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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgtcaaattattgctagaccaagtaattcatgttatgatgttgtttcaatttttcaatgcgtcagttgaaactgactgataacttattgttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG

Basic information

species Oryza sativa
transcript LOC_Os11g03380.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g03380.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G318871_T01 (Zea mays), 3'ss of exon 3
tatgtcaaattattgctagaccaagtaattcat-gttatgatgttgtttcaatttttcaatgcgtcagttgaaactgactgataacttattgttcctgt-----agCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG-------------------------------------
   || ||  |||    | |||    |||||   |  ||    |        |  |  |  || ||||||| |||||||   | |||| || ||  | |     |||| |||||||||||||| |||||||||||||||| |||| |  |||||| |||||| ||||||                                     
---gtgaagctata---aaacctgtaaattctccgccatttaatcaacattgtgatctatcgcttcagttgtaactgaccactgacttgttcttttttttacttagCTGCAATCGTCAGACATATCTAAAGATAAGCAAGTTGATCCAGCTTTAGCAGACACACTGAAGGTAATCATAGGAACTCATCTCTCTCAGATACTGTTCT

upper sequence: LOC_Os11g03380.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G017941_T01 (Zea mays), 3'ss of exon 4
tatgtcaaattattgctagaccaagtaattcatgttatgatgttgtttcaatttttcaa---tgcgtcagttgaaactgactgataacttattgttcctg---tagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG
   || | | | |   |      | ||  | |||   ||  ||||| | |        |    | |  ||||| |||||||   | |||| || ||  |    ||||||||||| |||||||| || ||||||||||||| |||| |  |||||| ||| ||  |||||
---gtgagaatgtc-ttctttttaata--taatgccctggggttgtcttaccccccgtagatcgagagagttgtaactgaccattgacttgttcttttttacttagCTACAATCATCAGACATATCGAAAGATAAGCAAGTTGATCCAGCTTTAGCAGATACATTGAAG

upper sequence: LOC_Os11g03380.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G410155_T01 (Zea mays), 3'ss of exon 3
tatgtcaaattattgctagaccaagtaattcat-gttatgatgttgtttcaatttttcaatgcgtcagttgaaactgactgataacttattgttcctgt------agCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG
    | ||  |||    | |||    |||||   |  ||    |        |  |  |  || ||||||| |||||||   |||||| || ||  | |      |||| |||||||||||||| |||||||||||||||| |||| |  |||||| |||||| ||||||
----tgaagctata---aaacctgcaaattctccgccatttaatcaacattgtgatctatcgcttcagttgtaactgaccactaacttgttctttttttttacttagCTGCAATCGTCAGACATATCTAAAGATAAGCAAGTTGATCCAGCTTTAGCAGACACACTGAAG

upper sequence: LOC_Os11g03380.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G179737_T02 (Zea mays), 3'ss of exon 4
tatgtcaaattattgctagaccaagtaattcatgttatgat-gttgtttcaatttttcaatgcgtcagttgaaactgactgataacttattgttcctgt-----agCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG
   || ||  |||        ||| |  | |    | | ||     ||   || | ||| |   ||||||| |||||||   | |||| || ||  | |     |||| |||||||||||||| |||||||||||||||| |||| |  |||||| |||||| ||||||
---gtgaagctataaaacctgcaaattctccgccatttaatcaacattgtgatctatcact---tcagttgtaactgaccattgacttgttcttttttttacttagCTGCAATCGTCAGACATATCTAAAGATAAGCAAGTTGATCCAGCTTTAGCAGACACACTGAAG

upper sequence: LOC_Os11g03380.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G371679_T01 (Zea mays), 3'ss of exon 5
tatgtcaaattattgctagaccaagtaattcat-gttatgatgttgtttcaatttttcaatgcgtcagttgaaactgactgataacttattgttcctgt-----agCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG------------
   || ||  |||    | |||    |||||   |  ||    |        |  |  |  || ||||||| |||||||   | |||| || ||  | |     |||| |||||||||||||| |||||||||||||||| |||| |  |||||| |||||| ||||||            
---gtgaagctata---aaacctgcaaattctccgccatttaatcaacattgtgatctatcgcttcagttgtaactgaccactgacttgttcttttttttacttagCTGCAATCGTCAGACATATCTAAAGATAAGCAAGTTGATCCAGCTTTAGCAGACACACTGAAGGTAATCATAGGC

upper sequence: LOC_Os11g03380.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G080404_T01 (Zea mays), 3'ss of exon 3
tatgtcaaattattgctagaccaagtaattca-tgttatgatgttgtttcaatttttcaatgcgtcagttgaaactgactgataacttattgttcctgta----gCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG-------------------------------------
   || ||  |||    | |||    |||||  ||  ||    |        |  |  |  || ||||||| |||||||   | |||| || ||  | ||    ||| |||||||||||||| |||||||||||||||| |||| |  |||||| |||||| ||||||                                     
--cgtgaagctata---aaacctgcaaattctctgccatttaatcaacattgtgatctatcgcttcagttgtaactgaccactgacttgttctttttttacttagCTGCAATCGTCAGACATATCTAAAGATAAGCAAGTTGATCCAGCTTTAGCAGACACACTGAAGGTAATCATAGGCACTCATCTCTCTTAGATACTGTTCT

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|4715628|gb|AU056744.1|AU056744
EST:     GGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGGCTCGAAG                         CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGT
genomic: GGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGG-CTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGT
EST: gi|33658304|gb|CF280918.1|CF280918
EST:     GATCATGCAAAGAG-GTTTGATGTTTGCAGTTCTTTTTCTTGGCTCGAAG                         CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
genomic: GATCATGCAAAGAGTGTT-GATGTT-GCAGTTCTTTTTCTTGGCTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
EST: gi|33658126|gb|CF280740.1|CF280740
EST:     AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG                         CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
genomic: AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
EST: gi|33690612|gb|CF318851.1|CF318851
EST:     AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG                         CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
genomic: AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
EST: gi|29672707|gb|CB668982.1|CB668982
EST:     AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG                         CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
genomic: AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
EST: gi|14714076|gb|AU198016.1|AU198016
EST:     AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG                         CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
genomic: AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
EST: gi|88312635|gb|CI587543.1|CI587543
EST:     AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG                         CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACT
genomic: AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACT
EST: gi|29663528|gb|CB659803.1|CB659803
EST:     AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG                         CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
genomic: AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
EST: gi|33679537|gb|CF307776.1|CF307776
EST:     AGGATCATGCAAAGAGGGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG                         CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACCTTAGTA
genomic: AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
EST: gi|29658170|gb|CB654445.1|CB654445
EST:     AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG                         CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
genomic: AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
EST: gi|88316617|gb|CI622863.1|CI622863
EST:     AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG                         CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGA
genomic: AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGA
EST: gi|58664366|gb|CK053052.1|CK053052
EST:     AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG                         CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
genomic: AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
EST: gi|58677950|gb|CK066637.1|CK066637
EST:     AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG                         CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
genomic: AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
EST: gi|88332593|gb|CI651753.1|CI651753
EST:     AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG                         CTACAATCGTCAGACATTTCTAAAGATAAGCAA
genomic: AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAA
EST: gi|29678424|gb|CB674699.1|CB674699
EST:     AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG                         CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
genomic: AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
EST: gi|33822526|gb|CF337070.1|CF337070
EST:     AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG                         CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
genomic: AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
EST: gi|86906721|gb|CI291169.1|CI291169
EST:     AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG                         CTACAATCGTCAGACATTTCTAAAGATA
genomic: AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTCTAAAGATA
EST: gi|33658022|gb|CF280636.1|CF280636
EST:     GGATCATGCAAAGAGTGTNTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG                         CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
genomic: GGATCATGCAAAGAGTGT-TGATGTTGCAGTTCTTTTTCTTGGCTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
EST: gi|58598104|gb|CK008632.1|CK008632
EST:     AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG                         CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
genomic: AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
EST: gi|88728556|gb|CI752066.1|CI752066
EST:     AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG                         CTACAATCGTCAGACATTTC
genomic: AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTC
EST: gi|88445308|gb|CI587202.1|CI587202
EST:     AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG                         CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTACTA
genomic: AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
EST: gi|29624905|gb|CB629916.1|CB629916
EST:     AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG                         CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
genomic: AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTA
EST: gi|2428191|gb|C72654.1|C72654
EST:     AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG                         CTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTAACTTTTAG
genomic: AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTA-CTTT-AG
EST: gi|58694105|gb|CK082792.1|CK082792
EST:     AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAG                         CTACAATCGTCAGACATTTCTAAANGATAAGCAAGCTGATTCTACTTTAGT
genomic: AGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTCTAAA-GATAAGCAAGCTGATTCTACTTTAGT

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), 66 (downstream exon)
Score: 42

TGTTCAAGGGAGGATCATGCAAAGAGTGTTGATGTTGCAGTTCTTTTTCTTGGCTCGAAGgtacttattg ... gttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcaatttttcaatgcgtcagttgaaactgactgataacttattgttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG
                                 tgataac  putative branch site (score: 42)
                                           ttgttcct  putative PPT
     atttttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgtcaaattattgctagaccaagtaattcatgttatgatgttgtttcaatttttcaatgcgtcagttgaaactgactgataacttattgttcctgtagCTACAATCGTCAGACATTTCTAAAGATAAGCAAGCTGATTCTACTTTAGTAGACACGCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - tattgct
- - - - - - - - -agaccaa
- - - - - - - - - - - - - -attcatg
- - - - - - - - - - - - - - - - - - atgatgt
- - - - - - - - - - - - - - - - - - - - - -tgtttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgactg