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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGACCAGTTTAAGCAGGAATTCTGCAAATTGTATGGCATGACATTGGAGCCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcgcctgatcattattttccgcttcacctttaccatttaatataaaccactagcattgtattacattctcttttttccttgaccatcattag

Basic information

species Oryza sativa
transcript LOC_Os05g06760.1
intron # 5
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g06760.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G177026_T02 (Zea mays), 5'ss of exon 5
TGGACCAGTTTAAGCAGGAATTCTGCAAATTGTATGGCATGACATTGGAGCCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatcctt-cgcctgatca--ttattttccgcttca--cctttaccatttaa-tataaaccactagcattgtatt-------acattctcttttttccttgaccatc-attag---
| |||   || ||||| || || ||||| || |||||||||||| | |||||| |||||||||| ||| |||||||||| || |||||||| ||||| |||||||||  |   || |    ||| |||   ||     | ||||    | || || |     |||| ||| | ||         || || | || |||||||||||  |||     
TTGACATTTTCAAGCAAGATTTTTGCAAGTTATATGGCATGACACTAGAGCCGCTGCTGAACATATATCTGCAAGCAGGCCTGACAGCTCTCAAGACCCCgtatcctcgcatgtgtttcacttacttttgtctatggtcttttattgctaaaatacagtttgctagtattatttttgttatggtatcctgtattgtccttgaccatttatttaaag

upper sequence: LOC_Os05g06760.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA20G38660.1 (Glycine max), 5'ss of exon 5
TGGACCAGTTTAAGCAGGAATTCTGCAAATTGTATGGCATGACATTGGAGCCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcgcctgatcattattttccgcttcacct-----ttaccatttaatataaaccactagcattgtattacattctcttttttccttgaccatcattag
||||||| || || ||||| |||||||| || ||||||||||| || ||||| ||||| || |||||| ||||||| || ||  | ||||| ||||||||||||||||   |   | |   | |      ||| ||      |    |||  | ||||    |  |||     || |||         | |  ||| |  |   
TGGACCAATTCAAACAGGAGTTCTGCAAGTTATATGGCATGACTTTAGAGCCCTTGCTCAATATCTATCTGCAAGCTGGCCTTTCTGCTCTCAAGACACCgtatcctttaacaacttaaactgtagattatcatctagaaactttttttttttctaaaatgtttacatacctata-attgaaacaccccttccaccctttt---

upper sequence: LOC_Os05g06760.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA10G43910.1 (Glycine max), 5'ss of exon 5
TGGACCAGTTTAAGCAGGAATTCTGCAAATTGTATGGCATGACATTGGAGCCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcgcctgat-------cat-----tattttccgcttcacctttaccatttaatataaaccactagcattgtattacattctcttttttccttgaccatcattag
||||||| || || ||||| |||||||| || ||||||||||| || ||||| ||||| || |||||| ||||||| || ||  | ||||| ||||||||||||||||    | |        |||     || ||    |  | |||  ||| |||   ||||| |  ||  |     |    ||  ||| |    ||||          
TGGACCAATTCAAACAGGAGTTCTGCAAGTTATATGGCATGACTTTAGAGCCCTTGCTCAATATCTATCTGCAAGCTGGCCTTTCTGCTCTCAAGACACCgtatcctttttttaaaatgcttgcatacatataattgaaacaccccctccaccctttccaataaatc-ttaaaaccacttggactttccttatccttttga----------

upper sequence: LOC_Os05g06760.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv13s0067g03560.t01 (Vitis vinifera), 5'ss of exon 5
TGGACCAGTTTAAGCAGGAATTCTGCAAATTGTATGGCATGACATTGGAGCCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcgcc--tgatcattattttccgcttcacctttaccatttaatataaaccactagcattgtattacattctcttttttccttgaccatcattag-
|||||||||| || ||||||||||| |  || |||||||||||  | ||||| |||||||| || ||| ||||||||||  |  | ||||| || || |||||||||    |  | |  | ||| |      |  |||| ||    || |   |    ||    |   |||||| ||   |  |   ||    ||    |  
TGGACCAGTTCAAACAGGAATTCTGTAGGTTATATGGCATGACTCTTGAGCCTTTGCTGAATATATATCTGCAAGCAGGCTTGTCTGCTCTAAAAACTCCgtatcctcattcatttactaatatatcgttgcttgccttcacatactagtt--agtggcttaagtgccattacagtcaggtcatatattttgaatttgcaaa

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|58680296|gb|CK068983.1|CK068983
EST:     CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
genomic: CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|89188363|gb|CI115612.1|CI115612
EST:     CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
genomic: CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|87031181|gb|CI259761.1|CI259761
EST:     CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
genomic: CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|86496175|gb|CI138808.1|CI138808
EST:     CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
genomic: CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|86522436|gb|CI162642.1|CI162642
EST:     TATGCAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
genomic: TATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|38483136|gb|CF966938.1|CF966938
EST:     CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
genomic: CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|86509560|gb|CI152193.1|CI152193
EST:     ATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
genomic: ATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|86432270|gb|CI085881.1|CI085881
EST:     TATATGCAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
genomic: TATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|87018975|gb|CI256860.1|CI256860
EST:     CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
genomic: CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|88989214|gb|CI042327.1|CI042327
EST:     CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
genomic: CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|88249284|gb|CI249133.1|CI249133
EST:     CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
genomic: CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|29626430|gb|CB631441.1|CB631441
EST:     CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
genomic: CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|86478019|gb|CI120652.1|CI120652
EST:     CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
genomic: CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|88836032|gb|CI371137.1|CI371137
EST:     TCACAGCTCTGAAGACACC                         ATTCTGGTTCGAT-GTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
genomic: TCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|287145|gb|D15950.1|D15950
EST:     CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
genomic: CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|58679080|gb|CK067767.1|CK067767
EST:     CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTTTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGA
genomic: CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGA
EST: gi|15849371|gb|BI797647.1|BI797647
EST:     CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCCAAGAAGACCCCTTATCCCTGCCTGG
genomic: CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|300215580|gb|HO088206.1|HO088206
EST:     CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
genomic: CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|89167966|gb|CI109170.1|CI109170
EST:     CTATATGCAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCGAAGAAGACCCCTTATCCCTGCCTGG
genomic: CTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|86427542|gb|CI072639.1|CI072639
EST:     CAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGGAGACCCCTTATCCCTGCCTGG
genomic: CAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|89187712|gb|CI115158.1|CI115158
EST:     CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCCAAGAAGACCCCTTATCCCTGCCTGG
genomic: CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|89188472|gb|CI115721.1|CI115721
EST:     CAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
genomic: CAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|3766555|gb|AU030665.1|AU030665
EST:     CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
genomic: CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|86866747|gb|CI343554.1|CI343554
EST:     CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
genomic: CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|86414065|gb|CI068272.1|CI068272
EST:     GGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
genomic: GGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|88989290|gb|CI043789.1|CI043789
EST:     CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
genomic: CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|88227774|gb|CI227254.1|CI227254
EST:     ATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
genomic: ATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
EST: gi|86867179|gb|CI343921.1|CI343921
EST:     CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACC                         ATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG
genomic: CCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGG

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: 56 (upstream exon), 73 (downstream exon)
Score: 36

TGGACCAGTTTAAGCAGGAATTCTGCAAATTGTATGGCATGACATTGGAGCCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcg ... ccatcattagATTCTGCTTCGATGGTAACTGCCCCAAAGAAGACCCCTTATCCCTGCCTGGCTTCCGGAAACTAGCAGAGCCGCTTCCATTCTCCAAGCAGCACCATTCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGACCAGTTTAAGCAGGAATTCTGCAAATTGTATGGCATGACATTGGAGCCGTTGCTGAACATCTATATGCAAGCAGGGCTCACAGCTCTGAAGACACCgtatccttcgcctgatcattattttccgcttcacctttaccatttaatataaaccactagcattgtattacattctcttttttccttgaccatcattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA