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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgttgtcaatctcctttggctaaacttagtatctgtagcattgcatatgaaactttcccaagattataatgaggtatgttttttccctgctttttctagGCAATCACTGTTGCTGGCACGAAGAAAAATGAGTCCATCTTCTCTGAAATCCAGAGCCAGGTGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTT

Basic information

species Oryza sativa
transcript LOC_Os05g45950.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g45950.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G115049_T01 (Zea mays), 3'ss of exon 2
---ttgttgtcaatctcctttggctaaact-tagtatctgtagcattgcatatgaaactttcccaagattataatgaggtatgttttttccctgctttttctagGCAATCACTGTTGCTGGCACGAAGAAAAATGAGTCCATCTTCTCTGAAATCCAGAGCCAGGTGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTT
   |  |||| ||| |  ||    |  |   |  ||| ||||  ||   ||||    |  | | |||       | || |||| |   |   |||| | | ||||| || |||| |||  |||||| |||| ||||  | |||||   |||||||||||||||| ||||| ||||||||||| | |||||||||||||||||||
gtttctttgttaatgtaattcttttggatagtgatatatgtacaatctgatatttttccctgcaaag--cggtgttagttatgatagctta-tgctgtgt-tagGCCATTACTGCTGCAAGCACGAGGAAAGATGAAGCTATCTTTAATGAAATCCAGAGCCAGCTGAAGCACAACAATGTGACTGTGGATGTGAAAGCAACTT
















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|29687058|gb|CB683333.1|CB683333
EST:     ACCACACGGACCAGAAGTTCACGCTCACCACCTACGCCGCGAACGGAGCT                         GCAATCACTGTTGCTGGCACGAAGAAAAATGAGTCCATCTTCTCTGAAATC
genomic: ACCACACGGACCAGAAGTTCACGCTCACCACCTACGCCGCGAACGGAGCTgtgagttcct ... ctttttctagGCAATCACTGTTGCTGGCACGAAGAAAAATGAGTCCATCTTCTCTGAAATC
EST: gi|33797474|gb|CF324597.1|CF324597
EST:     ACCACACGGACCAGAAGTTCACGCTCACCACCTACGCCGCGAACGGAGCT                         GCAATCACTGTTGCTGGCACGAAGAAAAATGAGTCCATCTTCTCTGAAATC
genomic: ACCACACGGACCAGAAGTTCACGCTCACCACCTACGCCGCGAACGGAGCTgtgagttcct ... ctttttctagGCAATCACTGTTGCTGGCACGAAGAAAAATGAGTCCATCTTCTCTGAAATC
EST: gi|24468749|gb|CA305698.1|CA305698
EST:     CACCACCTACGCCGCGAACGGAGCT                         GCAATCACTGTTGCTGGCACGAAGAAAAATGAGTCCATCTTCTCTGAAATC
genomic: CACCACCTACGCCGCGAACGGAGCTgtgagttcct ... ctttttctagGCAATCACTGTTGCTGGCACGAAGAAAAATGAGTCCATCTTCTCTGAAATC
EST: gi|313081113|gb|HO213699.1|HO213699
EST:     ACCACACGGACCAGAAGTTCACGCTCACCACCTACGCCGCGAACGGAGCT                         GCAATCACTGTTGCTGGCACGAAGAAAAATGAGTCCATCTTCTCTGAAATC
genomic: ACCACACGGACCAGAAGTTCACGCTCACCACCTACGCCGCGAACGGAGCTgtgagttcct ... ctttttctagGCAATCACTGTTGCTGGCACGAAGAAAAATGAGTCCATCTTCTCTGAAATC
EST: gi|58608189|gb|CK036222.1|CK036222
EST:     ACCACACGGACCAGAAGTTCACGCTCACCACCTACGCCGCGAACGGAGCT                         GCAATCACTGTTGCTGGCACGAAGAAAAATGAGTCCATCTTCTCTGGAATC
genomic: ACCACACGGACCAGAAGTTCACGCTCACCACCTACGCCGCGAACGGAGCTgtgagttcct ... ctttttctagGCAATCACTGTTGCTGGCACGAAGAAAAATGAGTCCATCTTCTCTGAAATC
EST: gi|38474605|gb|CF958738.1|CF958738
EST:     ACCACACGGACCAGAAGTTCACGCTCACCACCTACGCCGCGAACGGAGCT                         GCAATCACTGTTGCTGGCACGAAGAAAAATGAGTCCATCTTCTCTGAAATC
genomic: ACCACACGGACCAGAAGTTCACGCTCACCACCTACGCCGCGAACGGAGCTgtgagttcct ... ctttttctagGCAATCACTGTTGCTGGCACGAAGAAAAATGAGTCCATCTTCTCTGAAATC
EST: gi|3760364|gb|C97618.1|C97618
EST:     GGACCAGAAGTTCACGCTCACCACCTACGCCGCGAACGGAGCT                         GCAATCACTGTTGCTGGCACGAAGAAAAATGAGTCCATCTTCTCTGAAATC
genomic: GGACCAGAAGTTCACGCTCACCACCTACGCCGCGAACGGAGCTgtgagttcct ... ctttttctagGCAATCACTGTTGCTGGCACGAAGAAAAATGAGTCCATCTTCTCTGAAATC
EST: gi|163927541|gb|EG710729.1|EG710729
EST:     ACCACACGGACCAGAAGTTCACGCTCACCACCTACGCCGCGAACGGAGCT                         GCAATCACTGTTGCTGGCACGAAGAAAAATGAGTCCATCTTCTCTGAAATC
genomic: ACCACACGGACCAGAAGTTCACGCTCACCACCTACGCCGCGAACGGAGCTgtgagttcct ... ctttttctagGCAATCACTGTTGCTGGCACGAAGAAAAATGAGTCCATCTTCTCTGAAATC
EST: gi|33810860|gb|CF331321.1|CF331321
EST:     ACCACACGGACCAGAAGTTCACGCTCACCACCTACGCCGCGAACGGAGCT                         GCAATCACTGTTGCTGGCACGAAGAAAAATGAGTCCATCTTCTCTGAAATC
genomic: ACCACACGGACCAGAAGTTCACGCTCACCACCTACGCCGCGAACGGAGCTgtgagttcct ... ctttttctagGCAATCACTGTTGCTGGCACGAAGAAAAATGAGTCCATCTTCTCTGAAATC

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: 68 (upstream exon), 74 (downstream exon)
Score: 68

ATCTCCTGTATAGGGATTACCACACGGACCAGAAGTTCACGCTCACCACCTACGCCGCGAACGGAGCTgtgagttcct ... ctttttctagGCAATCACTGTTGCTGGCACGAAGAAAAATGAGTCCATCTTCTCTGAAATCCAGAGCCAGGTGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgaaactttcccaagattataatgaggtatgttttttccctgctttttctagGCAATCACTGTTGCTGGCACGAAGAAAAATGAGTCCATCTTCTCTGAAATCCAGAGCCAGGTGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTT
                              tatgttttttccctgc  CT-rich tract
               aagattataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgttgtcaatctcctttggctaaacttagtatctgtagcattgcatatgaaactttcccaagattataatgaggtatgttttttccctgctttttctagGCAATCACTGTTGCTGGCACGAAGAAAAATGAGTCCATCTTCTCTGAAATCCAGAGCCAGGTGAAGAACAACAATGTGTCCGTGGATGTGAAAGCAACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
ttgttgt
- - - - - - - - - - - - - - - - - - - -cattgca