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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGGAACATCGAACTATTTTAAAGGCCTTATGCTTATCTTATGCTATCTCATAGTTGCTGCGAGCTTCTTCGTACATGTTGATCCCGATTCAAgtaagtattttgtttggcattcaacctcgacaactatcccaaaactatttcaccagttctactggttcttaggtgtaatggtaaattagttatctatctg...

Basic information

species Oryza sativa
transcript LOC_Os03g27960.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g27960.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G053004_T01 (Zea mays), 5'ss of exon 10
GAAGGAACATCGAACTATTTTAAAGGCCTTATGCTTATCTTATGCTATCTCATAGTTGCTGCGAGCTTCTTCGTACATGTTGATCCCGATTCAAgtaagtattttgtttggcattcaacctcgacaactatcccaaaactatttcaccagttctactggttcttaggtgtaatggtaaattagttatctatctg----
||||| ||||| |||||||||||||| |||||||| ||||||||||| |||||||||||||| ||||| || || ||||| || || ||| ||||||||||| ||||||    ||   | | ||           ||||||   ||  |  |  |  ||||  | |   |    | || | |   || |   |     
GAAGGCACATCAAACTATTTTAAAGGTCTTATGCTCATCTTATGCTACCTCATAGTTGCTGCAAGCTTTTTTGTCCATGTCGACCCTGATGCAAgtaagtatcttgtttattgtttt-cttagatgcacgagagcaaactagacca--aaattgatgggttaatggaaatgcaag-aattaaaccatttggataaaaa

upper sequence: LOC_Os03g27960.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G046480_T01 (Zea mays), 5'ss of exon 11
GAAGGAACATCGAACTATTTTAAAGGCCTTATGCTTATCTTATGCTATCTCATAGTTGCTGCGAGCTTCTTCGTACATGTTGATCCCGATTCAAgtaagtattttgtttggcattcaacctcgacaactatcccaaaactatttcaccagttctactggttcttaggtgtaatggtaaattagttatctatctg------
||||| ||||| ||||||||||||||||||||||| ||||| ||||| |||||||| ||||| ||||||||||| ||||||||||| ||| ||||||||||  ||    || |||       | ||  |      |    | |  |  |    |  ||| ||   ||        ||| |||   || |   |       
GAAGGCACATCAAACTATTTTAAAGGCCTTATGCTCATCTTGTGCTACCTCATAGTCGCTGCAAGCTTCTTCGTCCATGTTGATCCTGATGCAAgtaagtacctt----ggtatt--gttctgtcagatgctgacagcaaactgaaaaaaaaatgatgggtcgatggaaatgcaataacttaagcatttggataaaaaaa

upper sequence: LOC_Os03g27960.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA13G44960.1 (Glycine max), 5'ss of exon 10
GAAGGAACATCGAACTATTTTAAAGGCCTTATGCTTATCTTATGCTATCTCATAGTTGCTGCGAGCTTCTTCGTACATGTTGATCCCGATTCAAgtaagtattttgtttggcattcaacctcgacaactatcccaaaactatttcacc---agttctactggttcttaggtgtaatggtaaattagttatctatctg-
|||||||| || || |||||||||||  | ||||||||  |||||||||| ||||||||||| || || ||||||||||| || ||  |   ||||  ||   ||     | ||  |      | |   |    | |  ||| | |     | |     ||  |||    | |     |   |   |  |  ||||  
GAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATTCTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAA---AAGTG-

upper sequence: LOC_Os03g27960.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA15G00380.1 (Glycine max), 5'ss of exon 10
GAAGGAACATCGAACTATTTTAAAGGCCTTATGCTTATCTTATGCTATCTCATAGTTGCTGCGAGCTTCTTCGTACATGTTGATCCCGATTCAAgtaagtattttgtttggcattcaacctcgacaactatcccaaaactatttca--ccagttctactgg----ttcttaggtgtaatggtaaattagttatctatctg
|||||||| || || |||||||||||  | ||||||||  |||||||||| ||||||||||| || || ||||||||||| || ||  |   ||||  ||   ||| |  | ||  |      | |   |    | |  ||| | |  |    ||||   |    | ||    |    |  |   ||||||   | |   
GAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAA---AAGTG-

upper sequence: LOC_Os03g27960.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA15G00380.2 (Glycine max), 5'ss of exon 10
GAAGGAACATCGAACTATTTTAAAGGCCTTATGCTTATCTTATGCTATCTCATAGTTGCTGCGAGCTTCTTCGTACATGTTGATCCCGATTCAAgtaagtattttgtttggcattcaacctcgacaactatcccaaaactatttca--ccagttctactgg----ttcttaggtgtaatggtaaattagttatctatctg--
|||||||| || || |||||||||||  | ||||||||  |||||||||| ||||||||||| || || ||||||||||| || ||  |   ||||  ||   ||| |  | ||  |      | |   |    | |  ||| | |  |    ||||   |    | ||    |    |  |   ||||||   | | |   
GAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAA---AAGTG-GTGAgttgctgagaatatactgcacagattcacagtagagttatataatgcagaatctagatgaatctcctctacttctctttttgcttagtttcatgtttcac

upper sequence: LOC_Os03g27960.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv09s0018g01840.t01 (Vitis vinifera), 5'ss of exon 11
GAAGGAACATCGAACTATTTTAAAGGCCTTATGCTTATCTTATGCTATCTCATAGTTGCTGCGAGCTTCTTCGTACATGTTGATCCCGATTCAAgtaagtattttgtttggcattcaacctcgacaactatcccaaaactatttcaccagttctactggttcttaggtgtaatggtaaattagttatctatctg------
||||| ||||| ||||||||||||||  | ||||||||  ||||||||||||||||||| || ||||| || ||||||||||| ||        ||||||   |||  ||   || |        ||  | |  |    ||  ||   | |  || ||  ||| |  |  | |  || | | | |  || |||       
GAAGGGACATCAAACTATTTTAAAGGTTTGATGCTTATTCTATGCTATCTCATAGTTGCAGCCAGCTTTTTTGTACATGTTGACCCTACAAAGGgtaagt---ttgactgaactttatttcaattaaaaaacagacctttacatcgttaatgatattg--tctaaatttcatttctacaattgct-cctgtcttgaaagg

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|88663369|gb|CI481268.1|CI481268
EST:     CTATCTCATAGTTGCTGCGAGCTTCTTCGTACATGTTGATCCCGATTC-A                         -A-GTAACAACAAGTGAAAGATCCGCAACAATTTGTGGAATGATAAGGGAT
genomic: CTATCTCATAGTTGCTGCGAGCTTCTTCGTACATGTTGATCCCGATTCAAgtaagtattt ... tgacctgaagCAGGTAACAACAAGTGAAAGATCCGCAACAATTTGTGGAATGATAAGGGAT
EST: gi|86841010|gb|CI335151.1|CI335151
EST:     TCATAGTTGCTGCGAGCTTCTTCGTACATTTTGATCCCGATTC-A                         -A-GTAACAACAAGTGAAAGATCCGCAACAATTTGTGGAATGATAAGGGAT
genomic: TCATAGTTGCTGCGAGCTTCTTCGTACATGTTGATCCCGATTCAAgtaagtattt ... tgacctgaagCAGGTAACAACAAGTGAAAGATCCGCAACAATTTGTGGAATGATAAGGGAT
EST: gi|88663342|gb|CI480446.1|CI480446
EST:     CTATCTCATAGTTGCTGCGAGCTTCTTCGTACATGTTGATCCCGATTC-A                         -A-GTAACAACAAGTGAAAGATCCGCAACAATTTGTGGAATGATAAGGGAT
genomic: CTATCTCATAGTTGCTGCGAGCTTCTTCGTACATGTTGATCCCGATTCAAgtaagtattt ... tgacctgaagCAGGTAACAACAAGTGAAAGATCCGCAACAATTTGTGGAATGATAAGGGAT
EST: gi|88661319|gb|CI453433.1|CI453433
EST:     CTATCTCATAGTTGCTGCGAGCTTCTTCGTACATGTTGATCCCGATTC-A                         -A-GTAACAACAAGTGAAAGATCCGCAACAATTTGTGGAATGATAAGGGAT
genomic: CTATCTCATAGTTGCTGCGAGCTTCTTCGTACATGTTGATCCCGATTCAAgtaagtattt ... tgacctgaagCAGGTAACAACAAGTGAAAGATCCGCAACAATTTGTGGAATGATAAGGGAT
EST: gi|33793120|gb|CF322441.1|CF322441
EST:     CTATCTCATAGTTGCTGCGAGCTTCTTCGTACATGTTGATCCCGATTCAA                         CAGGTAACAACAAGTGAAAGATCCGCAACAATTTGTGGAATGATAAGGGAT
genomic: CTATCTCATAGTTGCTGCGAGCTTCTTCGTACATGTTGATCCCGATTCAAgtaagtattt ... tgacctgaagCAGGTAACAACAAGTGAAAGATCCGCAACAATTTGTGGAATGATAAGGGAT
EST: gi|87020102|gb|CI277834.1|CI277834
EST:     CTATCTCATAGTTGCTGCGAGCTTCTTCGTACATGTTGATCCCGATTC-A                         -A-GTAACAACAAGTGAAAGATCCGCAACAATTTGTGGAATGATAAGGGAT
genomic: CTATCTCATAGTTGCTGCGAGCTTCTTCGTACATGTTGATCCCGATTCAAgtaagtattt ... tgacctgaagCAGGTAACAACAAGTGAAAGATCCGCAACAATTTGTGGAATGATAAGGGAT
EST: gi|25801152|gb|CA757113.1|CA757113
EST:     CTATCTCATAGTTGCTGCGAGCTTCTTCGTACATGTTGATCCCGATTC-A                         -A-GTAACAACAAGTGAAAGATCCGCAACAATTTGTGGAATGATAAGGGAT
genomic: CTATCTCATAGTTGCTGCGAGCTTCTTCGTACATGTTGATCCCGATTCAAgtaagtattt ... tgacctgaagCAGGTAACAACAAGTGAAAGATCCGCAACAATTTGTGGAATGATAAGGGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGGAACATCGAACTATTTTAAAGGCCTTATGCTTATCTTATGCTATCTCATAGTTGCTGCGAGCTTCTTCGTACATGTTGATCCCGATTCAAgtaagtattttgtttggcattcaacctcgacaactatcccaaaactatttcaccagttctactggttcttaggtgtaatggtaaattagttatctatctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT