||| |||||||||| ||||| ||||| |||||||| |||||||| ||||||||||| ||||||||||||||||||||||||||||||| |||  |||| |
--------------------------------------------------------------------------atgccttttcttaggg-----aaggacctttatttttctgc---------atgtctgtatgtctttatatgtca-acatatttttttcgttttg-cactgaccaacttg-tgagcagGCGCTGTTCCGTAAAATTGCTGCTGCCCTTCCTGGTATGGAGACACTCTCATCAGCGAAGCAGGAAGACATGGTTGATGTGAACTTGAGGTCTGGCAATG

upper sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 5
gtgtgcttaggaaaatataaatttcttgcatatcctttgtattacatcaggagattagcacgcgtgtagatctggcacattttcagaaagttcaaaatcgtgttcttttatttgggagatgctgaaatctgaat-tatttatgggtt-acatgggga-----taatttgtt-----ctgacattttttctcatgctgatcagGCGTTGTTCCGTAAGATTGCGGCTGCACTTCCTGGAATGGAGACCCTCTCATCAGCAAAGCAGGAAGACATGGTTGATGTGAACTTGAAGTCAAGCAACG
|| |||||  |||| ||||||||     ||||   || || | | ||    |   ||   |  | |   || ||     | |    |||||||| | | ||||  |||| ||||  |  | ||  | |||     | | |||| ||| | ||    |     || ||||||     ||||||        | || ||| |||||| |||||||||| ||||| ||||||||||||||||||||||| ||||||||||| || |||||||||||||||||||||||||||| |||  |||| |
gtatgcttcagaaa-tataaatt-----cataagtttggt-tcatatttacaatatacttctagagc--atgtgatttttatctgaaaagttcagagtagtgtgtttttctttgttaagtcctttattctctgcctgtctatgtgtttatatatcaacgtactagtttgttttgcgctgacaaccacaaacttg-tgagcagGCGCTGTTCCGTAAAATTGCTGCTGCACTTCCTGGAATGGAGACGCTCTCATCAGCGAAACAGGAAGACATGGTTGATGTGAACTTGAGGTCCGGCAATG

upper sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G04330.1 (Glycine max), 3'ss of exon 5
gtgtgcttaggaaaatataaatttcttgcatatcctttgtattacatcaggagattagcacgcgtgtagatctggcacattttcagaaagttcaaaatcgtgttcttttatttgggagatgctgaaatctgaattatttatgggttacatggggataatttgttctgacattttttctcatgctgatcagGCGTTGTTCCGTAAGATTGCGGCTGCACTTCCTGGAATGGAGACCCTCTCATCAGCAAAGCAGGAAGACATGGTTGATGTGAACTTGAAGTCAAGCAACG
                                                                        |  | |  ||||    |  |  || |    | ||| ||| |||    | || | || |   ||  || |   ||||    | ||  | |  ||  |||||| | |           ||||  | || || || ||||| || ||||| ||||||||||| || || || || ||||| || ||||||||||||||||| ||||| ||||| |  || |
------------------------------------------------------------------------tccctctctttcgtggaagt--aactgagatccttatatatgg----ttctaatatttctcttgcttctaacttac-catgtattttgttatccaacatttgtac-----------agGCCCTATTTCGAAAAATTGCTGCAGCACTACCTGGAATGGAAACACTATCTTCTGCAAAACAAGAAGACATGGTTGATGTAAACTTAAAGTCTACAAATG

upper sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA01G41100.1 (Glycine max), 3'ss of exon 5
gtgtgcttaggaaaatataaatttcttgcatatcctttgtattacatcaggagattagcacgcgtgtagatctggcacattttcagaaagttcaaaatcgtgttcttttatttgggagatgctgaaatctgaattatttatgggttacatggggataatttgttctgacattttttctcatgctgatcagGCGTTGTTCCGTAAGATTGCGGCTGCACTTCCTGGAATGGAGACCCTCTCATCAGCAAAGCAGGAAGACATGGTTGATGTGAACTTGAAGTCAAGCAACG
                                                                      ||   | |  ||||    |     |||  | | || || || |||    | || | || |   ||  || |   ||||         || | |||||   || ||   ||| |||  |||||  | || || || ||||| || ||| | ||||||||||| || || || || ||||| || ||||||||||||||||| ||||| ||||| |  |  |
----------------------------------------------------------------------tccccctctctttcgtggaa---gaaactgagatcctt-atatgg----ttctaatatttttcttgcttctaacttacc--------atgtattctg---ttattcgacat-ctgtacagGCCCTATTTCGAAAAATTGCTGCAGCATTACCTGGAATGGAAACACTATCTTCTGCAAAACAAGAAGACATGGTTGATGTAAACTTAAAGTCTACAACTG

upper sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv02s0012g00710.t01 (Vitis vinifera), 3'ss of exon 5
gtgtgcttaggaaaatataaatttcttgcatatcctttgtattacatcaggagattagcacgcgtgtagatctggcacattttcagaaagttcaaaatcgtgttcttttatttgggagatgctgaaatctgaattatttatgggttacatggggata-atttgttctgacattttttctcatgctgatcagGCGTTGTTCCGTAAGATTGCGGCTGCACTTCCTGGAATGGAGACCCTCTCATCAGCAAAGCAGGAAGACATGGTTGATGTGAACTTGAAGTCAAGCAACG
                                                                                     | |   ||     |  |   |  |||     |  |  || |  || | |   || |   |  | ||   ||  | || ||  |  |  |   |   |  ||  |||||  |||| || || ||||| || ||  | || |||||||| || || || ||||||||||| ||||||||||||||||||||  |||||||    |  |
-------------------------------------------------------------------------------------gtagtctctctccccagacatcctatagattaattattggatgctcactaggttgtaattatcttgatcatggaattctttggttacatgaaccttttttgtacagGCACTGTTTCGGAAAATTGCAGCAGCTTTACCAGGAATGGAAACACTTTCTTCAGCAAAGCAAGAAGACATGGTTGATGTGAATCTGAAGTCGTCAAGTG

upper sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv02s0012g00790.t01 (Vitis vinifera), 3'ss of exon 2
gtgtgcttaggaaaatataaatttcttgcatatcctttgtattacatcaggagattagcacgcgtgtagatctggcacattttcagaaagttcaaaatcgtgttcttttatttgggagatgctgaaatctgaattatttatgggtta--catggggataatttgttctgacattttttctcatgctgatcagGCGTTGTTCCGTAAGATTGCGGCTGCACTTCCTGGAATGGAGACCCTCTCATCAGCAAAGCAGGAAGACATGGTTGATGTGAACTTGAAGTCAAGCAACG---
                                                                               |  ||        || |      ||   ||| ||    |||||| |   ||   || |   ||  ||   |||||   |  || |||     |   ||| |||| |     ||||  |||| |  || ||||| |||  ||   | |||||||| || || || ||||| ||||| ||||||||||||||||||||| | |||||   || |    
------------------------------------------------------------------------------gtaatctctttccccagacatcctttagattaattcttggatgctca---ctaggttgtaactgtcttgatcatggaattctttggttaaatgaacctttttcatac-----agGCACTGTTTCAGAAAATTGCAGCTTTAC---CAGGAATGGAAACACTTTCTTCAGCCAAGCAAGAAGACATGGTTGATGTGAACCTAAAGTCTCCCAGCCTCA

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|25800647|gb|CA756608.1|CA756608
EST:     TCGGTGTGATGTTCATTGAAACCAGTGCTAAAGCTGGTTTTAACATTAAG                         GCGTTGTTCCGTAAGATTGCGGCTGCACTTCCTGGAATGGAAACCCTCTCA
genomic: TCGGTGTGATGTTCATTGAAACCAGTGCTAAAGCTGGTTTTAACATTAAGgtgtgcttag ... tgctgatcagGCGTTGTTCCGTAAGATTGCGGCTGCACTTCCTGGAATGGAGACCCTCTCA
EST: gi|58655172|gb|CK043852.1|CK043852
EST:     TTCATTGAAACCAGTGCT-AAGCTGGTTTTAACATTAAG                         GCGTTGTTCCGTAAGATTGCGGCTGCACTTCCTGGAGTGGAGACCCTCTCA
genomic: TTCATTGAAACCAGTGCTAAAGCTGGTTTTAACATTAAGgtgtgcttag ... tgctgatcagGCGTTGTTCCGTAAGATTGCGGCTGCACTTCCTGGAATGGAGACCCTCTCA
EST: gi|218500590|gb|FG953502.1|FG953502
EST:     CTGGTTTTAACATTAAG                         GCGTTGTTCCGTAAGATTGCGGCTGCACTTCCTGGAATGGAGACCCTCTCA
genomic: CTGGTTTTAACATTAAGgtgtgcttag ... tgctgatcagGCGTTGTTCCGTAAGATTGCGGCTGCACTTCCTGGAATGGAGACCCTCTCA
EST: gi|88981046|gb|CI021169.1|CI021169
EST:     GATGTTCATTGAAACCAGTGCTAAAGCTGGTTTTAACATTAAG                         GCGTTGTTCCGTAAGATTGCGGCTGCACTTCCTGGAATGGAGACCCTCTCA
genomic: GATGTTCATTGAAACCAGTGCTAAAGCTGGTTTTAACATTAAGgtgtgcttag ... tgctgatcagGCGTTGTTCCGTAAGATTGCGGCTGCACTTCCTGGAATGGAGACCCTCTCA
EST: gi|38470834|gb|CF954965.1|CF954965
EST:     TCGGTGTGATGTTCATTGAAACCAGTGCTAAAGCTGGTTTTAACATTAAG                         GCGTTGTTCCGTAAGATTGCGGCTGCACTTCCTGGAATGGAGACCCTCTCA
genomic: TCGGTGTGATGTTCATTGAAACCAGTGCTAAAGCTGGTTTTAACATTAAGgtgtgcttag ... tgctgatcagGCGTTGTTCCGTAAGATTGCGGCTGCACTTCCTGGAATGGAGACCCTCTCA

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: 71 (upstream exon), 75 (downstream exon)
Score: 60

GCAAGTCTCCATAGAGGAAGGAGAGGGCAAAGCGAAAGATCTCGGTGTGATGTTCATTGAAACCAGTGCTAAAGCTGGTTTTAACATTAAGgtgtgcttag ... tgctgatcagGCGTTGTTCCGTAAGATTGCGGCTGCACTTCCTGGAATGGAGACCCTCTCATCAGCAAAGCAGGAAGACATGGTTGATGTGAACTTGAAGTCAAGCAACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttatgggttacatggggataatttgttctgacattttttctcatgctgatcagGCGTTGTTCCGTAAGATTGCGGCTGCACTTCCTGGAATGGAGACCCTCTCATCAGCAAAGCAGGAAGACATGGTTGATGTGAACTTGAAGTCAAGCAACG
                           ttctgac  putative branch site (score: 60)
                                   ttttttctcatgct  CT-rich tract
                   ataatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgcttaggaaaatataaatttcttgcatatcctttgtattacatcaggagattagcacgcgtgtagatctggcacattttcagaaagttcaaaatcgtgttcttttatttgggagatgctgaaatctgaattatttatgggttacatggggataatttgttctgacattttttctcatgctgatcagGCGTTGTTCCGTAAGATTGCGGCTGCACTTCCTGGAATGGAGACCCTCTCATCAGCAAAGCAGGAAGACATGGTTGATGTGAACTTGAAGTCAAGCAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA