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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_Os07g07560.1
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




















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: 63 (upstream exon), 63 (downstream exon)
Score: 27

CATCGAAATGGAGGGAGTCATCAGGGCAACATGTTGATTATGACCAAAGGCCTGATATCTTTAGgttggcaata ... tttttttcagGGGTACAATTAGATATGCCAGTGTCCATGCCCATTTAGGCCGTACTGGTAGTAGGAGGGATGATTTAGAGTCATTGGCGTACACCCTTATATTTCTAATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatctgtctctcatatagtgctttttacttatttttatcttcgttttttttcagGGGTACAATTAGATATGCCAGTGTCCATGCCCATTTAGGCCGTACTGGTAGTAGGAGGGATGATTTAGAGTCATTGGCGTACACCCTTATATTTCTAATA
                   tgctttttacttattt  CT-rich tract
                      tttttacttattttta  TA-rich tract