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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGCCATCGTCCGCCTCACCCGCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAGgtcgcttcccttcttcttactagactgtccccctctctcgctcttactactgtgcccgcggatctgtatcaatcgacgatggatttcgccttggttgctg...

Basic information

species Oryza sativa
transcript LOC_Os05g19370.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g19370.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G180724_T01 (Zea mays), 5'ss of exon 2
CGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGCCATCGTCCGCCTCACCCGCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAGgtcg--cttcccttcttcttactagactgtccccctctctcgctcttactactgtgcccgcggatctgtatcaatcgacgatggatttcgccttggttgctg-
||||||||||||||||||| | ||||||||||||||||||||||||||  | |||||||||||||||||||||||||||||||||||||||||||||||||| |  |||| |   ||    |  | |        |     |   ||     |  |   | ||   || |   ||   ||    |||| |  || ||  ||| 
CGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGCCATCGTCCGCCTCACAAGGCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAGgtagatcttctcccattggcgcgtgccaactttgatgcgatggatttgtggatagggt-gtggtggtgcagggattaccgtc--atttaggattagtccctgt

upper sequence: LOC_Os05g19370.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G034794_T02 (Zea mays), 5'ss of exon 2
CGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGCCATCGTCCGCCTCACCCGCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAGgtcgcttcccttc--ttcttactagactgtccccctctctcgctcttactactgtgcccgcggatctgtatcaatcgacgatggatttcgccttggttgctg
||||||||||||||||||| | ||||||||||||||||||||||||||  | ||||| || || |||||||| ||||||||||||||||||||||||||||| | |  ||| |  | |  |    | || | | | |   |  |     |  ||       || |  |      |||  |   | |   |||  |   |   
CGTGCGCTGCTGGGAGTACAGGCAGCAGCCGGCCATCGTCCGCCTCACAAGGCCCACTCGTCCTGACAAGGCGCGCCGCCTCGGCTACAAGGCCAAGCAGgtagatctcctccagtgcagatcccattggcgcgcgcgaactttgacggtgatggatttatgggtaggggaaggtcggggggtggtgcagccgcgcaggg--

upper sequence: LOC_Os05g19370.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G084757_T02 (Zea mays), 5'ss of exon 1
CGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGCCATCGTCCGCCTCACCCGCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAGgtcgcttcccttcttcttactagactgtccccctctctcgctcttactactgtgcccgcggatctgtatcaatcgacgatggatttcgccttggttgctg--------
||||||||| ||||||||| | ||||||||||||||||||||||||||  | |||||||||||||||||||||||||||||||||| ||||||||||||||| | |      ||||| ||  |    ||||  | || ||  |  |||    || |   |||| |||    |  |  |  ||  | |     | |||| |        
CGTGCGCTGTTGGGAGTACAGGCAGCAGCCGGCCATCGTCCGCCTCACAAGGCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTTCAAGGCCAAGCAGgtagat------cttctcacgtgcagatcccattgtcgcgtgccaactttgatggcgatggatttgtgggcaggggggggggggtccagg--gattgccgaagagcta

upper sequence: LOC_Os05g19370.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G024354_T01 (Zea mays), 5'ss of exon 2
CGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGCCATCGTCCGCCTCACCCGCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAGgtcgcttcccttcttcttactagactgtccccctctctcgctct---tactactgtgcccgcggatctgtatcaatcgacgatggatttcgccttggttgctg
||||||||||||||||||| | ||||||||| ||||||||||||||||| | ||||||||||||||||||||||| || ||||||||||||||||||||||| | |   ||    | | |    |||| | | |  ||  | |    || |  |||       | |  ||      |    |   |||| |  || | | |||
CGTGCGCTGCTGGGAGTACAGGCAGCAGCCGTCCATCGTCCGCCTCACCAGGCCCACCCGCCCCGACAAGGCCCGTCGTCTCGGCTACAAGGCCAAGCAGgtaggtcttctcg--cctgccgctctgttctcttgcctgccgcgagatagtgatgtagaaataggttggtggagggcttgcagccatttaggatttgat-ctg

upper sequence: LOC_Os05g19370.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT4G17390.1 (Arabidopsis thaliana), 5'ss of exon 2
CGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGCCATCGTCCGCCTCACCCGCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAGgtcgcttcc--cttcttcttactagactgtccccctctctcgctcttactactgtgcccgcg--gatctgtatcaatcgacgatggatttcgccttggttgctg
 ||  | || |||||||| |||||||||||  |||| || || ||    || ||||| || ||||||||||| || || ||||||||||||||||||||||||  || |  |||||  | | |    |   |   |   | | | |   || |||    |     | |  |||| || ||     | ||  ||  ||  |    
GGTTAGGTGTTGGGAGTATCGCCAGCAGCCTTCCATTGTTCGTCTTGTTCGTCCCACTCGTCCCGACAAGGCTCGTCGTCTCGGCTACAAGGCCAAGCAGgtctttttcttcttctcttcattttggttatcaatttaataggtttaggtaatgttgttgaatcaagccttatcgattgattgctggttaagcggtgtct----

upper sequence: LOC_Os05g19370.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv16s0013g02020.t01 (Vitis vinifera), 5'ss of exon 2
CGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGCCATCGTCCGCCTCACCCGCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAGgtcgcttcccttcttcttac--tagactg---tccccctctctcgctcttactactgtgcccgcggatctgtatcaatcgacgatggatttcgccttggttgctg
 ||| | ||||||||||| |||||||| ||  | || ||  ||  ||| |||||||| || ||||| ||||| |||||| | ||||||||||||||||||||        || |||||||  | || ||   |       | |   | |||    ||     | |    ||| |        ||||   ||||  |  ||     
GGTGAGGTGCTGGGAGTATCGCCAGCACCCTTCAATTGTGTGCGCCACGCGCCCCACTCGACCCGATAAGGCTCGCCGCTTGGGCTACAAGGCCAAGCAGgttatcattgtttttcttacatttgattgcgattttttattttattttttatatttgaatttgggcgattgtgttcggttgtgatgatgttcgtttgtgt-----

upper sequence: LOC_Os05g19370.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EDP06755 (Chlamydomonas reinhardtii), 5'ss of exon 2
---------CGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGCCATCGTCCGCCTCACCCGCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAGgtcgcttcccttcttcttactagactgtccccctctctcgctcttactactg-tgcccgcggatctgtatcaatcgacgatggatttcgccttggttgctg
          |  ||| ||  ||  |||       ||| || |  |||   |  |  |   | |  ||||| || |||   |   || |  |   ||||||  |||  ||  |  |  |  || ||    |   |   | ||      |||| | ||| || |    |    | | | ||       |  |                   
CCCGGACAAGGCCCGCCGCCTGGGCTACAAGGCCAAGCAGGGCTACGTTGTCTACCGCGTGCGCGTCCGCCGCGGCAACCGCAAGCGGCCTGTGCACAAGgtaaagtcggcggaattgcagctcctcttgattttccactcccacaatgctcctgctaatgctaaatgtcactttttttcttgttttgcag-------------------

upper sequence: LOC_Os05g19370.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S68_114V6.1 (Physcomitrella patens), 5'ss of exon 2
CGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGCCATCGTCCGCCTCACCCGCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAGgtcgcttcccttcttcttactagactgtccccctctctcgctcttactactgtgcccgcggatctgtatcaatcgacgatggatttcgccttggttgctg--
 ||||| |||||||||||| | ||||  || |  ||||||||| |||| |||||  | || || |||||||||||||| || || |||||||||||||||||   |||     | | ||    |||||    |    |   |   |||  |  |  |    || |    ||   ||   |  | ||       ||||  |  
TGTGCGATGCTGGGAGTACAGGCAGCTCCCAGGAATCGTCCGCGTCACTCGCCCTTCTCGTCCTGACAAGGCCCGCCGTCTGGGTTACAAGGCCAAGCAGgtgctttcatggatccatatgtaactgttgtaccagatttgtggaacttgtaggttcttccatttc--acaggagatatttaaattttaaaaagttggaggg

upper sequence: LOC_Os05g19370.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S152_141V6.1 (Physcomitrella patens), 5'ss of exon 2
CGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGCCATCGTCCGCCTCACCCGCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAGgtc-gcttcccttcttcttactagactgtccccctctctcgctcttacta-ctgtgcccgcggatctgtatcaatcgacgatggatttcgccttggttgctg-
 |||||||||||||||||| | ||||  || | ||| |||||  |||| ||||| | ||| ||||||||||| |||||||| || || ||||||||||||||| |||| | |     |   | || | | |  |     |  |   |  | |||| |  |  |  |||  |  |    |  | | ||     || |    || 
TGTGCGCTGCTGGGAGTACAGGCAGCTCCCCGGCATTGTCCGTGTCACTCGCCCTAGCCGTCCCGACAAGGCTCGCCGCCTAGGGTATAAGGCCAAGCAGgtcagcttgcatctgaatctttcgagttttcgtcgaaagccatgaaagaatctgttcttgtagg-ctgcgtggagtagc--ttgtttcgaagttaggatttga

upper sequence: LOC_Os05g19370.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S134_151V6.1 (Physcomitrella patens), 5'ss of exon 2
CGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGCCATCGTCCGCCTCACCCGCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAGgtc-gcttcccttcttcttactagactgtccccctctctcgctcttactactgtgcccgcggatctgtatcaatcgacgatggatttcgccttggttgctg---
 || ||||||||||||||| | |||| ||| | ||| |||||| |||||||||| | |||||| |||||||| ||||| || || |||||||||||||||||| | ||   ||       || |  |   |     | | |    ||  | |||  | | |  |||  ||  ||| ||   | |    | |||||    |    
TGTTCGCTGCTGGGAGTACAGGCAGCTGCCCGGCATTGTCCGCGTCACCCGCCCTAGCCGCCCTGACAAGGCTCGCCGTCTTGGTTACAAGGCCAAGCAGgtcagtttggattagagacccttggtt--tcagtgtttttgtctgta--attgtttctgtgtgtctacatttatctacatggaacgctgtcttggacattaggg

upper sequence: LOC_Os05g19370.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S34_445V6.1 (Physcomitrella patens), 5'ss of exon 2
CGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGCCATCGTCCGCCTCACCCGCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAGgtcgcttcccttcttcttactagactgtccccctctctcgctcttact-actgtgcccgcgg-atctgtatcaatcgacgatggatttcgccttggttgctg-
 |||||||||||||||||| | ||||  || | |||||||||| |||| |||||  | || || |||||||| ||||| || || |||||||||||||||||   |        |   | | | || |   | |    |  |   | |          |  | || || ||   |    |||||   | || |    ||  | 
TGTGCGCTGCTGGGAGTACAGGCAGCTCCCCGGCATCGTCCGCGTCACTCGCCCTTCTCGGCCTGACAAGGCTCGCCGTCTAGGTTACAAGGCCAAGCAGgtacgtgttgagacttcaatttggctattttcttgcaccctttgcatttggaaaaattgtagcatttgaattgttt--tgatgg-cgtggcgtgaagtggcgt

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|15851744|gb|BI800020.1|BI800020
EST:     GCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAG                         GGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGGCAGGAAGAGGCCA
genomic: GCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAGgtcgcttccc ... ttgctttcagGGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGGCAGGAAGAGGCCA
EST: gi|27576894|gb|CA999588.1|CA999588
EST:     CCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAG                         GGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGGCAGGAAGAGGCCA
genomic: CCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAGgtcgcttccc ... ttgctttcagGGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGGCAGGAAGAGGCCA
EST: gi|10930664|gb|AU160938.1|AU160938
EST:     GCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAG                         GGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGGCAGGAAGAGGCCA
genomic: GCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAGgtcgcttccc ... ttgctttcagGGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGGCAGGAAGAGGCCA
EST: gi|25798204|gb|CA754173.1|CA754173
EST:     GCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAG                         GGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGGCAGGAAGAGGCCA
genomic: GCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAGgtcgcttccc ... ttgctttcagGGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGGCAGGAAGAGGCCA
EST: gi|58686451|gb|CK075138.1|CK075138
EST:     GCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAG                         GGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGGCAGGAAGAGGCCA
genomic: GCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAGgtcgcttccc ... ttgctttcagGGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGGCAGGAAGAGGCCA
EST: gi|5004067|gb|AU069216.1|AU069216
EST:     GGCTACAAGGCCAAGCAG                         GGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGNCAGGAAGAGGCCA
genomic: GGCTACAAGGCCAAGCAGgtcgcttccc ... ttgctttcagGGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGGCAGGAAGAGGCCA
EST: gi|55430973|gb|CV728491.1|CV728491
EST:     GCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAG                         GGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGGCAGGAAGAGGCCA
genomic: GCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAGgtcgcttccc ... ttgctttcagGGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGGCAGGAAGAGGCCA
EST: gi|88239646|gb|CI238808.1|CI238808
EST:     GACAAGGCCCGCCGCCTCGGCTACAAGTCCAAGCAG                         GGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGGCAGGAAGAGGCCA
genomic: GACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAGgtcgcttccc ... ttgctttcagGGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGGCAGGAAGAGGCCA

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: 52 (upstream exon), 67 (downstream exon)
Score: 24

CGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGCCATCGTCCGCCTCACCCGCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAGgtcgcttccc ... ttgctttcagGGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGGCAGGAAGAGGCCAGTGCCCAAGGGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATTACCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTGCGCTGCTGGGAGTACCGCCAGCAGCCGGCCATCGTCCGCCTCACCCGCCCCACCCGCCCCGACAAGGCCCGCCGCCTCGGCTACAAGGCCAAGCAGgtcgcttcccttcttcttactagactgtccccctctctcgctcttactactgtgcccgcggatctgtatcaatcgacgatggatttcgccttggttgctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcccgcg