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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggcaatattctctctgtacctgctatctgtctctcatatagtgctttttacttatttttatcttcgttttttttcagGGGTACAATTAGATATGCCAGTGTCCATGCCCATTTAGGCCGTACTGGTAGTAGGAGGGATGATTTAGAGTCATTGGCGTACACCCTTATATTTCTAATA

Basic information

species Oryza sativa
transcript LOC_Os07g07560.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G017204_T02 (Zea mays), 3'ss of exon 2
----------------------gttggcaatattctctctgtacctgctatctgtctctcatatagtgctttttacttatttttatcttcgtttttttt--cagGGGTACAATTAGATATGCCAGTGTCCATGCCCATTTAGGCCGTACTGGTAGTAGGAGGGATGATTTAGAGTCATTGGCGTACACCCTTATATTTCTAATA
                      |||||  ||||||||    || ||||  | |  |  | ||| | || | ||   | |  | |    | |||| ||||  ||| || |||||||||||||| ||||||||||||||||| ||  | |||||||||||||||||||||||||||| | |||| ||||||||||| ||  | |||
atcaacggcctgatatctttaggttggttatattctcat--tagctgcagttt-ccattaata-aatggtcttcgttaacctatcctcttgtttctttttgcagTGGAACAATTAGATATGCGAGTGTCCATGCCCATTTGGGGAGCACTGGTAGTAGGAGGGATGATTTAGAGTTACTGGCATACACCCTTATTTTCTTGATA

upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G110085_T01 (Zea mays), 3'ss of exon 4
gttggcaatattctctctgtacctgctatctgtctctcatatagtgctttttacttatttttatcttcgtttttttt--cagGGGTACAATTAGATATGCCAGTGTCCATGCCCATTTAGGCCGTACTGGTAGTAGGAGGGATGATTTAGAGTCATTGGCGTACACCCTTATATTTCTAATA
|||||  ||||||||    || ||||  | |  |  | ||| | || | ||   | |  | |    | |||| ||||  |||||| |||||||||||||| ||||||||||| ||||| || || |||||||||||||||||||||||||||||| | || ||||||||||| || || |||
gttggttatattctcat--tagctgcagttt-ccattaata-aatggtcttccttaacctatcctcttgtttctttttgcagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCACTCGCATACACCCTTATTTTCCTGATA

upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G017204_T01 (Zea mays), 3'ss of exon 1
gttggcaatattctctctgtacctgctatctgtctctcatatagtgctttttacttatttttatcttcgtttttttt--cagGGGTACAATTAGATATGCCAGTGTCCATGCCCATTTAGGCCGTACTGGTAGTAGGAGGGATGATTTAGAGTCATTGGCGTACACCCTTATATTTCTAATA
|||||  ||||||||    || ||||  | |  |  | ||| | || | ||   | |  | |    | |||| ||||  ||| || |||||||||||||| ||||||||||||||||| ||  | |||||||||||||||||||||||||||| | |||| ||||||||||| ||  | |||
gttggttatattctcat--tagctgcagttt-ccattaata-aatggtcttcgttaacctatcctcttgtttctttttgcagTGGAACAATTAGATATGCGAGTGTCCATGCCCATTTGGGGAGCACTGGTAGTAGGAGGGATGATTTAGAGTTACTGGCATACACCCTTATTTTCTTGATA

upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G458035_T01 (Zea mays), 3'ss of exon 7
gttggcaatattctctctgtacctgctatctgtctctcatatagtgctttttacttatttttatcttcgtttttttt--cagGGGTACAATTAGATATGCCAGTGTCCATGCCCATTTAGGCCGTACTGGTAGTAGGAGGGATGATTTAGAGTCATTGGCGTACACCCTTATATTTCTAATA
|||||  ||||||||    || ||| || ||  |  | ||| | || | ||   | |  | | |  | |||| ||||  |||||| |||||||||||||| ||||||||||| ||||| || || |||||||||||||||||||||||||||||| |||| ||||||||||| || || |||
gttggttatattctcat--tagctg-tagcttccattaata-aatggtcttccttaacctatcttcttgtttctttttgcagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCACTGGCATACACCCTTATTTTCCTGATA

upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G508368_T01 (Zea mays), 3'ss of exon 2
gttggcaatattctctctgtacctgctatctgtctctcatatagtgctttttacttatttttatcttcgttttttttcagGGGTACAATTAGATATGCCAGTGTCCATGCCCATTTAGGCCGTACTGGTAGTAGGAGGGATGATTTAGAGTCATTGGCGTACACCCTTATATTTCTAATA
|||||  ||||||||  |        | ||  |   | | || ||  |  |||     |  |||  |  | ||||| |||||| |||||||||||||| ||||||||||| ||||| ||  | |||||||||||||||||||||||||||| | |||| ||||||||||| || || |||
gttggttatattctcattagctgcagtttccattaataa-atggtcttcgttaacctatcctataatt-tctttttgcagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGTGCACTGGTAGTAGGAGGGATGATTTAGAGTTACTGGCATACACCCTTATTTTCCTGATA

upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G082099_T01 (Zea mays), 3'ss of exon 3
gttggcaatattctctctgtacctgctatctgtctctcatatagtgctttttacttatttttatcttcgttttttttc--agGGGTACAATTAGATATGCCAGTGTCCATGCCCATTTAGGCCGTACTGGTAGTAGGAGGGATGATTTAGAGTCATTGGCGTACACCCTTATATTTCTAATA
|||||  ||||||||    || |||| | ||  |  | ||| | || | ||   | |  | | |  | |||| ||||   ||||| |||||||||||||| ||||||||||| ||||| || || |||||||||||||||||||||||||||||| |||| ||||||||||| || || |||
gttggttatattctcat--tagctgc-agcttccattaata-aatggtcttccttaacctatcttcttgtttctttttggagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCAATGGCATACACCCTTATTTTCCTGATA

upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G480263_T01 (Zea mays), 3'ss of exon 5
--------------------gttggcaatattctctctgtacc-tgctatctgtctctcatatagtgcttttta-cttatttttatcttcgttttttttcagGGGTACAATTAGATATGCCAGTGTCCATGCCCATTTAGGCCGTACTGGTAGTAGGAGGGATGATTTAGAGTCATTGGCGTACACCCTTATATTTCTAATA
                     ||   |||||  |  |  || | |   || ||  |   | || ||  |  ||| | |||  |  | ||  | ||||| |||||| |||||||||||||| ||||||||||| ||||| ||  | |||||||||||||||||||||||||||||| || | ||||||||||| || || |||
cttggcaatattttagtttgcttctgaatatgattgcactatcatatcatgtgcttaggaaatggtcttccttaacctatcctcttgtt--tctttttgcagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGTGCACTGGTAGTAGGAGGGATGATTTAGAGTCACTGTCATACACCCTTATTTTCCTGATA

upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 9
gttggcaatattctctctgtacctgctatctgtctctcatatagtgctttttacttatttttatcttcgtttttttt--cagGGGTACAATTAGATATGCCAGTGTCCATGCCCATTTAGGCCGTACTGGTAGTAGGAGGGATGATTTAGAGTCATTGGCGTACACCCTTATATTTCTAATA
|||||  ||||||||    || ||||  | |  |  | ||| | || | ||   | |  | |    | |||| ||||  |||||| |||||||||||||| ||||||||||| ||||| || || |||||||||||||||||||||||||||||| |||| ||||||||||| || || |||
gttggttatattctcat--tagctgcagttt-ccattaata-aatggtcttccttaacctatcctcttgtttctttttgcagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCACTGGCATACACCCTTATTTTCCTGATA

upper sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 9
gttggcaatattctctctgtacctgctatctgtctctcatatagtgctttttacttatttttatcttcgttttttttcagGGGTACAATTAGATATGCCAGTGTCCATGCCCATTTAGGCCGTACTGGTAGTAGGAGGGATGATTTAGAGTCATTGGCGTACACCCTTATATTTCTAATA
|||||  ||||||||   | | | | | | |   |   | || | | | | ||     |  | |     | ||||| |||||| |||||||||||||| ||||||||||| ||||| || || |||||||||||||||||||||||||||||| |||| ||||||||||| || || || 
gttggtcatattctcatagcagcagtttttt--ttaataaatggcgttctgtaacctatcctcttggtttctttttgcagGGGAACAATTAGATATGCGAGTGTCCATGCTCATTTGGGGCGCACTGGTAGTAGGAGGGATGATTTAGAGTCACTGGCATACACCCTTATTTTCCTGATT

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|58659496|gb|CK048176.1|CK048176
EST:     GAGTCATCAGGGCAACATGTTGATTATGACCAAAGGCCTGATATCTTTAG                         GGGTACAATTAGATATGCCAGTGTCCATGCCCATTTAGGCCGTACTGGTAG
genomic: GAGTCATCAGGGCAACATGTTGATTATGACCAAAGGCCTGATATCTTTAGgttggcaata ... tttttttcagGGGTACAATTAGATATGCCAGTGTCCATGCCCATTTAGGCCGTACTGGTAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatctgtctctcatatagtgctttttacttatttttatcttcgttttttttcagGGGTACAATTAGATATGCCAGTGTCCATGCCCATTTAGGCCGTACTGGTAGTAGGAGGGATGATTTAGAGTCATTGGCGTACACCCTTATATTTCTAATA
                   tgctttttacttattt  CT-rich tract
                      tttttacttattttta  TA-rich tract