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

GCATATGAAAAGAAAACTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAGgttaggctttcagaacatgttaaataatctgttacttcttgtaatggtgcaagcgcacgcgaaattatctttgtttaaaggcttgatacaccttgatgag...

Basic information

species Oryza sativa
transcript LOC_Os03g58960.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g58960.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G027307_T01 (Zea mays), 5'ss of exon 6
GCATATGAAAAGAAAACTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAGgttaggctttcagaacatgttaaataatctgttacttcttgtaatggtgcaagcgcacgcgaaattatc-----tttgtttaaaggcttgatacaccttgatgag
|||||||| ||||| || || ||||  ||||| |||||| |||||||||||||||||||   ||||||||  || |   |   | |||  |  ||    ||||||   |||  |     ||       |||  ||        |  || |   ||  |||  | || ||| 
GCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAGgttaatctgtactagatttttagtt--tcaagaacttctgtcaattatttgctcgttt-tataatagtcaggcaccagcgtataactttattactgcatg-tga-

upper sequence: LOC_Os03g58960.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G001265_T01 (Zea mays), 5'ss of exon 6
GCATATGAAAAGAAAACTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAGgttaggctttcagaacatgttaaataatctgttacttcttgtaatggtgcaagcgcacgcgaaattatctttgtttaaaggcttgatacaccttgatgag---------
|||||||| ||||| || || ||||  ||||| |||||| |||||||||||||||||||   ||||||||| || | |    || || | |  | |   | || |  | |   |    || ||    | | ||    ||        ||  ||| | ||| ||||          
GCATATGAGAAGAAGACAACTCCACATTGGATATATGATCTTGGCCGGAAGAGGAATTTTGCTCAGgttagtctgt-attggatttttagt--tttaagaattttcatca-attatttgctcattttataataatcatgc-----acctacatatatcttcatgactgcatgtga
















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|29659672|gb|CB655947.1|CB655947
EST:     CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAG                         GTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
genomic: CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAGgttaggcttt ... ctgttaccagGTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
EST: gi|88291408|gb|CI529998.1|CI529998
EST:     TGATATTGGCCGGAAGAGGAATTTCATTCAG                         GTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
genomic: TGATATTGGCCGGAAGAGGAATTTCATTCAGgttaggcttt ... ctgttaccagGTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
EST: gi|86417491|gb|CI031700.1|CI031700
EST:     CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAAGTTCATTCAG                         GTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
genomic: CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAGgttaggcttt ... ctgttaccagGTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
EST: gi|86859035|gb|CI276977.1|CI276977
EST:     CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAG                         GTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
genomic: CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAGgttaggcttt ... ctgttaccagGTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
EST: gi|89168420|gb|CI109624.1|CI109624
EST:     GGCCGGAAGAGGAATTTCATTCAG                         GTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
genomic: GGCCGGAAGAGGAATTTCATTCAGgttaggcttt ... ctgttaccagGTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
EST: gi|86477714|gb|CI120347.1|CI120347
EST:     CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAG                         GTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGCAGAG
genomic: CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAGgttaggcttt ... ctgttaccagGTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
EST: gi|87012987|gb|CI297214.1|CI297214
EST:     CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAG                         GTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
genomic: CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAGgttaggcttt ... ctgttaccagGTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
EST: gi|29659673|gb|CB655948.1|CB655948
EST:     CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAG                         GTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
genomic: CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAGgttaggcttt ... ctgttaccagGTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
EST: gi|86261194|gb|CI004759.1|CI004759
EST:     CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAG                         GTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
genomic: CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAGgttaggcttt ... ctgttaccagGTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
EST: gi|27554328|gb|CA998228.1|CA998228
EST:     CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAG                         GTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACT
genomic: CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAGgttaggcttt ... ctgttaccagGTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACT
EST: gi|88991146|gb|CI108533.1|CI108533
EST:     CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAG                         GTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
genomic: CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAGgttaggcttt ... ctgttaccagGTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
EST: gi|88833273|gb|CI076756.1|CI076756
EST:     TGGCCGGAAGAGGAATTTCATTCAG                         GTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
genomic: TGGCCGGAAGAGGAATTTCATTCAGgttaggcttt ... ctgttaccagGTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
EST: gi|86500478|gb|CI143111.1|CI143111
EST:     CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAG                         GTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
genomic: CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAGgttaggcttt ... ctgttaccagGTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
EST: gi|88228048|gb|CI227528.1|CI227528
EST:     CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAG                         GTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
genomic: CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAGgttaggcttt ... ctgttaccagGTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
EST: gi|33812432|gb|CF332104.1|CF332104
EST:     TGTATGATATTGGCCGGAAGAGGAATTTCATTCAG                         GTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCCTGCGTACTCAGAAGA
genomic: TGTATGATATTGGCCGGAAGAGGAATTTCATTCAGgttaggcttt ... ctgttaccagGTTTTTGGAAATGACAAGAGGTATTGGTTCAT-CCCTGCGTACTCAGAAGA
EST: gi|86258794|gb|CI000023.1|CI000023
EST:     CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAG                         GTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
genomic: CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAGgttaggcttt ... ctgttaccagGTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
EST: gi|87018830|gb|CI256715.1|CI256715
EST:     CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAG                         GTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
genomic: CTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAGgttaggcttt ... ctgttaccagGTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
EST: gi|86417990|gb|CI032199.1|CI032199
EST:     TGGCCGGAAGAGGAATTTCATTCAG                         GTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG
genomic: TGGCCGGAAGAGGAATTTCATTCAGgttaggcttt ... ctgttaccagGTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAG

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: 56 (upstream exon), 72 (downstream exon)
Score: 12

GCATATGAAAAGAAAACTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAGgttaggcttt ... ctgttaccagGTTTTTGGAAATGACAAGAGGTATTGGTTCATCCCTGCGTACTCAGAAGAGGATTTGAGAAGAATGCCAGTTCTACAGGGCCTTGATTACCCTGTCAGGA




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATATGAAAAGAAAACTACGCCACGCTGGATGTATGATATTGGCCGGAAGAGGAATTTCATTCAGgttaggctttcagaacatgttaaataatctgttacttcttgtaatggtgcaagcgcacgcgaaattatctttgtttaaaggcttgatacaccttgatgag

- - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA