Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcagctggttaattaattaattactgtcacatgggaaagcaatcaatcagagagcatgatgctgtgttctaatggtgggggacattgtgatactggcagCATGTGGGGTCGAGCTGGCCACGGCGGGTTACGGCGTGTTCGGCATCGATTATGAGGGGCATGGCAAGTCCATGGGTGCCAGATGCTACATCCAGAAGTT

Basic information

species Oryza sativa
transcript LOC_Os05g29974.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g29974.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G306851_T02 (Zea mays), 3'ss of exon 3
-atcagctg-gttaattaattaattactgtcacatgggaaagcaatcaatcagagagcatgatgctgtgt-tctaatggtgggggacattgtgatactggcagCATGTGGGGTCGAGCTGGCCACGGCGGGTTACGGCGTGTTCGGCATCGATTATGAGGGGCATGGCAAGTCCATGGGTGCCAGATGCTACATCCAGAAGTT
 ||||     | | || |||   |  |  | | |  | |||    |   |  |   |||||||||      ||||| ||||||| |||  ||  ||||||||||||||||| |  |||||||||| || || || |||||||| || |||||||||||||| || |||||||||||||||||||| ||||||||||| |||||
gatcattgatgctcatgaatcgctagccttaaaaatgaaaactgctgggt--ggtggcatgatgccccccgtctaacggtggggaacac-gttttactggcagCATGTGGGATGAAGCTGGCCACAGCAGGGTATGGCGTGTTTGGTATCGATTATGAGGGCCACGGCAAGTCCATGGGTGCCAGGTGCTACATCCACAAGTT
















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|88342813|gb|CI640146.1|CI640146
EST:     GCTACGGCATGGAGGTCAGTGGCTTCATGAAAG                         CATGTGGGGTCGAGCTGGCCACGGCGGGTTACGGCGTGTTCGGCATCCATT
genomic: GCTACGGCATGGAGGTCAGTGGCTTCATGAAAGgtatacttcg ... atactggcagCATGTGGGGTCGAGCTGGCCACGGCGGGTTACGGCGTGTTCGGCATCGATT
EST: gi|88356078|gb|CI627526.1|CI627526
EST:     GCTACGGCATGGAGGTCAGTGGCTTCATGAAAG                         CATGTGGGGTCGAGCTGGCCACGGCGGGTTACGGCGTGTTCGGCATCGATT
genomic: GCTACGGCATGGAGGTCAGTGGCTTCATGAAAGgtatacttcg ... atactggcagCATGTGGGGTCGAGCTGGCCACGGCGGGTTACGGCGTGTTCGGCATCGATT
EST: gi|88368238|gb|CI575120.1|CI575120
EST:     GCTACGGCATGGAGGTCAGTGGCTTCATGAAAG                         CATGTGGGGTCGAGCTGGCCACGGCGGGTTACGGCGTGTTCGGCATCGATT
genomic: GCTACGGCATGGAGGTCAGTGGCTTCATGAAAGgtatacttcg ... atactggcagCATGTGGGGTCGAGCTGGCCACGGCGGGTTACGGCGTGTTCGGCATCGATT
EST: gi|88416988|gb|CI573703.1|CI573703
EST:     GTCAGTGGCTTCATGAAAG                         CATGTGGGGTCGAGCTGGCCACGGGGGGTTACGGCGTGTTCGGCATCGATT
genomic: GTCAGTGGCTTCATGAAAGgtatacttcg ... atactggcagCATGTGGGGTCGAGCTGGCCACGGCGGGTTACGGCGTGTTCGGCATCGATT
EST: gi|88760430|gb|CI769986.1|CI769986
EST:     GCTACGGCATGGAGGTCAGTGGCTTCATGAAAG                         CATGTGGGGTCGAGCTGGCCACGGCGGGTTACGGCGTGTTCGGCATCGATT
genomic: GCTACGGCATGGAGGTCAGTGGCTTCATGAAAGgtatacttcg ... atactggcagCATGTGGGGTCGAGCTGGCCACGGCGGGTTACGGCGTGTTCGGCATCGATT
EST: gi|29656345|gb|CB652620.1|CB652620
EST:     GCTACGGCATGGAGGTCAGTGGCTTCATGAAAG                         CATGTGGGGTCGAGCTGGCCACGGCGGGTTACGGCGTGTTCGGCATCGATT
genomic: GCTACGGCATGGAGGTCAGTGGCTTCATGAAAGgtatacttcg ... atactggcagCATGTGGGGTCGAGCTGGCCACGGCGGGTTACGGCGTGTTCGGCATCGATT
EST: gi|88743266|gb|CI766774.1|CI766774
EST:     GCTACGGCATGGAGGTCAGTGGCTTCATGAAAG                         CATGTGGGGTCGAGCTGGCCACGGCGGGTTACGGCGTGTTCGGCATCGATT
genomic: GCTACGGCATGGAGGTCAGTGGCTTCATGAAAGgtatacttcg ... atactggcagCATGTGGGGTCGAGCTGGCCACGGCGGGTTACGGCGTGTTCGGCATCGATT

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: 33 (upstream exon), 74 (downstream exon)
Score: 4

GCTACGGCATGGAGGTCAGTGGCTTCATGAAAGgtatacttcg ... atactggcagCATGTGGGGTCGAGCTGGCCACGGCGGGTTACGGCGTGTTCGGCATCGATTATGAGGGGCATGGCAAGTCCATGGGTGCCAGATGCTACATCCAGAAGTT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcagagagcatgatgctgtgttctaatggtgggggacattgtgatactggcagCATGTGGGGTCGAGCTGGCCACGGCGGGTTACGGCGTGTTCGGCATCGATTATGAGGGGCATGGCAAGTCCATGGGTGCCAGATGCTACATCCAGAAGTT
                      ttctaat  putative branch site (score: 4)
                      ttctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcagctggttaattaattaattactgtcacatgggaaagcaatcaatcagagagcatgatgctgtgttctaatggtgggggacattgtgatactggcagCATGTGGGGTCGAGCTGGCCACGGCGGGTTACGGCGTGTTCGGCATCGATTATGAGGGGCATGGCAAGTCCATGGGTGCCAGATGCTACATCCAGAAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- cagctgg
- - - - - - - - - - - - - - cacatgg
- - - - - - - - - - - - - - - - - - aaagcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgct