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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaatgcagaacttgactttcttgatgctgaataatctaaattggacatgttaactgattatatatggtctatatgttctatcagGTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTAGGATAGCTAGTGCAGCAAATGCTATTGTCTGAGCTTGTTTGAATGAATT

Basic information

species Oryza sativa
transcript LOC_Os03g04590.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g04590.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G123495_T01 (Zea mays), 3'ss of exon 3
--------gtaac--aatgcagaacttgactttcttgatgctgaataatctaaattggacatgttaactg-attatatatggtctatatgttctatcagGTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTAGGATAGCTAGTGCAGCAAATGCTATTGTCTGAGCTTGTTTGAATGAATT
        ||  |  | | ||  |       | | |  |  |||        |  ||  || |  | | |   |  | ||  |     |  | |  |||| ||||| ||||||||||| || || |||||||| |||||||||||||||||||| |||||||||||||||||||||||||||   |  | |   | |  
gtaagagtgtggcctacttcacgatgcagtctccctagttttgatctcctgtaggtg--cagggcagcagcgctgaacattttgctgctccttttgcagGATCTGCCATCACTGGACCTATTGGCAAGGAGTGCGCTGACCTTTGGCCTAGGATTGCTAGTGCAGCAAATGCTATTGTCTGATACTACTGGTTGGGAGG

upper sequence: LOC_Os03g04590.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G171181_T01 (Zea mays), 3'ss of exon 3
gtaacaatgcagaacttgactttcttgatgctgaataatctaaattggacatgttaactgattatatatggtctatatgt---tctatcagGTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTAGGATAGCTAGTGCAGCAAATGCTATTGTCTGAG--CTTGTTTGAATGAATT
     |    | ||| |||  ||| |    |   || | | || |      ||  ||   || | |     |    ||||   |||  |||||||||| ||||||||||| ||||| ||||||||||||||||||||||||||||| ||||||||||||||||| || || ||||  |||||| |||||    
---gtatgatacaacctgagattcctccatcatcatcagccaagtgctgtttggcaaggcatgaaacgaacttacaatgtctctcttgcagGTTCTGCAATCACTGGACCTATCGGCAAGGAGTGTGCTGACCTTTGGCCTAGGATCGCTAGTGCAGCAAATGCCATCGTTTGAGAGCTTGTTGGAATGTG--

upper sequence: LOC_Os03g04590.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G493312_T01 (Zea mays), 3'ss of exon 1
gtaacaatgcagaact-tgactttcttgatgctgaataatctaaattggacatgttaactgattatatatggtctatatgttctatcagGTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTAGGATAGCTAGTGCAGCAAATGCTATTGTCTGAG--CTTGTTTGAATGAATT
|||  |||     ||| | | |          ||       |   || | ||||  |  |||  |  |||     || |||  | | |||||| |||||||||||||| ||||| |||||||||||||| |||||||||||||| ||||| ||||||||  | || || ||||  |||| | ||||     
gtatgaattgtccactataattcctccagcattgggcctattctgtttggcatggca--tgacaaactatca--aatttgtcttgt-agGTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATCTTTGGCCTAGGATTGCTAGCGCAGCAAACACCATAGTTTGAGAGCTTGCTGGAATATG--

upper sequence: LOC_Os03g04590.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G150058_T02 (Zea mays), 3'ss of exon 1
gtaacaat-gcagaacttgactttcttgatgctgaataatctaaattggacatgttaactgattatatatggtctatatgttctatcagGTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTAGGATAGCTAGTGCAGCAAATGCTATTGTCTGAG--CTTGTTTGAATGAATT
|||  ||| |   |   | | |          ||       |   || | ||||  |  ||| ||  |||     || |||  |  ||||||| |||||||||||||| ||||| |||||||||||||| |||||||||||||| ||||| |||||||| || ||||| ||||  |||||| ||||     
gtatgaattgtccacaataattcctccagcattgggcctattctgtttggcatggca--tgactaactatca--aatttgtcttg-cagGTTCCGCTATCACTGGACCTATCGGCAAGGAGTGTGCTGATCTTTGGCCTAGGATTGCTAGCGCAGCAAACGCCATTGTTTGAGAGCTTGTTGGAATATG--

upper sequence: LOC_Os03g04590.3 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S280_69V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------------------------------------------------------------------------------gta-acaatgcagaacttgactttcttgatgctgaataatctaaattggacatgttaactgatt-atatatggtctatatgttctatcagGTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTAGGATAGCTAGTGCAGCAAATGCTATTGTCTGAGCTTGTTTGAATGAATT
                                                                                                |||     | |  | |   |  || |  | | |      | |    ||  | |  | | | | | |||  |  | |      | |  ||||||||||||||||||| || || ||||||||||| || ||  | ||||||||||| |||||||| || ||||| ||||||||||     | |    ||| 
gtacgcagatatttccctcaaatatctttgacgtcagattcgttttagcaaaagatccagttagcgaatgagaatgattggcagatatatgtcatcgtatgttgttcttatcggaatgttgtgcacgttatgacttttgggatgagcctactgatttactgataggttttttggcaacttttgcagGTTCTGCTATCACTGGTCCTATTGGGAAGGAGTGCGCCGATTTGTGGCCTAGGATTGCTAGTGCTGCCAATGCCATTGTCTGAGGGCAATAGTTGTAATA

upper sequence: LOC_Os03g04590.3 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S15_152V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------------------------------------------------------------------------------------gtaacaatgcagaacttgactttcttgatgctga-ataatctaaattggacatgttaactgattatat--atggtctatatgttctat-cagGTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTAGGATAGCTAGTGCAGCAAATGCTATTGTCTGAGCTTGTTTGA-ATGAATT
                                                                                                      || | | |       |  ||     |  | || |  | |  |   | |||| ||     |||| | |   ||| | |        | | ||||||||||||||||||| ||||| || || |||||||| ||| | ||||||||||| || ||||| || ||||||||||| ||||     | |    | || 
gtaatctcacttacatctatttgattttaggaaatacattcagttggtctgttctgtgaaatctgtcttacagtagttacctacttgattttaaagattacagtcatatttttttgttcaaccactcttgtactcatgtgaagttgttgggac-tggagtttgatcaaaccaatgtttttggcaacttgtgcagGTTCTGCTATCACTGGTCCCATTGGAAAAGAGTGTGCCGACTTGTGGCCTAGGATTGCCAGTGCTGCTAATGCTATTGTATGAGTGCAATAGTTGCGCAT-

upper sequence: LOC_Os03g04590.3 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S62_136V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------gtaacaatgcagaacttgactttcttgatgctgaat--aatctaaattggacatgttaact--gattatatatggtctatatgttctatcagGTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTAGGATAGCTAGTGCAGCAAATGCTATTGTCTGAGCTTGTTTGAATGAATT
                                             | |       ||     |    | | | ||     |  |   |  |||||    | | |    | || |   ||||    |||| |    ||||||||| ||||||||||| |||||||||||||| || ||| | ||||| ||||| || || || || || || ||||| ||||   ||      | | |
gtgagtgtatgcagccggtgcattgatggtgcagtctgcagattgggatgggcctagggggggggggtatagctgtaaggtggagggtggattggcagagctgatgagggttgtgcgtggttgtaatgtgc----agGTTCTGCCATCACTGGACCGATCGGGAAGGAGTGCGCAGACTTGTGGCCGAGGATTGCGAGCGCTGCCAACGCGATTGTTTGAGAGGGTAGTTTGGGAGT

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|25801894|gb|CA757855.1|CA757855
EST:     GTGAGATGAAAG                         GTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTA
genomic: GTGAGATGAAAGgtaacaatgc ... gttctatcagGTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTA
EST: gi|88453458|gb|CI563337.1|CI563337
EST:     ATAATGCTGGAGTGATTGTGAATCCTAAGGGTGAGATGAAAG                         GTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTA
genomic: ATAATGCTGGAGTGATTGTGAATCCTAAGGGTGAGATGAAAGgtaacaatgc ... gttctatcagGTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTA
EST: gi|55408901|gb|CV721277.1|CV721277
EST:     ATAATGCTGGAGTGATTGTGAATCCTAAGGGTGAGATGAAAG                         GTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTA
genomic: ATAATGCTGGAGTGATTGTGAATCCTAAGGGTGAGATGAAAGgtaacaatgc ... gttctatcagGTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTA
EST: gi|163925781|gb|EG714617.1|EG714617
EST:     ATAATGCTGGAGTGATTGTGAATCCTAAGGGTGAGATGAAAG                         GTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTA
genomic: ATAATGCTGGAGTGATTGTGAATCCTAAGGGTGAGATGAAAGgtaacaatgc ... gttctatcagGTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTA
EST: gi|427295|gb|D23379.1|D23379
EST:     GGAGTNATTGTNAATCCTAAGGGTGAGATGAAAG                         GTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTA
genomic: GGAGTGATTGTGAATCCTAAGGGTGAGATGAAAGgtaacaatgc ... gttctatcagGTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTA
EST: gi|88439490|gb|CI538662.1|CI538662
EST:     GGAGTGATTNTGAATCCTAAGGGTGAGATGAAAG                         GTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTA
genomic: GGAGTGATTGTGAATCCTAAGGGTGAGATGAAAGgtaacaatgc ... gttctatcagGTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTA
EST: gi|163920223|gb|EG709524.1|EG709524
EST:     ATAATGCTGGAGTGATTGTGAATCCTAAGGGTGAGATGAAAG                         GTTCTGGTGTCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTA
genomic: ATAATGCTGGAGTGATTGTGAATCCTAAGGGTGAGATGAAAGgtaacaatgc ... gttctatcagGTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTA
EST: gi|88278899|gb|CI397703.1|CI397703
EST:     ATAATGCTGGAGTGATTGTGAATCCTAAGGGTGAGATGAAAG                         GTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTA
genomic: ATAATGCTGGAGTGATTGTGAATCCTAAGGGTGAGATGAAAGgtaacaatgc ... gttctatcagGTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTA
EST: gi|11233510|gb|AU164922.1|AU164922
EST:     ATAATGCTGGAGTGATTGTGAANCCTAAGGGTGAGATGAAAG                         GTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTA
genomic: ATAATGCTGGAGTGATTGTGAATCCTAAGGGTGAGATGAAAGgtaacaatgc ... gttctatcagGTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTA
EST: gi|163926728|gb|EG713744.1|EG713744
EST:     ATAATGCTGGAGTGATTGTGAATCCTAAGGGTGAGATGAAAG                         GTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTA
genomic: ATAATGCTGGAGTGATTGTGAATCCTAAGGGTGAGATGAAAGgtaacaatgc ... gttctatcagGTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTA

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: 42 (upstream exon), 75 (downstream exon)
Score: 322

ATAATGCTGGAGTGATTGTGAATCCTAAGGGTGAGATGAAAGgtaacaatgc ... gttctatcagGTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTAGGATAGCTAGTGCAGCAAATGCTATTGTCTGAGCTTGTTTGAATGAATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataatctaaattggacatgttaactgattatatatggtctatatgttctatcagGTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTAGGATAGCTAGTGCAGCAAATGCTATTGTCTGAGCTTGTTTGAATGAATT
                                              ttctatc  CT-rich tract
                    ttaactgattatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacaatgcagaacttgactttcttgatgctgaataatctaaattggacatgttaactgattatatatggtctatatgttctatcagGTTCTGCTATCACTGGACCCATCGGGAAGGAGTGTGCTGACCTTTGGCCTAGGATAGCTAGTGCAGCAAATGCTATTGTCTGAGCTTGTTTGAATGAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT