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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttcttatcgggtgcttcccacgggcatctatgtgcaatgttctgataacatgccctgacagggattttggctctctacttggcggttgatgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG

Basic information

species Oryza sativa
transcript LOC_Os02g42540.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g42540.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G146786_T02 (Zea mays), 3'ss of exon 2
-------------------------------------ctttcttatcgggtgcttcccacgggcatctatgtgcaatgttctgataacatgccctgacagggattttggctctctacttggcggttgatgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
                                          | |    |   |||| |  || |||  ||| ||||||||| |||||||||||||||||||||||||| |||||||| || |||||||  | ||||||||| ||||||||||||||  ||||||| |||||||| || |||||||
tcacacgaggatgccttgcttttacttaaatgcttgatcaaatgactaagcatttccaataggtatcagtgtacaatgttcttataacatgccctgacagGGATTTTGGTTCTCTACTCGGTGGTTGATACCAACAGATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG

upper sequence: LOC_Os02g42540.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G146786_T01 (Zea mays), 3'ss of exon 2
ctttcttatcgggtgcttcccacgggcatctatgtgcaatgttctgataacatgccctgacagggattttggctctctacttggcggttgatgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
     | |    |   |||| |  || |||  ||| ||||||||| |||||||||||||||||||||||||| |||||||| || |||||||  | ||||||||| ||||||||||||||  ||||||| |||||||| || |||||||
tcaaatgactaagcatttccaataggtatcagtgtacaatgttcttataacatgccctgacagggattttggttctctactcggtggttgataccaacagATGCAAGAGGTTGCTGGTGATAGGGGAGGCTACCTTCACGGACGAGGAG

upper sequence: LOC_Os02g42540.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G33570.2 (Glycine max), 3'ss of exon 2
------------------------------------ctttc--ttatcgggtgcttcccacgggcatctatgtgcaatgttctgataacatgccctgacagggattttggctctct--acttggcggttgatgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
                                     ||||   | ||  |   ||     | |||  |    | | | | |||||||||||||| | ||||||| ||||||  ||  | | || || |||||    |||||||| ||||||||||| || || ||||||||||||||||| ||||| |
ttttctctcttggttatgtactgcctgtttttgctgttttcaactttcaagcaattttt-tgtgcaatttgagggattttgctgataacatgccccggcagGGATATTGGCTTCCTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGTGGAGGTTACCTTCATGGACGAGGCG

upper sequence: LOC_Os02g42540.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA09G28980.1 (Glycine max), 3'ss of exon 2
ctttcttatcgggtgcttcccacgggcatctatgtgcaatgttctgataacatgccctgacagggattttggctctct--acttggcggttgatgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
 |    | ||  |   ||     | |||  |    | | | | |||||||||||||| | ||||||| ||||||  ||  | | || || |||||    |||||||| ||||||||||| || || ||||||||||||||||| ||||| |
-tcaactttcaagcaattttt-tgtgcaatttgagggattttgctgataacatgccccggcagggatattggcttcctgtattgggtggctgatgcaagcagATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG

upper sequence: LOC_Os02g42540.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G33570.1 (Glycine max), 3'ss of exon 2
ctttcttatcgggtgcttcccacgggcatctatgtgcaatgttctgataacatgccctgacagggattttggctctct--acttggcggttgatgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
 |    | ||  |   ||     | |||  |    | | | | |||||||||||||| | ||||||| ||||||  ||  | | || || |||||    |||||||| ||||||||||| || || ||||||||||||||||| ||||| |
-tcaactttcaagcaattttt-tgtgcaatttgagggattttgctgataacatgccccggcagggatattggcttcctgtattgggtggctgatgcaagcagATGCAAGAGGTTGCTGGGGAGCGTGGAGGTTACCTTCATGGACGAGGCG

upper sequence: LOC_Os02g42540.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA09G28980.2 (Glycine max), 3'ss of exon 2
------------------------------------ctttc--ttatcgggtgcttcccacgggcatctatgtgcaatgttctgataacatgccctgacagggattttggctctct--acttggcggttgatgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
                                     ||||   | ||  |   ||     | |||  |    | | | | |||||||||||||| | ||||||| ||||||  ||  | | || || |||||    |||||||| ||||||||||| || || ||||||||||||||||| ||||| |
ttgcaaagcagaattttgtaattcttctgtatgtcgttttcaactttcaagcaattttt-tgtgcaatttgagggattttgctgataacatgccccggcagGGATATTGGCTTCCTGTATTGGGTGGCTGATGCAAGCAGATGCAAGAGGTTGCTGGGGAGCGCGGAGGTTACCTTCATGGACGAGGCG

upper sequence: LOC_Os02g42540.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G73350.2 (Arabidopsis thaliana), 3'ss of exon 2
--ctttcttatcgggtgcttcccacgggcatctatgtgcaatgttctgataacatgccctgacagggattttggctctct---acttggcggttgatgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
    |||||||      ||    |  || |         | | |||||||||| ||||| | |||||||   ||| |      | ||   ||||  ||   | ||||||| ||||||||||||||||| ||||| || |||||||| ||||| |
gtgattcttatgtttgactctatattgggactcg-----acttttctgataacttgccccggcagggataacggccccgccacattttctggttattgcatatagATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCG

upper sequence: LOC_Os02g42540.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G73350.3 (Arabidopsis thaliana), 3'ss of exon 2
----------------------------ctttcttatcgggtgcttcccacgggcatctatgtgc---------aatgttctgataacatgccctgacagggattttggctctct---acttggcggttgatgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
                              |   | |   ||| |||  | |     || | |           | | |||||||||| ||||| | |||||||   ||| |      | ||   ||||  ||   | ||||||| ||||||||||||||||| ||||| || |||||||| ||||| |
tatatctttgttagcattagtggttattgatgtgtgtgaagtgattcttatgtttgactctatattgggactcgacttttctgataacttgccccggcagGGATAACGGCCCCGCCACATTTTCTGGTTATTGCATATAGATGCAAGAGGTTGCTGGTGAACGTGGAGGCTATCTTCATGGACGAGGCG

upper sequence: LOC_Os02g42540.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv16s0039g00280.t01 (Vitis vinifera), 3'ss of exon 2
--ctttcttatcgggtgcttcccacgggcatctatgtgcaatgttctgataacatgccctgacagggattttggctct--ctacttggcggttgatgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
   | |||| ||      ||   | |    ||| ||   | | |||||||||||||||| | ||||||| |||||  |  ||||  || ||||||||    |||||||| |||||||| || ||||| ||||||||||||||||| ||||| |
acatctcttctct----ttttatatgacattctgtggagagttttctgataacatgccccggcagggatcttggcattgcctaccgggtggttgatgtgagcagATGCAAGAGGTTGCAGGGGAACGTGGAGGTTACCTTCATGGACGAGGCG

upper sequence: LOC_Os02g42540.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S88_45V6.1 (Physcomitrella patens), 3'ss of exon 3
ctttcttatcgggtgcttcccacgggcatctatgtgcaatgttc-tgataacatgccctgacagggattttggctctctacttggcggttg--atgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
   ||| |  |  |   | |   || |   |  ||  | ||    |  |||  | || |   || |||  |   | | || | |    |||  ||| | ||||||||||||||| ||||||||||| || || || |||||||| || ||||
--atctgaaggtatctatgctgtggtctggtgagtatactgagggtattaatttaccttcttagtgatgatccttgtttattggaacattgcgatggc-acagATGCAGGAGGTAGCTGGTGAACGTGGTGGATATCTTCATGGTCGTGGAG

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|88338650|gb|CI644107.1|CI644107
EST:     AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAG                         ATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
genomic: AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAGgttagaccgg ... atgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
EST: gi|88331773|gb|CI640804.1|CI640804
EST:     AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAG                         ATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
genomic: AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAGgttagaccgg ... atgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
EST: gi|88331772|gb|CI640803.1|CI640803
EST:     AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAG                         ATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
genomic: AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAGgttagaccgg ... atgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
EST: gi|88381604|gb|CI682270.1|CI682270
EST:     AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAG                         ATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
genomic: AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAGgttagaccgg ... atgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
EST: gi|88330892|gb|CI638300.1|CI638300
EST:     AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAG                         ATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
genomic: AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAGgttagaccgg ... atgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
EST: gi|88571094|gb|CI662467.1|CI662467
EST:     AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAG                         ATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
genomic: AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAGgttagaccgg ... atgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
EST: gi|88453631|gb|CI682502.1|CI682502
EST:     AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAG                         ATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
genomic: AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAGgttagaccgg ... atgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
EST: gi|88324974|gb|CI644986.1|CI644986
EST:     AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAG                         ATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
genomic: AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAGgttagaccgg ... atgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
EST: gi|88576151|gb|CI670296.1|CI670296
EST:     AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAG                         ATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
genomic: AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAGgttagaccgg ... atgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
EST: gi|27547521|gb|CA765797.2|CA765797
EST:     AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAG                         ATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGAGAGGAG
genomic: AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAGgttagaccgg ... atgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
EST: gi|88501795|gb|CI695478.1|CI695478
EST:     AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAG                         ATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
genomic: AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAGgttagaccgg ... atgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
EST: gi|88341833|gb|CI642977.1|CI642977
EST:     AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAG                         ATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
genomic: AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAGgttagaccgg ... atgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
EST: gi|33810840|gb|CF331311.1|CF331311
EST:     AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAG                         ATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
genomic: AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAGgttagaccgg ... atgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
EST: gi|88320199|gb|CI672378.1|CI672378
EST:     AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAG                         ATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
genomic: AGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAGgttagaccgg ... atgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG

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: 71 (upstream exon), 49 (downstream exon)
Score: 13

ATAGGAAGTGGGGGAAGGGGAAGGACAAGATTGATGATGAGGACATCACCTTCCAGCGCATGGTCGCAAAGgttagaccgg ... atgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gataacatgccctgacagggattttggctctctacttggcggttgatgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG
                    atttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttcttatcgggtgcttcccacgggcatctatgtgcaatgttctgataacatgccctgacagggattttggctctctacttggcggttgatgacgacagATGCAGGAGGTTGCTGGTGAACGGGGAGGTTACCTTCATGGGCGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - -tgcttcc
- - - - - - - - - - - -gggcatc
- - - - - - - - - - - - - - - tatgtgc
- - - - - - - - - - - - - - - - - - - -tgttctg
- - - - - - - - - - - - - - - - - - - - - - - - - catgccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcggttg