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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTCGATTTATGAAATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCGgtaaagctctctcattcgcaagtcttacttggtgtggtgtgtgcgcatactcactcacgctataatggttatctgactgcctgaattcgctttag

Basic information

species Oryza sativa
transcript LOC_Os03g63430.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63430.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G014116_T02 (Zea mays), 5'ss of exon 7
CTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTCGATTTATGAAATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCGgtaaag---ctctctcattcgcaagtcttacttggtgtggtgtgtgcgcatactcactcacgctataat-----ggttatctgactgcctgaattcgctt-tag
 |||||||| ||||||||||||||| |||||||||||||||| |||||| | |||||||| |||||| ||||||||||||||||| ||||||||||||||||| |    |||||||  || |||    |   |    |     |  |  | |  ||| ||      ||        |||||||||| ||| | |||  ||  ||
TTATTACTCTCACAACAATGATTACTTGGAAATCTGCCGTTGTTACAAGGCTATTTATGATATTCCAGCAATAAAAGAGGATCCAACAAAGTGGATACCGgtacacactctctctctctctcaacatgtgtatacacttccccgccctgacagacacccatcaaccaacccctcaattatctgactaccttatttcctttgcag

upper sequence: LOC_Os03g63430.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G013750_T03 (Zea mays), 5'ss of exon 7
CTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTCGATTTATGAAATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCGgtaaagctctctcattcgcaagtcttacttggtgtggtgtgtgcgcatactcactcacgctataatggttatctgactgcctgaattcgctttag--
 ||||||| ||||||||||||||||||||||||||| ||||| |||||| | |||||||| || ||| ||||||| || |||||| | |||||||||||||||   ||||||| |   || || |       |    | ||  | |  |  |||  || |   |||   ||||||||| ||| ||||| ||| |   
ATATTACTTGCACAACAATGATTACCTGGAAATCTGTCGTTGTTACAAGGCTATTTATGATATCCCAGCAATAAAGGAAGATCCAACCAAGTGGATACCGgta---ctctctc-tcaacatgtgt------atacactctg-acacccatccaccaacccctcaat---tatctgactaccttaattc-cttcacag

upper sequence: LOC_Os03g63430.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA05G32030.2 (Glycine max), 5'ss of exon 7
CTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTCGATTTATGAAATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCGgtaaagctctctcattcgcaagtcttacttggtgtggtgtgtgcgc-atactcactcacgctataatggttatctgactgcctgaattcgctttag
 ||||| || || ||||||||||| || ||||| ||||||||||||||| | || ||||| ||||||||  | ||||| || ||  | |||||||| || ||||  ||      ||  |   | ||    | |   ||   |  || ||| ||  |    ||  |||  ||||||   |   || |          
GTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGCAATATATGAGATTCCATCTGTCAAAGAAGACCCTGCCAAGTGGATTCCAgtaagccttctcttttttctgttattgtgagattctgttgttatgcgatattctgtttttctg-aata-ttatctt-ttatgtgtag---------

upper sequence: LOC_Os03g63430.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA06G15330.1 (Glycine max), 5'ss of exon 7
CTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTCGATTTATGAAATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCGgtaaagctctctcattcgcaagtcttacttggtgtggtgtgtgcgcatactcactcacgctataatggttatctgactgcctgaattcgctttag
 ||||| || || || |||||||| || ||||| ||||||||||||||| | || ||||| ||||||||  | |||||  |||   |  ||||||| || |||    |  |  | ||   | | ||| ||  | || |||  |    |  |  ||    || | |   || |||       |             
GTATTATTCCCATAAAAATGATTATCTTGAAATTTGCCGTTGCTACAAGGCAATATATGAGATTCCATCTGTCAAAGAAAATCTTGCCGAGTGGATTCCAgtaggctttccctactcttta-ttttattta-tctgttgtcagattgtgttt-ctttttctctgaatattttcttttcatgtag-----------

upper sequence: LOC_Os03g63430.2 (Oryza sativa), 5'ss of exon 7
lower sequence: AT5G09900.2 (Arabidopsis thaliana), 5'ss of exon 7
CTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTCGATTTATGAAATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCGgtaaagctctctcattcgcaagtcttacttggtgtggtgtgtgcgcatactcactcacgctataatggttatctgactgcctgaattcgctttag
 || || || || |||||||| ||| | |||||||||||| |||||||| |||| ||||| || || ||| |||||||   |||     ||||||| |||||||     |  | ||     |   ||  | || | || |     |        |   |  ||||   || | |||    |  ||    | ||||
GTACTATTCTCATAACAATGAGTACATTGAAATCTGCCGTAGCTACAAGGCGATATATGATATCCCTTCAGTAAAAGAAACTCCGGAGCAGTGGATTCCGgtaagctcatgccgttgattggatgta--tagt-tagtatacattctatagggttagtgtaataact-ttctttgatcttcaaaa----cattag

upper sequence: LOC_Os03g63430.2 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 5'ss of exon 7
CTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTCGATTTATGAAATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCGgtaaag---ctctctcattcgcaagtcttacttggtgtggtgtgtgcgcatactcactcacgctata-atggttatctgactgcctgaattcgctttag
 ||| |||| |||| |||||||||||| ||||| || ||| |||| ||| |||| |||||||| |||||  | | ||| |||||| |  |||||||||||||||||   || |  |||       | |  | |  |||  | |  | ||| ||||   ||  ||  |  | |                           
GTATCACTCCCACAGCAATGATTACCTTGAAATTTGTCGTAGCTATAAGGCGATATATGAAATCCCATCTGTCAGAGAAGATCCAGCTCAGTGGATACCGgtaaagaatcttttccatgtatgcctttgcccttttgtttttttggagca-actctaacaatctgcatgtag---------------------------

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|29658197|gb|CB654472.1|CB654472
EST:     ATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCG                         GTTCTTAGAAAGATCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATG
genomic: ATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCGgtaaagctct ... ttcgctttagGTTCTTAGAAAGATCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATG
EST: gi|29664786|gb|CB661061.1|CB661061
EST:     CGATTTATGAAATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCG                         GTTCTTAGAAAGATCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATG
genomic: CGATTTATGAAATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCGgtaaagctct ... ttcgctttagGTTCTTAGAAAGATCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATG
EST: gi|29620777|gb|CB625788.1|CB625788
EST:     GATCCATCAAAGTGGATACCG                         GTTCTTAGAAAGATCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATG
genomic: GATCCATCAAAGTGGATACCGgtaaagctct ... ttcgctttagGTTCTTAGAAAGATCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATG
EST: gi|29645308|gb|CB650315.1|CB650315
EST:     CGATTTATGAAATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCG                         GTTCTTAGAAAGATCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATG
genomic: CGATTTATGAAATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCGgtaaagctct ... ttcgctttagGTTCTTAGAAAGATCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATG
EST: gi|29637545|gb|CB642554.1|CB642554
EST:     CGATTTATGAAATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCG                         GTTCTTAGAAAGATCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATG
genomic: CGATTTATGAAATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCGgtaaagctct ... ttcgctttagGTTCTTAGAAAGATCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATG
EST: gi|29664785|gb|CB661060.1|CB661060
EST:     GATTTATGAAATTCCATNCA-TAAAAGAGGATCCATCAAAGTGGATACCG                         GTTCTTAGAAAGATCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCG
genomic: GATTTATGAAATTCCAT-CAATAAAAGAGGATCCATCAAAGTGGATACCGgtaaagctct ... ttcgctttagGTTCTTAGAAAGATCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCG
EST: gi|33797492|gb|CF324606.1|CF324606
EST:     CGATTTATGAAATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCG                         GTTCTTAGAAAGATCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATG
genomic: CGATTTATGAAATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCGgtaaagctct ... ttcgctttagGTTCTTAGAAAGATCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATG
EST: gi|117217926|gb|CT845200.1|CT845200
EST:     CGATTTATGAAATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCG                         GTTCTTAGAAAGATCTGTTGGTATTTGGTGTTGGCGC-TCATGATCCGATG
genomic: CGATTTATGAAATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCGgtaaagctct ... ttcgctttagGTTCTTAGAAAGATCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATG
EST: gi|29664483|gb|CB660758.1|CB660758
EST:     ATCAATAAAAGAGGATCCATCAAAGTGGATACCG                         GTTCTTAGAAAGATCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATG
genomic: ATCAATAAAAGAGGATCCATCAAAGTGGATACCGgtaaagctct ... ttcgctttagGTTCTTAGAAAGATCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATG
EST: gi|300215653|gb|HO088279.1|HO088279
EST:     CGATTTATGAAATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCG                         GTTCTTAGAAAGATCTGTTGGTATTTGGTGTTGGCGCCTCATGATCAGATG
genomic: CGATTTATGAAATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCGgtaaagctct ... ttcgctttagGTTCTTAGAAAGATCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATG

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: 57 (upstream exon), 73 (downstream exon)
Score: 74

CTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTCGATTTATGAAATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCGgtaaagctct ... ttcgctttagGTTCTTAGAAAGATCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATGCAATCAAGCCTTCTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTCGATTTATGAAATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCGgtaaagctctctcattcgcaagtcttacttggtgtggtgtgtgcgcatactcactcacgctataatggttatctgactgcctgaattcgctttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA