Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatgcctaagagtggtggatcatagttgccttttgctgtattgtcagttgctgatttgattcacaaacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTTATTGTGACAAGCATTGATGGAAGAAATGGACAGGCTAAACAG

Basic information

species Oryza sativa
transcript LOC_Os05g04340.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G155836_T01 (Zea mays), 3'ss of exon 2
-------------------gtattatgcctaagagtggtggatcatagttgcct----tttgctgtattgtcagttgctgatttgattcacaaacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTTATTGTGACAAGCATTGATGGAAGAAATGGACAGGCTAAACAG
                    | ||    | |  | || |   |  | | |||       |  || | |  |  |||     |||| || | |||    ||||||| |||| || || || ||||||||||||||| | || ||||||||| | || ||||| ||||||||||| |||||||| ||||| || |||
gtaatctcatctcccccgaatgtttcatcaattattgctttctggtgggtgctcagtgctcactttgtatttggtttggtttttgtttgaaaaaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATCATAGTGACCAGCATTGATGGGAGAAATGGGCAGGCAAAGCAG
















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|88736332|gb|CI759840.1|CI759840
EST:     ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
EST: gi|12622374|gb|AU172587.1|AU172587
EST:     ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
EST: gi|88308962|gb|CI654245.1|CI654245
EST:     ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATAGTTGTCAATGGCA
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGTCAATGGCA
EST: gi|29628929|gb|CB633940.1|CB633940
EST:     ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATAGGTGTCAATGGCAATGGGACAGAACCTGGTCATATT
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
EST: gi|88400318|gb|CI591008.1|CI591008
EST:     ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
EST: gi|88350886|gb|CI619144.1|CI619144
EST:     ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
EST: gi|88298568|gb|CI563563.1|CI563563
EST:     ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
EST: gi|88423830|gb|CI609861.1|CI609861
EST:     ACCGGCTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
EST: gi|86883938|gb|CI309910.1|CI309910
EST:     ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
EST: gi|86901784|gb|CI310546.1|CI310546
EST:     ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
EST: gi|88350866|gb|CI619124.1|CI619124
EST:     ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACC
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACC
EST: gi|88389101|gb|CI595335.1|CI595335
EST:     ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATAGTTGT
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGT
EST: gi|58601571|gb|CK012099.1|CK012099
EST:     ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATATT
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
EST: gi|58663289|gb|CK051975.1|CK051975
EST:     ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATATT
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
EST: gi|33658344|gb|CF280957.1|CF280957
EST:     ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
EST: gi|29630931|gb|CB635940.1|CB635940
EST:     ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATATT
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
EST: gi|58603162|gb|CK013690.1|CK013690
EST:     ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATATT
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
EST: gi|29626488|gb|CB631499.1|CB631499
EST:     ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATACTTGTCAATGGCAATGGGACAGAACCTGGTCATATT
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
EST: gi|88354859|gb|CI614137.1|CI614137
EST:     ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
EST: gi|29629558|gb|CB634567.1|CB634567
EST:     ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATATT
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
EST: gi|25798115|gb|CA754076.1|CA754076
EST:     ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
EST: gi|58598716|gb|CK009244.1|CK009244
EST:     ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATATT
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
EST: gi|88342816|gb|CI640149.1|CI640149
EST:     ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATAGTTGTCAATGGCAATG
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATG
EST: gi|88412181|gb|CI573457.1|CI573457
EST:     ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
EST: gi|88395838|gb|CI593040.1|CI593040
EST:     ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAG                         GACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT
genomic: ACCGACTTCCGAATGAGATGAGCAATATGAGTATAAGGGATGATAATAAGgtattatgcc ... aacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catagttgccttttgctgtattgtcagttgctgatttgattcacaaacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTTATTGTGACAAGCATTGATGGAAGAAATGGACAGGCTAAACAG
                                 atttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattatgcctaagagtggtggatcatagttgccttttgctgtattgtcagttgctgatttgattcacaaacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTTATTGTGACAAGCATTGATGGAAGAAATGGACAGGCTAAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA