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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgtcccagagcttgattgtcttgttccgtgaatgacgcgccattgctacattacttttcatgactgattttcttttctgttcaatcacattgtcaaagATTGAATTGGAGGACCCGTTGGAAAATCTTGGAGTGAAGCTGGTCAGACAGGCTGGTGCCAGGACGAACGATGTTGCTGGTGATGGTTGTACCACTTCCA

Basic information

species Oryza sativa
transcript 13114.m00140
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: 13113.m00214 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G042253_T01 (Zea mays), 3'ss of exon 1
actgtcccagagcttgat-tgtcttgttccgtgaatgacgcgccattgctacattacttttcatgactgattttcttttctgttcaatcacattgt-----caaagATTGAATTGGAGGACCCGTTGGAAAATCTTGGAGTGAAGCTGGTCAGACAGGCTGGTGCCAGGACGAACGATGTTGCTGGTGATGGTTGTACCACTTCCA
||| | | ||| ||| |||||| || | | | || || || | ||| | ||| | ||||||||| ||| ||||| |||||||| || || || |||||||||||||||||||||||| |||||||||| || ||||| || ||| |||| || |||||||||||||| ||||
--tgtactaatatgagatgcttctcgttccg---atcatgtcctttttctg-atcatgttttaatacttccaatgcccatgtatcaatcacactgtgtcattcaagATCGAATTGGAAGATCCATTAGAAAATCTTGGAGTGAAGCTGGTCCGACAGGCTGGAGCAAGGACCAATGATATTGCAGGAGATGGTTGTACCACATCCA

upper sequence: 13113.m00214 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G13980.1 (Glycine max), 3'ss of exon 2
-actgtcccagagcttgattgtcttgttccgtgaatgacgcgccattgctacattacttttcatgactgattttcttttctgttcaatcacattgtcaaagATTGAATTGGAGGACCCGTTGGAAAATCTTGGAGTGAAGCTGGTCAGACAGGCTGGTGCCAGGACGAACGATGTTGCTGGTGATGGTTGTACCACTTCCA
||| | || | || | || | ||| | | || | |||| ||| | | | || ||| | || || | ||||||||||||| || |||||||||||| ||||||| || |||| ||||| |||||||| | ||||| || ||||||||||| | || || ||
tgttgtttgtgtagtttaatgaacttctctat-aatcaggtctaataacaacatggttttgtgccttttgtatgaacttagtttccctaacgttatatcagATTGAATTGGAAGATCCGTTGGAAAATGTTGGAGTTAAATTGGTGAGACAAGCTGGTGCTAAAACGAATGACCAAGCTGGTGATGGCTCAACTACATCTG

upper sequence: 13113.m00214 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA01G09520.1 (Glycine max), 3'ss of exon 2
-actgtcccagagcttgattgtcttgttccgtgaatgacgcgccattgctacattacttttcatgactgattttcttttctgtt-caatcacattgtcaaagATTGAATTGGAGGACCCGTTGGAAAATCTTGGAGTGAAGCTGGTCAGACAGGCTGGTGCCAGGACGAACGATGTTGCTGGTGATGGTTGTACCACTTCCA
| | || | || | ||| | ||| | || | |||| ||| | ||| | | |||| | | | || | ||||||||||||| || |||||||||||| ||||||| || |||| ||||| |||||||| | || ||||| ||||||||||| | || || ||
tgtggcttgtgtagtttaatgaacttttctat-aatctggtctaataacaacatggttttgtgcc-ttaattatgaaatttgtttccctaatgttatatcagATTGAATTGGAAGATCCGTTGGAAAATGTTGGAGTTAAATTGGTGAGACAAGCTGGTGCTAAAACCAACGACCAAGCTGGTGATGGCTCAACTACATCTG

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|58612717|gb|CK040429.1|CK040429
EST:     AGTACGGCCCTCCCAAGATCGTCAACGATGGGGAGACGGTCCTCAAGGAG                         ATTGAATTGGAGGACCCGTTGGAAAATCTTGGAGTGAAGCTGGTCAGACAG
genomic: AGTACGGCCCTCCCAAGATCGTCAACGATGGGGAGACGGTCCTCAAGGAGgtaatgtgcc ... attgtcaaagATTGAATTGGAGGACCCGTTGGAAAATCTTGGAGTGAAGCTGGTCAGACAG
EST: gi|58608898|gb|CK036931.1|CK036931
EST:     AGTACGGNCCTCCCAAGATCGTCAACGATGGGGAGACGGTCCTCAAGGAG                         ATTGAATTGGAGGACCCGTTGGAAAATCTTGGAGTGAAGCTGGTCAGACAG
genomic: AGTACGGCCCTCCCAAGATCGTCAACGATGGGGAGACGGTCCTCAAGGAGgtaatgtgcc ... attgtcaaagATTGAATTGGAGGACCCGTTGGAAAATCTTGGAGTGAAGCTGGTCAGACAG
EST: gi|58693360|gb|CK082047.1|CK082047
EST:     AGTACGGCCCTCCCAAGATCGTCAACGATGGGGAGACGGTCCTCAAGGAG                         ATTGAATTGGAGGACCCGTTGGAAAATCTTGGAAGTGAAGCTGGTCAGACA
genomic: AGTACGGCCCTCCCAAGATCGTCAACGATGGGGAGACGGTCCTCAAGGAGgtaatgtgcc ... attgtcaaagATTGAATTGGAGGACCCGTTGGAAAATCTTGGA-GTGAAGCTGGTCAGACA
EST: gi|58691467|gb|CK080154.1|CK080154
EST:     AGTACGGCCCTCCCAAGATCGTCAACGATGGGGAGACGGTCCTCAAGGAG                         ATTGAATTGGAGGACCCGTTGGAAAATCTTGGAGTGAAGCTGGTCAGACAG
genomic: AGTACGGCCCTCCCAAGATCGTCAACGATGGGGAGACGGTCCTCAAGGAGgtaatgtgcc ... attgtcaaagATTGAATTGGAGGACCCGTTGGAAAATCTTGGAGTGAAGCTGGTCAGACAG

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: 39 (upstream exon), 46 (downstream exon)
Score: 3

GGTCGGGGTGACGCTGGGGCCCAAGGGGAGGAACGTGGTGCTGAGCAACAAGTACGGCCCTCCCAAGATCGTCAACGATGGGGAGACGGTCCTCAAGGAGgtaatgtgcc ... attgtcaaagATTGAATTGGAGGACCCGTTGGAAAATCTTGGAGTGAAGCTGGTCAGACAGGCTGGTGCCAGGACGAACGATGTTGCTGGTGATGGTTGTACCACTTCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctacattacttttcatgactgattttcttttctgttcaatcacattgtcaaagATTGAATTGGAGGACCCGTTGGAAAATCTTGGAGTGAAGCTGGTCAGACAGGCTGGTGCCAGGACGAACGATGTTGCTGGTGATGGTTGTACCACTTCCA
                  gactgat  putative branch site (score: 3)
 attttctttt  TA-rich tract