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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTTCTCTACACTCCAGATGCAGATTTTTCATGTTTTTCAGACCTTGCACTTTCATCTCCTGCTGACTACTACATTGAAGGACAAGGTTCCTTGATCCAgtaaggctactttctcttccatgttctttgcttttgtggtctggaattaagtttgaccattcagtgttcttgacatttgatatcattcactattgtagct...

Basic information

species Oryza sativa
transcript LOC_Os07g10490.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g10490.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G454952_T01 (Zea mays), 5'ss of exon 11
ATCTTCTCTACACTCCAGATGCAGATTTTTCATGTTTTTCAGACCTTGCACTTTCATCTCCTGCTGACTACTACATTGAAGGACAAGGTTCCTTGATCCAgtaaggctactttctcttccatgttct-ttgcttttgtggtctggaattaagtttgaccattcagtgttcttgacatttgatatcattcactattgtagct
| ||| | |||||  | |||||||| ||||| |||||||| |||||||| || |||||||||||||| |||||||||||||| ||||||||| |||||||||||| ||||| | |      | |    ||  | |  || |||| || |   ||   |  |||   |       ||| ||                     
ACCTTTTGTACACGGCGGATGCAGACTTTTCCTGTTTTTCGGACCTTGCTCTCTCATCTCCTGCTGATTACTACATTGAAGGGCAAGGTTCCCTGATCCAgtaagtctactcttttccaagtatcaaattaatgtcttgctctgcaaatgtattcacc--ttccacgcctaattcatctgcag------------------

upper sequence: LOC_Os07g10490.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA10G30220.1 (Glycine max), 5'ss of exon 11
ATCTTCTCTACACTCCAGATGCAGATTTTTCATGTTTTTCAGACCTTGCACTTTCATCTCCTGCTGACTACTACATTGAAGGACAAGGTTCCTTGATCCAgtaaggctactttctcttccatgttctttgcttttgtggtctggaattaagt-ttgaccattcagtgttcttgacatttgatatcattcactattgtagct-
| |||||||| || || |||||||||||||| || ||| |||||||||||||||||||||| |  || || |||||||| |||||||| || ||| |||||||||  |   |  |||| ||  ||||    |||      |    || |  | || |||    | | || || |     ||| | ||| | |    |   | 
ACCTTCTCTATACACCCGATGCAGATTTTTCTTGCTTTGCAGACCTTGCACTTTCATCTCCAGAGGATTATTACATTGAGGGACAAGGATCATTGCTCCAgtaagtgtttgtaatcttgcac-ttctaaattttcacttccattcatgagttgtttacctgaaaatatt-ttaaggaaagatttaattaagtgacttgcttg

upper sequence: LOC_Os07g10490.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA20G37170.1 (Glycine max), 5'ss of exon 11
ATCTTCTCTACACTCCAGATGCAGATTTTTCATGTTTTTCAGACCTTGCACTTTCATCTCCTGCTGACTACTACATTGAAGGACAAGGTTCCTTGATCCAgtaaggctactttctcttccatgttctttgcttttgtggtctggaattaagtttgaccattcagtgttcttgacatttgatatcattcactattgtagct----
| |||||||| || || |||||||||||||| || ||| |||||||||||||||||||||| |  || || |||||||| |||||||| || ||| |||||||||  |  || |  |  ||   |  |   ||||    ||      | ||||      || |   |  || | |    | ||  || | | || |   |    
ACCTTCTCTATACACCCGATGCAGATTTTTCTTGCTTTGCAGACCTTGCACTTTCATCTCCAGAAGATTATTACATTGAGGGACAAGGATCATTGCTCCAgtaag--tgtttgcaatctcacacttctaaattttcacttccattcatgagttgtttacttgaaaataatttataagaaagat--ttaagtgttttgcttgagt

upper sequence: LOC_Os07g10490.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv14s0030g01740.t01 (Vitis vinifera), 5'ss of exon 11
ATCTTCTCTACACTCCAGATGCAGATTTTTCATGTTTTTCAGACCTTGCACTTTCATCTCCTGCTGACTACTACATTGAAGGACAAGGTTCCTTGATCCAgtaaggctactttctcttccatgttctttgcttttgtggtctgga--attaagtttgaccattc-agtgttcttgacatttgatatcattcactattgtagct
|||| || ||||| ||||| ||||| || || || ||| | || || |||||||||||||| |  || ||||||||||| ||||||||||| ||| |||||||||   | |||   |    | |  |||  |  |   || |  |  |||||   |    |||  | |||  ||    ||||| || || ||  |        
ATCTCCTTTACACCCCAGACGCAGACTTCTCTTGCTTTGCCGATCTAGCACTTTCATCTCCAGAAGATTACTACATTGAGGGACAAGGTTCATTGCTCCAgtaagcgaaattttcttcttgtttgttttattactactgtttttatcattaatactcttgattttaatgtgtttctattttgagataatacaaaacaacc---

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|163925596|gb|EG710761.1|EG710761
EST:     CTTTCATCTCCTGCTGACTACTACATTGAAGGACAAGGTTCCTTGATCCA                         AGCTGTGCTAATCCCTGGCGATCCTTACATGCCATTGCCGAATGAGGAGAT
genomic: CTTTCATCTCCTGCTGACTACTACATTGAAGGACAAGGTTCCTTGATCCAgtaaggctac ... tcatttgtagAGCTGTGCTAACCCCTGGCGATCCTTACATGCCATTGCCGAATGAGGAGAT
EST: gi|300215694|gb|HO088320.1|HO088320
EST:     CTTTCATCTCCTGCTGACTACTACATTGAAGGACAAGGTTCCTTGATCCA                         AGCTGTGCTAACCCCTGGCGATCCTTACATGCCATTGCCGAATGAGGAGAT
genomic: CTTTCATCTCCTGCTGACTACTACATTGAAGGACAAGGTTCCTTGATCCAgtaaggctac ... tcatttgtagAGCTGTGCTAACCCCTGGCGATCCTTACATGCCATTGCCGAATGAGGAGAT
EST: gi|29629811|gb|CB634820.1|CB634820
EST:     CTTTCATCTCCTGCTGACTACTACATTGAAGGACAAGGTTCCTTGATCCA                         AGCTGTGCTAACCCCTGGCGATCCTTACATGCCATTGCCGAATGAGGAGAT
genomic: CTTTCATCTCCTGCTGACTACTACATTGAAGGACAAGGTTCCTTGATCCAgtaaggctac ... tcatttgtagAGCTGTGCTAACCCCTGGCGATCCTTACATGCCATTGCCGAATGAGGAGAT
EST: gi|29675444|gb|CB671719.1|CB671719
EST:     CTTTCATCTCCTGCTGACTACTACATTGAAGGACAAGGTTCCTTGATCCA                         AGCTGTGCTAACCCCTGGCGATCCTTACATGCCATTGCCGAATGAGGAGAT
genomic: CTTTCATCTCCTGCTGACTACTACATTGAAGGACAAGGTTCCTTGATCCAgtaaggctac ... tcatttgtagAGCTGTGCTAACCCCTGGCGATCCTTACATGCCATTGCCGAATGAGGAGAT
EST: gi|29683969|gb|CB680244.1|CB680244
EST:     GGACAAGGTTCCTTGCCT-CT                         AGCTGTGCTAACCCCTGGCGATCCTTACATGCCATTGCCGAATGAGGAGA
genomic: GGACAAGGTTCCTTG-ATCCAgtaaggctac ... tcatttgtagAGCTGTGCTAACCCCTGGCGATCCTTACATGCCATTGCCGAATGAGGAGA
EST: gi|29656822|gb|CB653097.1|CB653097
EST:     CTTTCATCTCCTGCTGACTACTACATTGAAGGACAAGGTTCCTTGATCCA                         AGCTGTGCTAACCCCTGGCGATCCTTACATGCCATTGCCGAATGAGGAGAT
genomic: CTTTCATCTCCTGCTGACTACTACATTGAAGGACAAGGTTCCTTGATCCAgtaaggctac ... tcatttgtagAGCTGTGCTAACCCCTGGCGATCCTTACATGCCATTGCCGAATGAGGAGAT
EST: gi|58685253|gb|CK073940.1|CK073940
EST:     CTTTCATCTCCTGCTGACTACTACATTGAAGGACAAGGTTCCTTGATCCA                         AGCTGTGCTAACCCCTGGCGATCCTTACATGCCATTGCCGAATGAGGAGAT
genomic: CTTTCATCTCCTGCTGACTACTACATTGAAGGACAAGGTTCCTTGATCCAgtaaggctac ... tcatttgtagAGCTGTGCTAACCCCTGGCGATCCTTACATGCCATTGCCGAATGAGGAGAT
EST: gi|29675446|gb|CB671721.1|CB671721
EST:     CTTTCATCTCCTGCTGACTACTACATTGAAGGACAAGGTTCCTTGATCCA                         AGCTGTGCTAACCCCTGGCGATCCTTACATGCCATTGCCGAATGAGGAGAT
genomic: CTTTCATCTCCTGCTGACTACTACATTGAAGGACAAGGTTCCTTGATCCAgtaaggctac ... tcatttgtagAGCTGTGCTAACCCCTGGCGATCCTTACATGCCATTGCCGAATGAGGAGAT
EST: gi|4714783|gb|AU055900.1|AU055900
EST:     CTTTCATCTCCTGCTGACTACTACATTGAAGGACAAGGTTCCTTGATCCA                         AGCTGTGCTAACCCCTGGCGATCCTTACATGCCATTGCCGAATGAGGAGAT
genomic: CTTTCATCTCCTGCTGACTACTACATTGAAGGACAAGGTTCCTTGATCCAgtaaggctac ... tcatttgtagAGCTGTGCTAACCCCTGGCGATCCTTACATGCCATTGCCGAATGAGGAGAT
EST: gi|8956710|gb|BE230513.1|BE230513
EST:     CTTTCATCTCCTGCTGACTACTACATTGAAGGACAGGGTTCCTTGATCCA                         AGCTGTGCTAACCCCTGGCGATCCTTACATGCCATTGCCGAATGAGGAGAT
genomic: CTTTCATCTCCTGCTGACTACTACATTGAAGGACAAGGTTCCTTGATCCAgtaaggctac ... tcatttgtagAGCTGTGCTAACCCCTGGCGATCCTTACATGCCATTGCCGAATGAGGAGAT

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: 74 (upstream exon), 73 (downstream exon)
Score: 72

ATCTTCTCTACACTCCAGATGCAGATTTTTCATGTTTTTCAGACCTTGCACTTTCATCTCCTGCTGACTACTACATTGAAGGACAAGGTTCCTTGATCCAgtaaggctac ... tcatttgtagAGCTGTGCTAACCCCTGGCGATCCTTACATGCCATTGCCGAATGAGGAGATAATTAGCAAGGTTCAAAAGCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTTCTCTACACTCCAGATGCAGATTTTTCATGTTTTTCAGACCTTGCACTTTCATCTCCTGCTGACTACTACATTGAAGGACAAGGTTCCTTGATCCAgtaaggctactttctcttccatgttctttgcttttgtggtctggaattaagtttgaccattcagtgttcttgacatttgatatcattcactattgtagct

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