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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttagatatggtttgctcattgcttaataaagttgttgaagtagcacagagtcatcttatcatgctttgtagctcaacgctattgttcttgaacacagGTTCCATGTAGATAAGATGTCCTCTGCACACGTGTATTTGAGATTAAATAAAGGTCAGACAATGGATGACATAAGTGAAGGTGTGCTTGAAGATTGTGCC

Basic information

species Oryza sativa
transcript LOC_Os05g13440.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g13440.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G157332_T07 (Zea mays), 3'ss of exon 1
--attttagatatggtttgctcattgcttaataaagttgttgaa-gtagcacagagtcatcttatcatgctttgtagctcaacgctattgttcttgaacacagGTTCCATGTAGATAAGATGTCCTCTGCACACGTGTATTTGAGATTAAATAAAGGTCAGACAATGGATGACATAAGTGAAGGTGTGCTTGAAGATTGTGCC
   || || ||||  ||  ||  ||||  | |  | ||  | |    |  | | | | |     || |||||  || || ||  ||  | |   |||  |||||||||||||||||||||||||||||||||| |||||| ||||||| |||||||||||  ||||||||||||| ||||| ||| |||| ||||| ||||| 
cttttgtacatatcattgactt-ttgcaaattccattttcttattaaaatatacaattaaga-gtcgtgcttcttaccttaa-actggtttgggtgattacagGTTCCATGTAGATAAGATGTCCTCTGCACATGTGTATGTGAGATTGAATAAAGGTCAATCAATGGATGACATGAGTGAGGGTTTGCTGGAAGACTGTGCG

upper sequence: LOC_Os05g13440.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv04s0008g03810.t01 (Vitis vinifera), 3'ss of exon 1
--attttagatatggtttgctcattgcttaataaagttgttgaagtagcacagagtcatcttatcatgctttgtagctcaacgctattgttc-ttgaacacagGTTCCATGTAGATAAGATGTCCTCTGCACACGTGTATTTGAGATTAAATAAAGGTCAGACAATGGATGACATAAGTGAAGGTGTGCTTGAAGATTGTGCC
   | |||  | ||  |    ||| ||||| |    || ||     ||  |   ||  |||| ||| |      |||   | |  |  | |  || | | |||||| ||||| |||||||||||||| || || || ||| | |||||  | || ||||||||||| ||||| |||||||||||| | || || |||||||| 
ttctcttaagtttgaatcatgcat-gcttagttttttttttttttcagttccatgttttctt-tca-gtcaaagagcgttatggaagggcttatttatcgcagGTTTCATGTGGATAAGATGTCCTCAGCCCATGTTTATGTAAGATTGCACAAGGGTCAGACAATTGATGATATAAGTGAAGGTTTACTGGAGGATTGTGCT
















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|88727931|gb|CI749443.1|CI749443
EST:     AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTG                         GTTCCATGTAGATAAGATGTCCTCTG
genomic: AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTGgtaacttccc ... ttgaacacagGTTCCATGTAGATAAGATGTCCTCTG
EST: gi|88570263|gb|CI661438.1|CI661438
EST:     AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTG                         GTTCCATGTAGATTAGATGTCCTCTGCACACGTG
genomic: AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTGgtaacttccc ... ttgaacacagGTTCCATGTAGATAAGATGTCCTCTGCACACGTG
EST: gi|58663146|gb|CK051832.1|CK051832
EST:     AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTG                         GTTCCATGTAGATAAGATGTCCTCTGCACACGTGTATTTGAGATTAAATAA
genomic: AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTGgtaacttccc ... ttgaacacagGTTCCATGTAGATAAGATGTCCTCTGCACACGTGTATTTGAGATTAAATAA
EST: gi|33659404|gb|CF282017.1|CF282017
EST:     AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTG                         GTTCCATGTAGATAAGATGTCCTCTGCACACGTGTATTTGAGATTAAATAA
genomic: AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTGgtaacttccc ... ttgaacacagGTTCCATGTAGATAAGATGTCCTCTGCACACGTGTATTTGAGATTAAATAA
EST: gi|33808581|gb|CF330176.1|CF330176
EST:     AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTG                         GTTCCATGTAGATAAGATGTCCTCTTCACACGTGTATTTGAGATTAAATAA
genomic: AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTGgtaacttccc ... ttgaacacagGTTCCATGTAGATAAGATGTCCTCTGCACACGTGTATTTGAGATTAAATAA
EST: gi|88349520|gb|CI653799.1|CI653799
EST:     AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTG                         GTTCCATGTAGATAAGATGTCCTCTGCACACGTGTATTTGAGATTAAATAA
genomic: AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTGgtaacttccc ... ttgaacacagGTTCCATGTAGATAAGATGTCCTCTGCACACGTGTATTTGAGATTAAATAA
EST: gi|88342124|gb|CI636482.1|CI636482
EST:     AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTG                         GTTCCATGTAGATTAGATGTC
genomic: AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTGgtaacttccc ... ttgaacacagGTTCCATGTAGATAAGATGTC
EST: gi|88582454|gb|CI699868.1|CI699868
EST:     AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTG                         GTTCCATGTAGATAAGAT
genomic: AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTGgtaacttccc ... ttgaacacagGTTCCATGTAGATAAGAT
EST: gi|88588559|gb|CI706384.1|CI706384
EST:     AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTG                         GTTCCATGTAGATNAGATGTCCTCTGCAC
genomic: AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTGgtaacttccc ... ttgaacacagGTTCCATGTAGATAAGATGTCCTCTGCAC
EST: gi|88440830|gb|CI693400.1|CI693400
EST:     AAGTCCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTG                         GTTCCATGTAGATAAGATGTCCTCCGCACACGTGTATTTGAGAT
genomic: AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTGgtaacttccc ... ttgaacacagGTTCCATGTAGATAAGATGTCCTCTGCACACGTGTATTTGAGAT
EST: gi|88376943|gb|CI639268.1|CI639268
EST:     AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTG                         GTTCCATGTAGATAAGATGTCCTCTGCACACGTGTATTTGAGATTAAATAA
genomic: AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTGgtaacttccc ... ttgaacacagGTTCCATGTAGATAAGATGTCCTCTGCACACGTGTATTTGAGATTAAATAA
EST: gi|88364521|gb|CI644599.1|CI644599
EST:     AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTG                         GTTCCATGTAGATAAGATGTCCTCTGCACACGTGTA
genomic: AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTGgtaacttccc ... ttgaacacagGTTCCATGTAGATAAGATGTCCTCTGCACACGTGTA
EST: gi|58683841|gb|CK072528.1|CK072528
EST:     AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTG                         GTTCCATGTAGATAAGATGTCCTCTGCACACGTGTATTTGAGATTAAATAA
genomic: AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTGgtaacttccc ... ttgaacacagGTTCCATGTAGATAAGATGTCCTCTGCACACGTGTATTTGAGATTAAATAA
EST: gi|88336614|gb|CI656885.1|CI656885
EST:     AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTG                         GTTCCATGTAGATAAGATGNTC-TCTGCACA
genomic: AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTGgtaacttccc ... ttgaacacagGTTCCATGTAGATAAGATG-TCCTCTGCACA
EST: gi|163926796|gb|EG715084.1|EG715084
EST:     AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTG                         GTTCCATGTAGATAAAATGTCCTCTGCACACGTGTATTTGAGATTAAATAA
genomic: AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTGgtaacttccc ... ttgaacacagGTTCCATGTAGATAAGATGTCCTCTGCACACGTGTATTTGAGATTAAATAA
EST: gi|396941371|gb|HO188580.1|HO188580
EST:     AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTG                         GTTCCATGTAGATAAGATGTCCTCTGCACACGTGTATTTGAGATTAAATAA
genomic: AAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTGgtaacttccc ... ttgaacacagGTTCCATGTAGATAAGATGTCCTCTGCACACGTGTATTTGAGATTAAATAA

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: 62 (upstream exon), 55 (downstream exon)
Score: 46

TCAAGGTGCGGCCCGAGGCCGGCGACTACACCATCTTCATGGGTCTCGACAAGTTCGAGAACGAGGACCTCATCAAGTACGGCTTCCCCGAGGACATCTGgtaacttccc ... ttgaacacagGTTCCATGTAGATAAGATGTCCTCTGCACACGTGTATTTGAGATTAAATAAAGGTCAGACAATGGATGACATAAGTGAAGGTGTGCTTGAAGATTGTGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcacagagtcatcttatcatgctttgtagctcaacgctattgttcttgaacacagGTTCCATGTAGATAAGATGTCCTCTGCACACGTGTATTTGAGATTAAATAAAGGTCAGACAATGGATGACATAAGTGAAGGTGTGCTTGAAGATTGTGCC
                                       ttgttctt  CT-rich tract
          atcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttagatatggtttgctcattgcttaataaagttgttgaagtagcacagagtcatcttatcatgctttgtagctcaacgctattgttcttgaacacagGTTCCATGTAGATAAGATGTCCTCTGCACACGTGTATTTGAGATTAAATAAAGGTCAGACAATGGATGACATAAGTGAAGGTGTGCTTGAAGATTGTGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - -tgctcat
- - - - - - - - - - - tgcttaa
- - - - - - - - - - - - - - - - - -tgttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtagct