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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCCTCCTTTCAGCTTGTGTTTGCACCGATTGATGATTTCCCAGATGAAACTCCATTGATTTCTTCTGGCTTCCGTGTTATACCACTTGATATGAAAACAgttaagtgctgccaaattccaaattacattatccattacccttttgactgttccctaggtccatatgtgctttatttgctgttgcattaatctgtgatga...

Basic information

species Oryza sativa
transcript LOC_Os03g01890.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01890.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G158742_T01 (Zea mays), 5'ss of exon 1
ATCCTCCTTTCAGCTTGTGTTTGCACCGATTGATGA---TTTCCCAGATGAAACTCCATTGATTTCTTCTGGCTTCCGTGTTATACCACTTGATATGAAAACAgttaagtgctgccaaattccaaattacattatccattaccct-tttgactgttccct--aggtccatatgtgctttatttgctgttgcattaatctgtgatga
   |||||| ||||||||||||||||||||||||||   ||| || |||||  ||||||||||||| ||| |||| ||||| |||||||||||||||||||||||||||     | ||   | | ||| | || ||  || |  |  |||   | || ||  |  ||| | | |  | | ||| |  ||    | |    |     
---CTCCTTCCAGCTTGTGTTTGCACCGATTGATGAGCATTTTCCGGATGATGCTCCATTGATTTCCTCTAGCTTTCGTGTCATACCACTTGATATGAAAACAgttaagcatcactaa---caacatttccttttctttttcgttgcttgggcggtcgcttcatttccttgtctattatgtttacgattatccttaggactatctc

upper sequence: LOC_Os03g01890.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G042250_T03 (Zea mays), 5'ss of exon 15
ATCCTCCTTTCAGCTTGTGTTTGCACCGATTGATGA---TTTCCCAGATGAAACTCCATTGATTTCTTCTGGCTTCCGTGTTATACCACTTGATATGAAAACAgttaagtgctgccaaattccaaattacattatccattaccct-tttgactgttccct--aggtccatatgtgctttatttgctgttgcattaatctgtgatga
   |||||| ||||||||||||||||| ||||||||   ||| || |||||  ||||||||||||| |||||||| ||||| |||||||||||||||||||||||||||     | ||   | | ||||| || ||  || |  |  |||   | || ||  |  ||| | | |  | | ||| |  ||   ||||    |  |  
---CTCCTTCCAGCTTGTGTTTGCACCAATTGATGAGCATTTTCCGGATGATGCTCCATTGATTTCCTCTGGCTTTCGTGTCATACCACTTGATATGAAAACAgttaagcatcactaa---caacattaccttttctttttcgttgcttgggcggtcgcttcatttccttgtctattatgtttacaattatcttaagactttctcc

upper sequence: LOC_Os03g01890.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G109987_T05 (Zea mays), 5'ss of exon 14
ATCCTCCTTTCAGCTTGTGTTTGCACCGATTGATGA---TTTCCCAGATGAAACTCCATTGATTTCTTCTGGCTTCCGTGTTATACCACTTGATATGAAAACAgttaagtgctgccaaattccaaattacattatccattaccctt-ttgactgttccctaggtccatatgtgctttatttgctgttgcattaatctgtgatga--
   |||||| ||||||||||||||||| ||||||||   ||||||||||||  |||||||||||||||||||||| ||||| |||||||||||| ||||||||||||||   ||||||   | | ||||| || ||| ||    |  |||  ||  |    | | ||| |     |   ||    ||  | | |||  | |     
---CTCCTTCCAGCTTGTGTTTGCACCAATTGATGAGCATTTCCCAGATGATGCTCCATTGATTTCTTCTGGCTTTCGTGTCATACCACTTGATGTGAAAACAgttaagcattgccaa---caacattaccttttccctttttttccttgcttgggcagccgcttcatttccttgtctattatgtttataattatccttaacatgt

upper sequence: LOC_Os03g01890.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G098704_T01 (Zea mays), 5'ss of exon 1
ATCCTCCTTTCAGCTTGTGTTTGCACCGATTGATGA---TTTCCCAGATGAAACTCCATTGATTTCTTCTGGCTTCCGTGTTATACCACTTGATATGAAAACAgttaagtgctgccaaattccaaattacattatccattaccct-tttgactgttccct--aggtccatatgtgctttatttgctgttgcattaatctgtgatga
   |||||| ||||||||||||||||||||||||||   ||| || |||||  ||||||||||||| ||| |||| | ||| |||||||||||||||||||||||||||     | ||   | | ||| | || ||  || |  |  |||   | || ||  |  ||| | | |  | | ||| |  ||    | |    |     
---CTCCTTCCAGCTTGTGTTTGCACCGATTGATGAGCATTTTCCGGATGATGCTCCATTGATTTCCTCTAGCTTTCATGTCATACCACTTGATATGAAAACAgttaagcatcactaa---caacatttccttttctttttcgttgcttgggcggtcgcttcatttccttgtctattatgtttacgattatccttaggactatctc

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|58612749|gb|CK040461.1|CK040461
EST:     CTCCATTGATTTCTTCTGGCTTCCGTGTTATACCACTTGATATGAAAACA                         GATGGTGCATCCTCTGGTAGGACATTA
genomic: CTCCATTGATTTCTTCTGGCTTCCGTGTTATACCACTTGATATGAAAACAgttaagtgct ... tttcatgcagGATGGTGCATCCTCTGGTAGGACATTA
EST: gi|218500446|gb|FG953830.1|FG953830
EST:     CCAC-TGATAT-AAAACA                         GATGGTGCATCCTCTGGTAGGACATTA-ATTTGGCATCTAGTCTTGAAGTA
genomic: CCACTTGATATGAAAACAgttaagtgct ... tttcatgcagGATGGTGCATCCTCTGGTAGGACATTAGATTTGGCATCTAGTCTTGAAGTA
EST: gi|58683794|gb|CK072481.1|CK072481
EST:     CTCCATTGATTTCTTCTGGCTTCCGTGTTATACCACTTGATATGAAAACA                         GATGGTGCATCCTCTGGTAGGACATTAGATTTGGCATCTAGTCTTGAAGTA
genomic: CTCCATTGATTTCTTCTGGCTTCCGTGTTATACCACTTGATATGAAAACAgttaagtgct ... tttcatgcagGATGGTGCATCCTCTGGTAGGACATTAGATTTGGCATCTAGTCTTGAAGTA
EST: gi|58669786|gb|CK058472.1|CK058472
EST:     CTCCATTGATTTCTTCTGGCTTCCGTGTTATACCACTTGATATGAAAACA                         GATGGTGCATCCTCTGGTAGGACATTAGATTTGGCATCTAGTCTTGAAGTA
genomic: CTCCATTGATTTCTTCTGGCTTCCGTGTTATACCACTTGATATGAAAACAgttaagtgct ... tttcatgcagGATGGTGCATCCTCTGGTAGGACATTAGATTTGGCATCTAGTCTTGAAGTA

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: 56 (upstream exon), 70 (downstream exon)
Score: 19

ATCCTCCTTTCAGCTTGTGTTTGCACCGATTGATGATTTCCCAGATGAAACTCCATTGATTTCTTCTGGCTTCCGTGTTATACCACTTGATATGAAAACAgttaagtgct ... tttcatgcagGATGGTGCATCCTCTGGTAGGACATTAGATTTGGCATCTAGTCTTGAAGTAGGTTCAGCAACAGCTCAAGCCTCCGGAGATGCATCTGCAGATGATTGTA




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