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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattggttttttgatcgctaataaaccatttggcatataattagctcttggccaaccgatggggcccttgttcttgtaatgactcatttccgttgttcagGTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAGCAAACACATATACCCCTGAGTTCCTCACCAAG

Basic information

species Oryza sativa
transcript LOC_Os07g04990.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g04990.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G111954_T03 (Zea mays), 3'ss of exon 7
------------------cattggtttt---ttgatcgctaataaaccatttggcatataattagctcttggccaaccgatggggcccttgttcttgtaatgactcatttccgttgttcagGTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAGCAAACACATATACCCCTGAGTTCCTCACCAAG
                  |  | || ||   || | |  |  | |     | |      |||    |  |          |     |    ||  || | ||| |  || || |  ||||||||||||| |||| || |||||||||||||| || ||||| |||||||||||||||||||| ||||||||||||||| |||||
gtaaagagcccaatcatgcgatcgtgttaaatttaacagttttgatttgatggaagcccaatccatttgttttgttttttttcaatctcgttttctgcactgatttgttcccatgattcagGTGTTCTGACAGGTAAGTACACTCCAGAAAACCCCCCTACTGGTCCTCGAGCAAACACATACACCCCTGAGTTCCTCGCCAAG
















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|88368695|gb|CI675516.1|CI675516
EST:     TTGTGATGAGCTTGGCATCACCCTGATTGCTTATTCCCCAATAGCCCAAG                         GTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAG
genomic: TTGTGATGAGCTTGGCATCACCCTGATTGCTTATTCCCCAATAGCCCAAGgtgagaacca ... cgttgttcagGTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAG
EST: gi|313083769|gb|HO213899.1|HO213899
EST:     TTGTGATGAGCTTGGCATCACCCTGATTGCTTATTCCCCAATAGCCCAAG                         GTGTTCTGTCAGGAAAATACACTC
genomic: TTGTGATGAGCTTGGCATCACCCTGATTGCTTATTCCCCAATAGCCCAAGgtgagaacca ... cgttgttcagGTGTTCTGTCAGGAAAATACACTC
EST: gi|95101321|gb|CI693066.1|CI693066
EST:     TTGTGATGAGCTTGGCATCACCCTGATTGCTTATTCCCCAATAGCCCAAG                         GTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAG
genomic: TTGTGATGAGCTTGGCATCACCCTGATTGCTTATTCCCCAATAGCCCAAGgtgagaacca ... cgttgttcagGTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAG
EST: gi|29686327|gb|CB682602.1|CB682602
EST:     TTGTGATGAGCTTGGCATCACCCTGATTGCTTATTCCCCAATAGCCCAAG                         GTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAG
genomic: TTGTGATGAGCTTGGCATCACCCTGATTGCTTATTCCCCAATAGCCCAAGgtgagaacca ... cgttgttcagGTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAG
EST: gi|86892489|gb|CI311960.1|CI311960
EST:     TTGTGATGAGCTTGGCATCACCCTGATTGCTTATTCCCCAATAGCCCAAG                         GTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAG
genomic: TTGTGATGAGCTTGGCATCACCCTGATTGCTTATTCCCCAATAGCCCAAGgtgagaacca ... cgttgttcagGTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAG
EST: gi|29686352|gb|CB682627.1|CB682627
EST:     TTGTGATGAGCTTGGCATCACCCTGATTGCTTATTCCCCAATAGCCCAAG                         GTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAG
genomic: TTGTGATGAGCTTGGCATCACCCTGATTGCTTATTCCCCAATAGCCCAAGgtgagaacca ... cgttgttcagGTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAG
EST: gi|29684749|gb|CB681024.1|CB681024
EST:     TTGTGATGAGCTTGGCATCACCCTGATTGCTTATTCCCCAATAGCCCAAG                         GTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAG
genomic: TTGTGATGAGCTTGGCATCACCCTGATTGCTTATTCCCCAATAGCCCAAGgtgagaacca ... cgttgttcagGTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAG
EST: gi|29685611|gb|CB681886.1|CB681886
EST:     TTGTGATGAGCTTGGCATCACCCTGATTGCTTATTCCCCAATAGCCCAAG                         GTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAG
genomic: TTGTGATGAGCTTGGCATCACCCTGATTGCTTATTCCCCAATAGCCCAAGgtgagaacca ... cgttgttcagGTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAG
EST: gi|29685612|gb|CB681887.1|CB681887
EST:     TTGTGATGAGCTTGGCATCACCCTGATTGCTTATTCCCCAATAGCCCAAG                         GTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAG
genomic: TTGTGATGAGCTTGGCATCACCCTGATTGCTTATTCCCCAATAGCCCAAGgtgagaacca ... cgttgttcagGTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAG
EST: gi|86838940|gb|CI330354.1|CI330354
EST:     TGATGAGGCTTGGCATCACCCTGATTGCTTATTCCCCAATAGCCCAAG                         GTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAG
genomic: TGATGA-GCTTGGCATCACCCTGATTGCTTATTCCCCAATAGCCCAAGgtgagaacca ... cgttgttcagGTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAG

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: 75 (upstream exon), 74 (downstream exon)
Score: 62

AACTACAGCCTAATATACAGGACTCCTGAGTTGAATGGTGTGAAGGCAGCTTGTGATGAGCTTGGCATCACCCTGATTGCTTATTCCCCAATAGCCCAAGgtgagaacca ... cgttgttcagGTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAGCAAACACATATACCCCTGAGTTCCTCACCAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttggccaaccgatggggcccttgttcttgtaatgactcatttccgttgttcagGTGTTCTGTCAGGAAAATACACTCCAGAAAAACCTCCTACCGGTCCTCGAGCAAACACATATACCCCTGAGTTCCTCACCAAG
                                     ctcatttcc  CT-rich tract
                            ttgtaat  TA-rich tract