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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattgactttacaccaactactccacttttgttgcctttactgtaaattgaacattatttttccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATGAAGAACCCACCTGCCCAGCACCTTTCAGCTTTGATTTTGAGCAACCATC

Basic information

species Oryza sativa
transcript LOC_Os10g38950.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G127141_T01 (Zea mays), 3'ss of exon 5
gtacattgactttacaccaactactccacttttgttgcctttactgtaaattgaa----cattatttttccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATGAAGAACCCACCTGCCCAGCACCTTTCAGCTTTGATTTTGAGCAACCATC
||||  || ||| |  | |   |||  | |  || || ||| ||| |||| | ||    | || ||||   ||||||||||||||||||| ||||| |||||||||||||| |||||||| |||||||| ||||| |||||||| ||||||||||||||||||||||||||||||||
gtac-ctgccttcatgcaagtcactttattagtggtggcttaactataaactcaaagaccttttttttcatatgcagTTGATGAGGCTCTGCATCATCCATACTTGGCTTCACTTCATGAGATCAATGATGAACCTACCTGCCCTGCACCTTTCAGCTTTGATTTTGAGCAACCATC

upper sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA18G47140.1 (Glycine max), 3'ss of exon 5
------------------gtacattgac--tttacaccaact--actccacttttgttgcctttactgtaaattgaacattattttt----ccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATGAAGAACCCACCTGCCCAGCACCTTTCAGCTTTGATTTTGAGCAACCATC-
                   | || | |   |||| | |   |  | |    ||||||     ||  | | ||| | |  ||| || |    |  ||||||| | || |||||   |||||||||||||||  |||||||||| || ||||| |||||    |||     ||||||||| |||||||||||||||||||| 
tgaatgttgacaatttatctgcaataatcttttatagctgttggattttctttttgtatatatttttattaatcgtatgttacttatgatgctttgcagtTAAAGAAGCTCTGTGTCACCCATACTTGGCACCTCTTCATGATATTAATGAGGAACCTGTTTGCGTTAGACCTTTCAGTTTTGATTTTGAGCAACCATCT

upper sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA09G39190.1 (Glycine max), 3'ss of exon 5
-------------------gtacattgac--tttacaccaactac-tccacttttgttgcct-ttactgtaaattgaacattattttt----ccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATGAAGAACCCACCTGCCCAGCACCTTTCAGCTTTGATTTTGAGCAACCATC
                    | || | |   |||| | | | |   |   ||||| ||   | ||  | | ||| | || ||| || |    |  ||||||||| || |||||   |||||||||||||||| |||||||||| || ||||| |||||  | |||     ||||||||| ||||||||||||||||||||
ttgaatgtcgacaatatatatgcagtaatcttttatagctattggattttctttttttatatatttttattaatcgtacgttacttatgacgctttgcagTTGAAGAAGCTCTGTGTCACCCATACTTGGCTCCTCTTCATGATATTAATGAGGAACCTGCTTGCGTTAGACCTTTCAGTTTTGATTTTGAGCAACCATC

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|86903057|gb|CI324527.1|CI324527
EST:     AAGCAGACGGATAACTG                         TTGATGAGGCTGTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
genomic: AAGCAGACGGATAACTGgtacattgac ... ttccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
EST: gi|86874392|gb|CI316758.1|CI316758
EST:     TCTGTTAGAGAAAATGGCTGGTGGGTGACCCAAGCAGACGGATAACTG                         TTGATGAGGCTGCTTCATCACCCAATACGTGGCTTCTCTTCATGACATCAA
genomic: TCTGTTAGAGAAAAT-GCTGGTGTTTGACCCAAGCAGACGGATAACTGgtacattgac ... ttccatgcagTTGATGAGGCT-CTTCATCACCC-ATACTTGGCTTCTCTTCATGACATCAA
EST: gi|29614257|gb|CB619270.1|CB619270
EST:     CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTG                         TTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
genomic: CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTGgtacattgac ... ttccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
EST: gi|23512837|gb|BU672858.1|BU672858
EST:     CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTG                         TTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
genomic: CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTGgtacattgac ... ttccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
EST: gi|86421256|gb|CI057245.1|CI057245
EST:     CCCAAGCAGACGGATAACTG                         TTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
genomic: CCCAAGCAGACGGATAACTGgtacattgac ... ttccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
EST: gi|89187007|gb|CI053410.1|CI053410
EST:     CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTG                         TTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
genomic: CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTGgtacattgac ... ttccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
EST: gi|29614216|gb|CB619229.1|CB619229
EST:     CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTG                         TTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
genomic: CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTGgtacattgac ... ttccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
EST: gi|58654323|gb|CK043003.1|CK043003
EST:     CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTG                         TTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
genomic: CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTGgtacattgac ... ttccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
EST: gi|88955671|gb|CI091960.1|CI091960
EST:     CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTG                         TTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
genomic: CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTGgtacattgac ... ttccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
EST: gi|33815274|gb|CF333489.1|CF333489
EST:     CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTG                         TTGATGAGGCTCTTCATTCACCCATACTTGGCTTCTCTTCATGACATCAAT
genomic: CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTGgtacattgac ... ttccatgcagTTGATGAGGCTCTTCA-TCACCCATACTTGGCTTCTCTTCATGACATCAAT
EST: gi|88990538|gb|CI107925.1|CI107925
EST:     CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTG                         TTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
genomic: CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTGgtacattgac ... ttccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
EST: gi|88218611|gb|CI218460.1|CI218460
EST:     CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTG                         TTGATGAGGCTCTTCATCACCCATACTTGGCCTCTCTTCATGACATCAATG
genomic: CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTGgtacattgac ... ttccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
EST: gi|25807128|gb|CA763089.1|CA763089
EST:     CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTG                         TTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
genomic: CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTGgtacattgac ... ttccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
EST: gi|27578107|gb|CB000802.1|CB000802
EST:     CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTG                         TTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
genomic: CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTGgtacattgac ... ttccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
EST: gi|89181927|gb|CI113433.1|CI113433
EST:     CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTG                         TTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
genomic: CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTGgtacattgac ... ttccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
EST: gi|86853233|gb|CI326328.1|CI326328
EST:     CGATCTGTTAGAGAAAATGCTGGTGTTT-ACCCAAGCAGACGGATAACTG                         TTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
genomic: CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTGgtacattgac ... ttccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
EST: gi|29688024|gb|CB684299.1|CB684299
EST:     CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTG                         TTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
genomic: CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTGgtacattgac ... ttccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
EST: gi|86258736|gb|CI065089.1|CI065089
EST:     CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTG                         TTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
genomic: CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTGgtacattgac ... ttccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
EST: gi|88976887|gb|CI257583.1|CI257583
EST:     CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTG                         TTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
genomic: CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTGgtacattgac ... ttccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
EST: gi|86488872|gb|CI131505.1|CI131505
EST:     CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTG                         TTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
genomic: CGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTGgtacattgac ... ttccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
EST: gi|86496784|gb|CI139417.1|CI139417
EST:     GACGGATAACTG                         TTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG
genomic: GACGGATAACTGgtacattgac ... ttccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATG

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: 67 (upstream exon), 62 (downstream exon)
Score: 25

CCAAGGCAGGACTTCCGCTTGCGCTTCCGCAACATGTCTGCTGGTGCAGTCGATCTGTTAGAGAAAATGCTGGTGTTTGACCCAAGCAGACGGATAACTGgtacattgac ... ttccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATGAAGAACCCACCTGCCCAGCACCTTTCAGCTTTGATTTTGAGCAACCATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactactccacttttgttgcctttactgtaaattgaacattatttttccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATGAAGAACCCACCTGCCCAGCACCTTTCAGCTTTGATTTTGAGCAACCATC
                                       ttatttttcc  CT-rich tract
                          tgtaaattgaacatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacattgactttacaccaactactccacttttgttgcctttactgtaaattgaacattatttttccatgcagTTGATGAGGCTCTTCATCACCCATACTTGGCTTCTCTTCATGACATCAATGAAGAACCCACCTGCCCAGCACCTTTCAGCTTTGATTTTGAGCAACCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT