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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtttgtcttatccatgctaagtatggttgtattcctgctcagatttaaaatgacagataatatatttttttaactgatcttgtgttaaaaactgtgcagGCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAG

Basic information

species Oryza sativa
transcript LOC_Os10g38970.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g38970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G162292_T01 (Zea mays), 3'ss of exon 2
------------tgtttgtcttatcc-atgctaagtatggttgtattcctgctcagatttaaaatgacagataatatatttttttaactgatcttgtgttaaaaactgtgcagGCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAG
            ||||  |   | |  | ||  || ||| |||| ||    || || ||| ||||| ||   ||  || | |||||     |||         |||  |||||| ||||| ||||| ||||||||||| |||||||| |||||||| ||||||||||||||||||||||||
aatttttatctatgttgctagcaccagaggcctagcatgattgtgttt---cttaggtttgaaatgccatg-aacttactcttttattctgtct---------aaccttgcagGTTGGGTGAATCGCTTTGCCAATGCCGGTGATACTGCTGTGGTTGTTGCTGAGAACACAGCAGTTAAG

upper sequence: LOC_Os10g38970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G162292_T02 (Zea mays), 3'ss of exon 2
------------tgtttgtcttatcc-atgctaagtatggttgtattcctgctcagatttaaaatgacagataatatatttttttaactgatcttgtgttaaaaactgtgcagGCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAG--------------------------------
            ||||  |   | |  | ||  || ||| |||| ||    || || ||| ||||| ||   ||  || | |||||     |||         |||  |||||| ||||| ||||| ||||||||||| |||||||| |||||||| ||||||||||||||||||||||||                                
aatttttatctatgttgctagcaccagaggcctagcatgattgtgttt---cttaggtttgaaatgccatg-aacttactcttttattctgtct---------aaccttgcagGTTGGGTGAATCGCTTTGCCAATGCCGGTGATACTGCTGTGGTTGTTGCTGAGAACACAGCAGTTAAGGTAATTTCAGAATTTGTTGCTGTGATACAATG

upper sequence: LOC_Os10g38970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G29860.1 (Glycine max), 3'ss of exon 2
tgtttgtcttatccatgctaagtatggttgtattcctgctc--agatttaaaatgacagataatatattttt---ttaactg-atcttgtgttaaaaactgtg-cagGCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAG
       ||||   | |     ||  |   |  |||  ||   | |||     |     | | ||  |||||   |  |||| || || |        |  || |||||||||| ||| | |||||||||||||||||||| ||  ||| ||| ||||  || |||||| |   |
-------cttagtgaaggaggttaaagcattgatccatcttgtaaattattgtttctgtacagtacttttttgcttccactgtatattcttacggcttccatgacagGCTGGGTGAATAGGTTTGCCAATGCTGGTGATACTGCCATGGAAGTGGCTGGAAATACAGCATTACGG

upper sequence: LOC_Os10g38970.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA09G24630.1 (Glycine max), 3'ss of exon 2
tgtttgtcttatccatgct-aagtatggttgtattcctgctcagatttaaaatgacag-ataatatattt---ttttaactg-atcttgtgttaaaaactgtg-cagGCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAG
        | |   | | | ||| || | |  || |    |  || |||      | | | | ||  |||   |||  ||||  | || |   ||   |  || |||| ||||||||| | |||||||||||||||||||| ||| ||| ||| ||||  || |||||| |   |
-------gtgaaggaggtttaagcattgatccatccaacttgtgaattattgcttctgtacattacttttctgtttccactgtgtattcttacaacttccatgacagGTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGG

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|33816213|gb|CF333954.1|CF333954
EST:     CCCAAGCTCCCAG                         GCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
genomic: CCCAAGCTCCCAGgtaaggggat ... aactgtgcagGCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
EST: gi|33804321|gb|CF328035.1|CF328035
EST:     GCGACGTGCTCTGCGAGGGGCTCGCCGTCCCCAAGCTCCCAG                         GCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
genomic: GCGACGTGCTCTGCGAGAGGCTCGCCGTCCCCAAGCTCCCAGgtaaggggat ... aactgtgcagGCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
EST: gi|29682951|gb|CB679226.1|CB679226
EST:     CCACTTCTGCGACGTGTTTTGCGAGAGGCTCGCCGTCCCCAAGCTCCCAG                         GCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
genomic: CCACTTCTGCGACGTGCTCTGCGAGAGGCTCGCCGTCCCCAAGCTCCCAGgtaaggggat ... aactgtgcagGCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
EST: gi|3761045|gb|C98299.1|C98299
EST:     CCATTTCTGCGACGTGCTCTGCGAGAGGCTCGCCGTCCCCAAGCTCCCAG                         GCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
genomic: CCACTTCTGCGACGTGCTCTGCGAGAGGCTCGCCGTCCCCAAGCTCCCAGgtaaggggat ... aactgtgcagGCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
EST: gi|6850181|gb|AU082300.1|AU082300
EST:     TGCGACGTGCTCTGCGANAGGCTCGCCGTCCCCAAGCTCCCAG                         GCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
genomic: TGCGACGTGCTCTGCGAGAGGCTCGCCGTCCCCAAGCTCCCAGgtaaggggat ... aactgtgcagGCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
EST: gi|88977233|gb|CI024970.1|CI024970
EST:     CGTGCTCTGCGAGAGGCTCGCCGTCCCCAAGCTCTCAG                         GCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
genomic: CGTGCTCTGCGAGAGGCTCGCCGTCCCCAAGCTCCCAGgtaaggggat ... aactgtgcagGCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
EST: gi|33814559|gb|CF333144.1|CF333144
EST:     GCGAGAGGCTCGCCGTCCCCCAAGCTCCCAG                         GCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
genomic: GCGAGAGGCTCGCCGT-CCCCAAGCTCCCAGgtaaggggat ... aactgtgcagGCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
EST: gi|86259224|gb|CI010525.1|CI010525
EST:     GCGAGAGGCTCGCCGTCCCCAAGCTCCCAG                         GCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
genomic: GCGAGAGGCTCGCCGTCCCCAAGCTCCCAGgtaaggggat ... aactgtgcagGCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
EST: gi|33804319|gb|CF328034.1|CF328034
EST:     CCACTTCTGCGACGTGCTCTGCGAGGGGCTCGCCGTCCCCAAGCTCCCAG                         GCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
genomic: CCACTTCTGCGACGTGCTCTGCGAGAGGCTCGCCGTCCCCAAGCTCCCAGgtaaggggat ... aactgtgcagGCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
EST: gi|163920984|gb|EG710397.1|EG710397
EST:     CCACTTCTGCGACGTGCTCTGCGAGAGGCTCGCCGTCCCCAAGCTCCCAG                         GCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
genomic: CCACTTCTGCGACGTGCTCTGCGAGAGGCTCGCCGTCCCCAAGCTCCCAGgtaaggggat ... aactgtgcagGCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
EST: gi|88243897|gb|CI243019.1|CI243019
EST:     ACGTGCTCTGCGAGAGGCTCGCCGTCCCCAAGCTCCCAG                         GCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
genomic: ACGTGCTCTGCGAGAGGCTCGCCGTCCCCAAGCTCCCAGgtaaggggat ... aactgtgcagGCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
EST: gi|13420451|gb|AU174541.1|AU174541
EST:     CCACTTCTGCGACGTGCTCTGCGAGAGGCTCGCCGTCCCCAAGCTCCCAG                         GCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGG
genomic: CCACTTCTGCGACGTGCTCTGCGAGAGGCTCGCCGTCCCCAAGCTCCCAGgtaaggggat ... aactgtgcagGCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGG
EST: gi|33817055|gb|CF334366.1|CF334366
EST:     CCACTTCTGCGACGTGCTCTGCGAGAGGCTCGCCGTCCCCAAGCTCCCAG                         GCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
genomic: CCACTTCTGCGACGTGCTCTGCGAGAGGCTCGCCGTCCCCAAGCTCCCAGgtaaggggat ... aactgtgcagGCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
EST: gi|218505580|gb|FG966210.1|FG966210
EST:     CCACTTCTGCGACGTGCTCTGCGAGAGGCTCGCCGTCCCCAAGCTCCCAG                         GCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG
genomic: CCACTTCTGCGACGTGCTCTGCGAGAGGCTCGCCGTCCCCAAGCTCCCAGgtaaggggat ... aactgtgcagGCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTG

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: 44 (upstream exon), 65 (downstream exon)
Score: 4

AGCCGCGAGTGGCCGGGACACTCCTACGACCTCCTCTCCAGGAACTGCAACCACTTCTGCGACGTGCTCTGCGAGAGGCTCGCCGTCCCCAAGCTCCCAGgtaaggggat ... aactgtgcagGCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaaatgacagataatatatttttttaactgatcttgtgttaaaaactgtgcagGCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAG
            ataatatattttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtttgtcttatccatgctaagtatggttgtattcctgctcagatttaaaatgacagataatatatttttttaactgatcttgtgttaaaaactgtgcagGCTGGGTTAATCGTTTTGCCAATGCTGGTGATACCGCTGTGGTAGTTGCTGAGAACACAGCAGTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
tgtttgt
- - - - - -tccatgc
- - - - - - - - - - - -atggttg
- - - - - - - - - - - - - - - - - cctgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtgtt