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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattattagatcgatactattctgcagagttcaacgcttggccttatgttctctcaatcttttggagcactcacattttgccatcttacaaattatacagGATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACATGCCCTGAGCTAGTAGGGAGGTGTTCAATTGTCCGTGAACTTCATGTAT

Basic information

species Oryza sativa
transcript LOC_Os04g40840.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g40840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G359735_T01 (Zea mays), 3'ss of exon 7
--aattattagatcgatactattctgcagagttcaacgcttggccttatgttctctcaatcttttgga-gcactcacattttgccatcttacaaattatacagGATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACATGCCCTGAGCTAGTAGGGAGGTGTTCAATTGTCCGTGAACTTCATGTAT
    || || |||  | ||||       | ||  |||   | |  |  |  ||| |  |  ||    |   ||||||| ||| |  | | |  |||| ||||||||||||| || || ||| |||| ||||| ||||||||||| ||||||||||||||||| || |||||||||||||||||||| ||||| |||||||| |
ccttttgtttgatgaagactagc--aatgggtctaacaaatagtttgttagtcttttgagtttagcaatagactcacaatttact-tttcatgaattttacagGATATCCTGATCGGGCTGTTGCGCTTGCGTAAATGTGGCCGTAATGTTACATGCCCTGAACTTGTAGGGAGGTGTTCAATTGTGCGTGAGCTTCATGTCT

upper sequence: LOC_Os04g40840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G100872_T01 (Zea mays), 3'ss of exon 7
--aattattagatcgatactattctgcagagttcaacgcttggccttatgttctctcaatcttttggagcactcacattttgccatcttacaaattatacagGATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACATGCCCTGAGCTAGTAGGGAGGTGTTCAATTGTCCGTGAACTTCATGTAT
   |||  |    |   |  | |  |   || | | |     | | || | |   | |   |        ||||||| ||| |  | | |  |||| ||||||||||||| || || ||| |||| ||||| ||||||||||| ||||||||||||||||| || |||||||||||||||||||| ||||| |||||||| |
gatattccttttgctcaatgaatgggtctagctaaccataatgtcgta-gcttcttgagcttagcaatatactcacaatttact-tttcatgaattttacagGATATCCTGATCGGCCTGTTGCGCTTGCGTAAATGTGGCCGTAATGTTACATGCCCTGAACTTGTAGGGAGGTGTTCAATTGTTCGTGAGCTTCATGTCT

upper sequence: LOC_Os04g40840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA04G36790.1 (Glycine max), 3'ss of exon 7
aattattagatcgatactattctgcagagttcaacgcttggccttatgttctctcaatcttttggagcactcacattttgccatcttacaaattata--cagGATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACATGCCCTGAGCTAGTAGGGAGGTGTTCAATTGTCCGTGAACTTCATGTAT
   || |  ||   |    || | |    || ||        |    |   | |   ||      |||| | || || ||  | ||  |   || ||  |||||||||||| ||||| || ||||| |||||||||||||||||||   ||| || || |||||  | |||| |||||| ||||| |||||||| || || |
--gtagttcataactggccttgttccttctttaattgcaaatcaagagggatgtgtctcaaacacagcaatgaccttgtgtgaactctctgcttgtaaacagGATATCCTTGTTGGTTTGTTGCGACTGCGAAAATGTGGCCGCAACACTACTTGTCCAGAGCTTATGGGGAAGTGTTCTATTGTTCGTGAACTCCACGTTT

upper sequence: LOC_Os04g40840.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA06G18150.1 (Glycine max), 3'ss of exon 7
aattattagatcgatactattctgcagagttcaacgcttggccttatgttctctcaatcttttggagcactcacattttgccatcttacaaattata--cagGATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACATGCCCTGAGCTAGTAGGGAGGTGTTCAATTGTCCGTGAACTTCATGTAT
  | ||    |   | || |  |    | |  |  |    |  |      || |   ||      |||| | || || |   | ||  |   || ||  |||||||||||| ||||| || ||||  |||||||||||||||||||    || || || |||||  | |||| |||||| ||||| |||||||| ||||| |
--tcatatttttccttctttaattgtaaatcaagagggacgtgtctcaacctgttgctcaaacacagcaatgaccttgtctgaactctctgcttgtaaacagGATATCCTTGTTGGTTTGTTGCGGCTGCGAAAATGTGGCCGCAACACAACTTGTCCAGAGCTTATGGGGAAGTGTTCTATTGTTCGTGAACTCCATGTTT

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|33810915|gb|CF331348.1|CF331348
EST:     CTTCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAG                         GATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
genomic: CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAGgtacatatat ... aattatacagGATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
EST: gi|88907490|gb|CI090284.1|CI090284
EST:     CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAG                         GATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
genomic: CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAGgtacatatat ... aattatacagGATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
EST: gi|86887320|gb|CI313223.1|CI313223
EST:     CTCCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAG                         GATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
genomic: CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAGgtacatatat ... aattatacagGATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
EST: gi|29682940|gb|CB679215.1|CB679215
EST:     CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAG                         GATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
genomic: CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAGgtacatatat ... aattatacagGATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
EST: gi|29666831|gb|CB663106.1|CB663106
EST:     CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAG                         GATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
genomic: CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAGgtacatatat ... aattatacagGATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
EST: gi|29682941|gb|CB679216.1|CB679216
EST:     CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAG                         GATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
genomic: CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAGgtacatatat ... aattatacagGATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
EST: gi|89186014|gb|CI047883.1|CI047883
EST:     AGGATACACAGCAG                         GATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
genomic: AGGATACACAGCAGgtacatatat ... aattatacagGATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
EST: gi|27577984|gb|CB000679.1|CB000679
EST:     CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAG                         GATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
genomic: CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAGgtacatatat ... aattatacagGATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
EST: gi|88226125|gb|CI226041.1|CI226041
EST:     CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAG                         GATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
genomic: CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAGgtacatatat ... aattatacagGATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
EST: gi|218500846|gb|FG954979.1|FG954979
EST:     CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAG                         GATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
genomic: CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAGgtacatatat ... aattatacagGATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
EST: gi|27576345|gb|CA999039.1|CA999039
EST:     CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAG                         GATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
genomic: CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAGgtacatatat ... aattatacagGATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
EST: gi|88983019|gb|CI250623.1|CI250623
EST:     CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAG                         GATATCCTTATTGGTTTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
genomic: CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAGgtacatatat ... aattatacagGATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
EST: gi|33810913|gb|CF331347.1|CF331347
EST:     CTTCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAG                         GATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
genomic: CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAGgtacatatat ... aattatacagGATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
EST: gi|86543899|gb|CI184105.1|CI184105
EST:     CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAG                         GATATCCTTATTGGTCTTCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
genomic: CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAGgtacatatat ... aattatacagGATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
EST: gi|86485804|gb|CI128437.1|CI128437
EST:     CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAG                         GATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
genomic: CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAGgtacatatat ... aattatacagGATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
EST: gi|87035159|gb|CI189781.1|CI189781
EST:     CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAG                         GATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA
genomic: CTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAGgtacatatat ... aattatacagGATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACA

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: 55 (upstream exon), 70 (downstream exon)
Score: 22

CCATCACAAAATTAGACCTGACGAAGTAGAGCTTGTTAGGCGTGACTATGCTGCAAATGAGGGCTGGGAGACCTTTCTCTCATACGAGGATACACAGCAGgtacatatat ... aattatacagGATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACATGCCCTGAGCTAGTAGGGAGGTGTTCAATTGTCCGTGAACTTCATGTAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttctctcaatcttttggagcactcacattttgccatcttacaaattatacagGATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACATGCCCTGAGCTAGTAGGGAGGTGTTCAATTGTCCGTGAACTTCATGTAT
                                     atcttacaaattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattattagatcgatactattctgcagagttcaacgcttggccttatgttctctcaatcttttggagcactcacattttgccatcttacaaattatacagGATATCCTTATTGGTCTGCTGCGATTGCGAAAATGTGGCCGCAATGTTACATGCCCTGAGCTAGTAGGGAGGTGTTCAATTGTCCGTGAACTTCATGTAT

- - - - - - - - - -ttctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgccatc