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'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAATTTGTGAAATCTGGTTTGCCATGTCTTGGATTCTTGATCAATTCCCCAAGTGGTTTCCTATCGAGAGAGAGACTTACCTTGATCGATTGACATTGAGgttggttactgttactagctaggtatacttgttatccatcattctgaattaccaagactaattgtttgcttttatag

Basic information

species Oryza sativa
transcript LOC_Os07g24190.3
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g24190.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G028353_T02 (Zea mays), 5'ss of exon 6
TAATTTGTGAAATCTGGTTTGCCATGTCTTGGATTCTTGATCAATTCCCCAAGTGGTTTCCTATCGAGAGAGAGACTTACCTTGATCGATTGACATTGAGgttggttactgttactagctaggtatacttgttatccatcattctgaattaccaagactaattgtttgcttttatag
| || |||||||||||||||||||||||||||||||||||||||||||| |||||||| ||||| ||||||||||||||||| || ||  || || ||||||| ||  ||||||| | |||   ||   |    ||  |   | |   ||     || |||||| |||  |  ||||
TTATCTGTGAAATCTGGTTTGCCATGTCTTGGATTCTTGATCAATTCCCAAAGTGGTTCCCTATAGAGAGAGAGACTTACCTAGACCGGCTGTCACTGAGgttagtcgctgttaccacctacaaatctataccttctcttccttttgttt--tgtgattaattgcttgtctggatag

upper sequence: LOC_Os07g24190.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G025231_T02 (Zea mays), 5'ss of exon 6
TAATTTGTGAAATCTGGTTTGCCATGTCTTGGATTCTTGATCAATTCCCCAAGTGGTTTCCTATCGAGAGAGAGACTTACCTTGATCGATTGACATTGAGgttggttactgttactagctaggtatacttgttatccatcattctgaattaccaagactaattgtttgcttttatag
| || |||||||||||||||||||||||||||||||||||||||||||| |||||||| ||||| ||||||||||||||||| || ||  || || ||||||| ||| ||||| | | |||   ||| | |   ||  || | |||   |    |||||||||  |||  |  ||||
TTATCTGTGAAATCTGGTTTGCCATGTCTTGGATTCTTGATCAATTCCCAAAGTGGTTCCCTATTGAGAGAGAGACTTACCTAGACCGGCTGTCACTGAGgttagttgctgttgccacctactaatattagccttc--tcttcctgttgttttgagactaattacttgtatggatag
















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|33678973|gb|CF307212.1|CF307212
EST:     AAGTGGTTTCCTATCGAGAGAGAGACTTACCTTGATCGATTGACATTGAG                         GTTTGACAAGGAAGGCCAAACATCTCAACTTGCACCAATCGATTTCTTTGT
genomic: AAGTGGTTTCCTATCGAGAGAGAGACTTACCTTGATCGATTGACATTGAGgttggttact ... gcttttatagGTTTGACAAGGAAGGCCAAACATCTCAACTTGCACCAATCGATTTCTTTGT
EST: gi|58657578|gb|CK046258.1|CK046258
EST:     AAGTGGTTTCCTATCGAGAGAGAGACTTACCTTGATCGATTGACATTGAG                         GTTTGACAAGGAAGGCCAAACATCTCAACTTGCACCAATCGATTTCTTTGT
genomic: AAGTGGTTTCCTATCGAGAGAGAGACTTACCTTGATCGATTGACATTGAGgttggttact ... gcttttatagGTTTGACAAGGAAGGCCAAACATCTCAACTTGCACCAATCGATTTCTTTGT
EST: gi|29681197|gb|CB677472.1|CB677472
EST:     AAGTGGTTTCCTATCGAGAGAGAGACTTACCTTGATCGATTGACATTGAG                         GTTTGACAAGGAAGGCCAAACATCTCAACTTGCACCAATCGATTTCTTTGT
genomic: AAGTGGTTTCCTATCGAGAGAGAGACTTACCTTGATCGATTGACATTGAGgttggttact ... gcttttatagGTTTGACAAGGAAGGCCAAACATCTCAACTTGCACCAATCGATTTCTTTGT
EST: gi|29680102|gb|CB676377.1|CB676377
EST:     AAGTGGTTTCCTATCGAGAGAGAGACTTACCTTGATCGATTGACATTGAG                         GTTTGACAAGGAAGGCCAAACATCTCAACTTGCACCAATCGATTTCTTTGT
genomic: AAGTGGTTTCCTATCGAGAGAGAGACTTACCTTGATCGATTGACATTGAGgttggttact ... gcttttatagGTTTGACAAGGAAGGCCAAACATCTCAACTTGCACCAATCGATTTCTTTGT
EST: gi|29624917|gb|CB629928.1|CB629928
EST:     ACCTGGTTTCCTATCGAGAGAGAGACTTACCTTGATCGATTGACATTGAG                         GTTTGACAAGGAAGGCCAAACATCTCAACTTGCACCAATCGATTTCTTTGT
genomic: AAGTGGTTTCCTATCGAGAGAGAGACTTACCTTGATCGATTGACATTGAGgttggttact ... gcttttatagGTTTGACAAGGAAGGCCAAACATCTCAACTTGCACCAATCGATTTCTTTGT
EST: gi|58693391|gb|CK082078.1|CK082078
EST:     AAGTGGTTTCCTATCGAGAGAGAGACTTACCTTGATCGATTGACATTGAG                         GTTTGACAAGGAAGGCCAAACATCTCAACTTGCACCAATCGATTTCTTTGT
genomic: AAGTGGTTTCCTATCGAGAGAGAGACTTACCTTGATCGATTGACATTGAGgttggttact ... gcttttatagGTTTGACAAGGAAGGCCAAACATCTCAACTTGCACCAATCGATTTCTTTGT
EST: gi|29635077|gb|CB640086.1|CB640086
EST:     GATCGATTGACATTGAG                         GTGTGACAAGGAAGGCCAAACATCTCAACTTGCACCAATCGATTTCTTTGT
genomic: GATCGATTGACATTGAGgttggttact ... gcttttatagGTTTGACAAGGAAGGCCAAACATCTCAACTTGCACCAATCGATTTCTTTGT
EST: gi|29681223|gb|CB677498.1|CB677498
EST:     AAGTGGTTTCCTATCGAGAGAGAGACTTACCTTGATCGATTGACATTGAG                         GTTTGACAAGGAAGGCCAAACATCTCAACTTGCACCAATCGATTTCTTTGT
genomic: AAGTGGTTTCCTATCGAGAGAGAGACTTACCTTGATCGATTGACATTGAGgttggttact ... gcttttatagGTTTGACAAGGAAGGCCAAACATCTCAACTTGCACCAATCGATTTCTTTGT
EST: gi|29632077|gb|CB637086.1|CB637086
EST:     GATCGATTGACATTGAG                         GTTTGACAAGGAAGGCCAAACATCTCAACTTGCACCAATCGATTTCTTTGT
genomic: GATCGATTGACATTGAGgttggttact ... gcttttatagGTTTGACAAGGAAGGCCAAACATCTCAACTTGCACCAATCGATTTCTTTGT

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), 75 (downstream exon)
Score: 62

TAATTTGTGAAATCTGGTTTGCCATGTCTTGGATTCTTGATCAATTCCCCAAGTGGTTTCCTATCGAGAGAGAGACTTACCTTGATCGATTGACATTGAGgttggttact ... gcttttatagGTTTGACAAGGAAGGCCAAACATCTCAACTTGCACCAATCGATTTCTTTGTCAGTACTGTTGATCCCTTGAAGGAACCTCCTTTGGTCACAGCAAACACT




<











<


<