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

gtaagcagatggccatctccatttaccactcttgttaacgagcacgcgtaattaacccacatttgaaatgcagGTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTGAAGCTGAGTGACGGCTACTACGTCATGGACCCAGCTAAGGCCGTGGATA

Basic information

species Oryza sativa
transcript LOC_Os03g51080.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g51080.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G826838_T01 (Zea mays), 3'ss of exon 3
--------------------------gtaagcagatggccatctccatt-------taccactcttgttaacgagc-acgcgtaattaacccacatttgaaatgcagGTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTGAAGCTGAGTGACGGCTACTACGTCATGGACCCAGCTAAGGCCGTGGATA
                           | |  |||   |   ||||| |       |  ||  | | | |   | | || | |   |   |        ||||||||||||||||||||||||||||||| ||||||||||| ||||| ||||||||||||||||| |||||||||||||||||||||||    ||||| ||||| |
gtaaggaaactgcaatccagttctttctgaatagaccacgtactccagtgctcctatgacaagcatttcatttaccgactcatcggtgtgcttggcgaaaaatgcagGTTTGCTGGGAGAAGTTCGCGCGCTACTTCGAGGTCGAGCTGAAGGAAGTGAAGCTGAGCGACGGCTACTACGTCATGGACCCGCAGAAGGCAGTGGACA

upper sequence: LOC_Os03g51080.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ36644 (Selaginella moellendorffii), 3'ss of exon 3
----------------gtaagcagatggccatctccatt-taccactcttgttaacgagcacgc-gtaattaacccacatttgaaatgcagGTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTGAAGCTGAGTGACGGCTACTACGTCATGGACCCAGCTAAGGCCGTGGATA
                 |  |   |||    | |   || | |  || || ||   ||| | || |  |       |       |   ||||||||||||||||| ||||| || ||||| || || |||||||||||||||||||||||  | |  |||||||| ||||| |||   ||||| ||||| |
gttggtttctcttcagtttcgtcaatgaagttttgttttgtgcatcttttcttggagagaatgctgagaactgttgatgaaatcaccacagGTTTGCTGGGAGAAATTCGCTCGCTACTTTGAAGTGGAGCTCAAGGAAGTGAAGCTGAGCAAGGATTACTACGTGATGGATCCACACAAGGCGGTGGAGA

upper sequence: LOC_Os03g51080.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ18071 (Selaginella moellendorffii), 3'ss of exon 3
--------gtaagcagat--ggccatctccattta--ccactcttgttaacgagcacgcgtaatta-acccacatttgaaatg--cagGTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTGAAGCTGAGTGACGGCTACTACGTCATGGACCCAGCTAAGGCCGTGGATA
         |   ||| |  | ||||     |||   |  || || ||   ||| | |  |  | | | |      ||||||   ||||||||||||||||||||||| || ||||| || || |||||||||||||||||||||||  | |  |||||||| ||||| |||   ||||| ||||| |
gttggtttctcttcagtttcgtccatgaagttttgtgcatcttttcttggagagaatgaatgctgagaactgttgatgaaattaccagGTTTGCTGGGAGAAGTTCGCTCGCTACTTTGAAGTGGAGCTCAAGGAAGTGAAGCTGAGCAAGGATTACTACGTGATGGATCCACACAAGGCGGTGGAGA

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|58690704|gb|CK079391.1|CK079391
EST:     CCGGCAAGCCATGCGACAAGCCTAACATTGTCACCGGCGCCAATGTCCAA                         GTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTG
genomic: CCGGCAAGCCATGCGACAAGCCTAACATTGTCACCGGCGCCAATGTCCAAgtaagcagat ... tgaaatgcagGTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTG
EST: gi|29617567|gb|CB622579.1|CB622579
EST:     CCGGCAAGCCATGCGACAAGCCTAACATTGTCACCGGCGCCAATGTCCAA                         GTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTG
genomic: CCGGCAAGCCATGCGACAAGCCTAACATTGTCACCGGCGCCAATGTCCAAgtaagcagat ... tgaaatgcagGTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTG
EST: gi|8336367|gb|BE040860.1|BE040860
EST:     CCGGCAAGCCATGCGACAAGCCTAACATTGTCACCGGCGCCAATGTCCAA                         GTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTG
genomic: CCGGCAAGCCATGCGACAAGCCTAACATTGTCACCGGCGCCAATGTCCAAgtaagcagat ... tgaaatgcagGTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTG
EST: gi|29659446|gb|CB655721.1|CB655721
EST:     CCGGCAAGCCATGCGACAAGCCTAACATTGTCACCGGCGCCAATGTCCAA                         GTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTG
genomic: CCGGCAAGCCATGCGACAAGCCTAACATTGTCACCGGCGCCAATGTCCAAgtaagcagat ... tgaaatgcagGTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTG
EST: gi|117217697|gb|CT845092.1|CT845092
EST:     CCGGCAAGCCATGCGACAAGCCTAACATTGTCACCGGCGCCAATGTCCAA                         GTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTG
genomic: CCGGCAAGCCATGCGACAAGCCTAACATTGTCACCGGCGCCAATGTCCAAgtaagcagat ... tgaaatgcagGTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTG
EST: gi|58692856|gb|CK081543.1|CK081543
EST:     CCGGCAAGCCATGCGACAAGCCTAACATTGTCACCGGCGCCAATGTCCAA                         GTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCT
genomic: CCGGCAAGCCATGCGACAAGCCTAACATTGTCACCGGCGCCAATGTCCAAgtaagcagat ... tgaaatgcagGTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCT
EST: gi|2309713|gb|C25868.1|C25868
EST:     CCGGCAAGCCATGCGACAAGNCTAACATTGTCACCGGNGNCAATGTCCAA                         GTTTTCTGGGAGAAGTT
genomic: CCGGCAAGCCATGCGACAAGCCTAACATTGTCACCGGCGCCAATGTCCAAgtaagcagat ... tgaaatgcagGTTTGCTGGGAGAAGTT
EST: gi|29613133|gb|CB618146.1|CB618146
EST:     CCGGCAAGCCATGCGACAAGCCTAACATTGTCACCGGCGCCAATGTCCAA                         GTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTG
genomic: CCGGCAAGCCATGCGACAAGCCTAACATTGTCACCGGCGCCAATGTCCAAgtaagcagat ... tgaaatgcagGTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTG
EST: gi|88304126|gb|CI599814.1|CI599814
EST:     CCGGCAAGCCATGCGACAAGCCTAACATTGTCACCGGCGCCAATGTTCAA                         GTTTGTTGGGAGA-GTTCGGGCGATACTTCGAGGTTGAGCTCAAGGAAGT
genomic: CCGGCAAGCCATGCGACAAGCCTAACATTGTCACCGGCGCCAATGTCCAAgtaagcagat ... tgaaatgcagGTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGT
EST: gi|58667690|gb|CK056376.1|CK056376
EST:     CCGGCAAGCCATGCGACAAGCCTAACATTGTCACCGGCGCCAATGTCCAA                         GTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTG
genomic: CCGGCAAGCCATGCGACAAGCCTAACATTGTCACCGGCGCCAATGTCCAAgtaagcagat ... tgaaatgcagGTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTG
EST: gi|29659019|gb|CB655294.1|CB655294
EST:     CCGGCAAGCCATGCGACAAGCCTAACATTGTCACCGGCGCCAATGTCCAA                         GTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTG
genomic: CCGGCAAGCCATGCGACAAGCCTAACATTGTCACCGGCGCCAATGTCCAAgtaagcagat ... tgaaatgcagGTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTG
EST: gi|58696140|gb|CK084827.1|CK084827
EST:     CCGGCAAGCCATGCGACAAGCCTAACATTGTCACCGGCGCCAATGTCCAA                         GTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTG
genomic: CCGGCAAGCCATGCGACAAGCCTAACATTGTCACCGGCGCCAATGTCCAAgtaagcagat ... tgaaatgcagGTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTG
EST: gi|33799654|gb|CF325690.1|CF325690
EST:     CTAACATTGTCACCGGCGCCAATGTCCAA                         GTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTG
genomic: CTAACATTGTCACCGGCGCCAATGTCCAAgtaagcagat ... tgaaatgcagGTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTG

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), 74 (downstream exon)
Score: 64

GCTCGCCGGTTTGGCCTTCAAGAGGAGGTGGCAGAACAAGATGAAGGCAGCCGGCAAGCCATGCGACAAGCCTAACATTGTCACCGGCGCCAATGTCCAAgtaagcagat ... tgaaatgcagGTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTGAAGCTGAGTGACGGCTACTACGTCATGGACCCAGCTAAGGCCGTGGATA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatttaccactcttgttaacgagcacgcgtaattaacccacatttgaaatgcagGTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTGAAGCTGAGTGACGGCTACTACGTCATGGACCCAGCTAAGGCCGTGGATA
                               aattaac  putative branch site (score: 64)
                                          atttgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcagatggccatctccatttaccactcttgttaacgagcacgcgtaattaacccacatttgaaatgcagGTTTGCTGGGAGAAGTTCGCGCGATACTTCGAGGTTGAGCTCAAGGAAGTGAAGCTGAGTGACGGCTACTACGTCATGGACCCAGCTAAGGCCGTGGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA