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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttgctcctatttcagtttttttattaaaagaagttcaacccttgaatttcaatttctttaccctttctcttgttacaaagtcttcttgataactgtagGGTACCGTAGTACTTGTTTTCCAACCAGCTGAGGAAGGTGGTGGTGGGGCAAAGAAAATGATAGATGATGGAGCTGTGGAAAATATAGAGGCCATTTTTG

Basic information

species Oryza sativa
transcript LOC_Os01g37960.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g37960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G090779_T01 (Zea mays), 3'ss of exon 2
ggttgctcctatttcagtttttttattaaaagaagttcaacccttgaatttcaatttctttaccc-tttctcttgttacaaa---gtcttcttgataactgtagGGTACCGTAGTACTTGTTTTCCAACCAGCTGAGGAAGGTGGTGGTGGGGCAAAGAAAATGATAGATGATGGAGCTGTGGAAAATATAGAGGCCATTTTTG
 ||| | || || |||||| |   || ||  |   |   | | ||||||||  ||  |  ||    ||||| | ||||  ||    | ||||| || | |||||||||| ||||| ||||| ||||||||||||||||||||||| |||||||| |||||||||||||| ||  ||||||||||||| ||||| ||||||||||
-gtttcgcccatatcagttat---atgaactgtcttgtgatctttgaatttttatcaccctatgaatttctatggttatgaatatattttctttatcaatgtagGGTACAGTAGTTCTTGTCTTCCAACCAGCTGAGGAAGGTGGCGGTGGGGCCAAGAAAATGATAGAAGACAGAGCTGTGGAAAACATAGATGCCATTTTTG

upper sequence: LOC_Os01g37960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G21080.1 (Glycine max), 3'ss of exon 3
ggttgctcctatttcagtttttttattaaaagaagttcaacccttgaatttcaatttctttaccctttctcttg------ttacaaagtctt---cttgataactg--tagGGTACCGTAGTACTTGTTTTCCAACCAGCTGAGGAAGGTGGTGGTGGGGCAAAGAAAATGATAGATGATGGAGCTGTGGAAAATATAGAGGCCATTTTTG
          | | || |  ||   | |  |  |||  |  |  |||  |    | |||| | ||| |||| ||      | ||||| || |   |||| |  ||   ||||| ||  | || ||||||||||||||||| |||||||| ||||  ||||| ||||||||  |||||  ||||||  | || ||| |    || || ||||
----------actccaatgcttaagtcactaacagtg-actcagtgacatatgttgtcttcatcctctctcatggatccctaacaaattcattatcttgctgtctaaatagGGAACTATTGTTCTTGTTTTCCAACCAGCAGAGGAAGGAGGTGCAGGGGCTAAGAAAATTTTAGATACTGGAGCCTTAGATAATGTTATTGCTATCTTTG

upper sequence: LOC_Os01g37960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G21050.1 (Glycine max), 3'ss of exon 2
ggttgctcctatttcagtttttttattaaaagaagttcaacccttgaatttcaatttctt-taccctttctcttgttacaaagtcttcttgataactg--tagGGTACCGTAGTACTTGTTTTCCAACCAGCTGAGGAAGGTGGTGGTGGGGCAAAGAAAATGATAGATGATGGAGCTGTGGAAAATATAGAGGCCATTTTTG
  ||     | |||   || || | ||     |  ||   | || || | | || || |  ||   |      |    ||   |||| ||| |  ||   ||||| || || || ||||||||||||||||| |||||||| ||||  ||||| |||||||| ||||||  ||||||  | || ||| |    || || ||||
-cttaactttgtttagattgttatgttgtgctactttt--ctctggattgttaagttatgatatgatgatagattcatcattatcttgttgttgtctaaatagGGAACTGTTGTTCTTGTTTTCCAACCAGCAGAGGAAGGAGGTGCAGGGGCTAAGAAAATTATAGATTCTGGAGCCTTAGATAATGTTACTGCTATCTTTG

upper sequence: LOC_Os01g37960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G21040.1 (Glycine max), 3'ss of exon 2
ggttgctcctatttcagtttttttattaaaagaagttcaacccttgaatttcaatttctttaccctttctcttg---ttacaaagtcttcttgataactgtagGGTACCGTAGTACTTGTTTTCCAACCAGCTGAGGAAGGTGGTGGTGGGGCAAAGAAAATGATAGATGATGGAGCTGTGGAAAATATAGAGGCCATTTTTG
  | |   ||   | |    |  || |   |    || | |  ||   ||    | |||| | | | | || ||        |    ||| | |||  |  |||| || || || ||||||||||||||||| |||||||| ||||| ||||| ||||||||  |||||| ||||||  | |||||| |    || || ||||
-ctcgacactcactaaagcctgctactcttac--ttttatctgttatgttctgttatcttcatcttctgtcatggatccctgataaattcattatatttacagGGGACTGTTGTTCTTGTTTTCCAACCAGCCGAGGAAGGAGGTGGAGGGGCTAAGAAAATTTTAGATGCTGGAGCCTTAGAAAATGTTACTGCTATCTTTG

upper sequence: LOC_Os01g37960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G21030.1 (Glycine max), 3'ss of exon 2
ggttgctcctatttcagtttttttattaaaagaagttcaacccttgaatttcaatttctttaccctttctc----ttgttacaaagtc----ttcttg-ataactgtagGGTACCGTAGTACTTGTTTTCCAACCAGCTGAGGAAGGTGGTGGTGGGGCAAAGAAAATGATAGATGATGGAGCTGTGGAAAATATAGAGGCCATTTTTG
        | | ||| | |  |||| ||  | |  |  ||   |    ||    | | |  ||||| || |    || | | ||  ||    || |||  | |   ||||| || ||||| ||||||||||||||||| |||||||| ||||| ||||| ||||||||  |||||| ||||||  | |||||| | |  || |||||||
--------ccacttctgctactttactatgaaatatg-aattgtcttgttctcttgtttccaccctgtcccagatttatgataatttcattatttttgtgtcaaaatagGGAACTGTAGTTCTTGTTTTCCAACCAGCAGAGGAAGGAGGTGGAGGGGCTAAGAAAATTTTAGATGCTGGAGCCTTAGAAAATGTCGCAGCTATTTTTG

upper sequence: LOC_Os01g37960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G51760.1 (Arabidopsis thaliana), 3'ss of exon 2
ggttgctcctatttcag--tttttttattaaaagaagttcaacccttgaatttca-----atttctttaccctttct-cttgttacaaagtcttcttgataactgtagGGTACCGTAGTACTTGTTTTCCAACCAGCTGAGGAAGGTGGTGGTGGGGCAAAGAAAATGATAGATGATGGAGCTGTGGAAAATATAGAGGCCATTTTTG
| ||  |  |    | |  ||||  || |   | || || |  |  |  |  |||     || | |  |  |||    ||||||  | | | ||||||||      |||| || || || || ||||||||||||||||||||||| || || || |||||||| ||  | || | |||||   |||| ||| |    || || ||||
gtttagttttgacactggattttcctagttttaaaatttgagtctgtcgaaatcatcatgatgtttggattcttgaaacttgttggaca-ttttcttgat-----cagGGCACAGTGGTTCTAGTTTTCCAACCAGCTGAGGAAGGAGGAGGAGGTGCAAAGAAGATTGTGGAGGCTGGAGTGTTGGAGAATGTGAGTGCAATCTTTG

upper sequence: LOC_Os01g37960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv09s0002g02630.t01 (Vitis vinifera), 3'ss of exon 2
---ggttgctcctatttcagtttttttattaaaagaagttcaacccttgaatttcaatttctttaccctttctcttgttacaaagtcttcttgataactgt-agGGTACCGTAGTACTTGTTTTCCAACCAGCTGAGGAAGGTGGTGGTGGGGCAAAGAAAATGATAGATGATGGAGCTGTGGAAAATATAGAGGCCATTTTTG
         |||||||||    || || |    | || |       || | |     ||||||| || ||| | || ||      |||| |  || | | | |||| || ||  | |||||||| ||||||||||| ||||| ||||| ||||||||||||||  |||||| |||||   | |||||| |  | || || ||||
attcaagcttcctatttcttccttcttttgtggataaatga----ttttattccttttttcttttccttttttttttttttttcttcttttatattattatcagGGAACAGTCATTCTTGTTTTTCAACCAGCTGAAGAAGGAGGTGGAGGGGCAAAGAAAATTTTAGATGCTGGAGTACTAGAAAATGTGAATGCTATCTTTG

upper sequence: LOC_Os01g37960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv11s0016g02700.t01 (Vitis vinifera), 3'ss of exon 2
ggttgctcctatttcagtttttttattaaaagaagttcaacccttgaatttcaatttctt---taccctttctcttgttacaaagtcttcttgataactgtagGGTACCGTAGTACTTGTTTTCCAACCAGCTGAGGAAGGTGGTGGTGGGGCAAAGAAAATGATAGATGATGGAGCTGTGGAAAATATAGAGGCCATTTTTG
   || || |  | | || |   ||  |    ||||   |     ||||    || ||||   |        | |||| |  |   ||||| | |  |  ||||| || || || |||||||||||||| ||||||||| | |  || ||||||||||||||| ||||   ||||    |||| || || || ||||| ||||
--ctgttcatgatactgtatcagtaagatggtaagtaatattgcagaatactcatgtcttctatggaagaaattttgtgattatcgcttct-ggtttcaatagGGAACAGTCGTTCTTGTTTTCCAACCGGCTGAGGAACGAGACGGAGGGGCAAAGAAAATGTTAGAAACTGGAATATTGGAGAACATTGATGCCATCTTTG

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|58688291|gb|CK076978.1|CK076978
EST:     TGCTGTTGGGTTCTG-CAGGATACTTCAGGAACACCGTGATGAGCTGAAG                         GGTACCGTAGTACTTGTTTTCCAACCAGCTGAGGAAGGTGGTGGTGGGGCA
genomic: TGCTGTTGGGTTCTGCCAGGATACTTCAGGAACACCGTGATGAGCTGAAGgttggctaaa ... ataactgtagGGTACCGTAGTACTTGTTTTCCAACCAGCTGAGGAAGGTGGTGGTGGGGCA
EST: gi|29663359|gb|CB659634.1|CB659634
EST:     TGCTGTTGGGTTCTGCCAGGATACTTCTCGAACACCGTGATGAGCTGAAG                         GGTACCGTAGTACTTGTTTTCCAACC
genomic: TGCTGTTGGGTTCTGCCAGGATACTTCAGGAACACCGTGATGAGCTGAAGgttggctaaa ... ataactgtagGGTACCGTAGTACTTGTTTTCCAACC
EST: gi|218485087|gb|FG957004.1|FG957004
EST:     TGCTGTTGGGTTCTGCCAGGATACTTCAGGAACACCGTGATGAGCTGAAG                         GGTACCGTAGTACTTGTTTTCCAACCAGCTGAGGAAGGTGGTGGTGGGGCA
genomic: TGCTGTTGGGTTCTGCCAGGATACTTCAGGAACACCGTGATGAGCTGAAGgttggctaaa ... ataactgtagGGTACCGTAGTACTTGTTTTCCAACCAGCTGAGGAAGGTGGTGGTGGGGCA
EST: gi|218497348|gb|FG955372.1|FG955372
EST:     TGCTGTTGGGTTCTGCCAGGATACTTCAGGAACACCGTGATGAGCTGAAG                         GGTACCGTA-TACTTGTTTTCCAACCAGCTGAGGAAGGTGGTGGTGGGGCA
genomic: TGCTGTTGGGTTCTGCCAGGATACTTCAGGAACACCGTGATGAGCTGAAGgttggctaaa ... ataactgtagGGTACCGTAGTACTTGTTTTCCAACCAGCTGAGGAAGGTGGTGGTGGGGCA
EST: gi|58601345|gb|CK011873.1|CK011873
EST:     TGCTGTTGGGTTCTGCCAGGATACTTCAGGAACACCGTGATGAGCTGAAG                         GGTACCGTAGTACTTGTTTTCCAACCAGCTGAGGAAGGTGGTGGTGGGGCA
genomic: TGCTGTTGGGTTCTGCCAGGATACTTCAGGAACACCGTGATGAGCTGAAGgttggctaaa ... ataactgtagGGTACCGTAGTACTTGTTTTCCAACCAGCTGAGGAAGGTGGTGGTGGGGCA
EST: gi|58658282|gb|CK046962.1|CK046962
EST:     TGCTGTTGGGTTCTGCCAGGATACTTCAGGAACACCGTGATGAGCTGAAG                         GGTACCGTAGTACT
genomic: TGCTGTTGGGTTCTGCCAGGATACTTCAGGAACACCGTGATGAGCTGAAGgttggctaaa ... ataactgtagGGTACCGTAGTACT
EST: gi|58684058|gb|CK072745.1|CK072745
EST:     TGCTGTTGGGTTCTGCCAGGATACTTCAGGAACACCGTGATGAGCTGAAG                         GGTACCGTAGTACTTGTTTTCCAACCAGCTGAGGAAGGTGGTGGTGGGGCA
genomic: TGCTGTTGGGTTCTGCCAGGATACTTCAGGAACACCGTGATGAGCTGAAGgttggctaaa ... ataactgtagGGTACCGTAGTACTTGTTTTCCAACCAGCTGAGGAAGGTGGTGGTGGGGCA

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: 72 (upstream exon), 72 (downstream exon)
Score: 60

TAAAGTGCCTGGAAAGATGCATGGGTGTGGTCACGATGCACATGTTGCTATGCTGTTGGGTTCTGCCAGGATACTTCAGGAACACCGTGATGAGCTGAAGgttggctaaa ... ataactgtagGGTACCGTAGTACTTGTTTTCCAACCAGCTGAGGAAGGTGGTGGTGGGGCAAAGAAAATGATAGATGATGGAGCTGTGGAAAATATAGAGGCCATTTTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatttcaatttctttaccctttctcttgttacaaagtcttcttgataactgtagGGTACCGTAGTACTTGTTTTCCAACCAGCTGAGGAAGGTGGTGGTGGGGCAAAGAAAATGATAGATGATGGAGCTGTGGAAAATATAGAGGCCATTTTTG
                                           tgataac  putative branch site (score: 60)
       aatttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttgctcctatttcagtttttttattaaaagaagttcaacccttgaatttcaatttctttaccctttctcttgttacaaagtcttcttgataactgtagGGTACCGTAGTACTTGTTTTCCAACCAGCTGAGGAAGGTGGTGGTGGGGCAAAGAAAATGATAGATGATGGAGCTGTGGAAAATATAGAGGCCATTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- ttgctcc
- - - - - - - - - - - - - -aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcttg