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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCGAGGGCGACACGGGGCCGCTCGTCTACCCGGCCGGCTTCCTCTACGTTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAGgtcgccgattgtcttcttgtctgctctgttctttccttggctcctcgccttcttcatgtgctcagttgtgctaaattttgatgagttgttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g07720.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g07720.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G066362_T02 (Zea mays), 5'ss of exon 3
GATCGAGGGCGACACGGGGCCGCTCGTCTACCCGGCCGGCTTCCTCTACGTTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAGgtcgccgattg------tcttcttgtctgc------tctgttctttccttggctcctcgc-cttcttcatg------tgctcagttgtgcta-aattttgatgagttg--ttgcag
||||||||| ||||| |||||  | |||||||||||||| ||||||||||| ||||||||| | ||| | || || |  ||||  |||||||| || |||||| | | |        |||  || || ||      ||  |||||   |||  ||||| | | || |||||      ||    |  ||| |  ||   |||||||||    |||||
GATCGAGGGAGACACAGGGCCATTGGTCTACCCGGCCGGATTCCTCTACGTCTACTCCGCCGTTAAGTTCCTTACGGGAGGCCGCGTCTTCCCTGCTCAGgtcacggctcagccaaatctgtttatcagcacgaactcgtttcttctgttgcttcctcccacctcatcatggtcagatgtctggcagtgttttaagactgatgagtttgtctgcag
















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|88368729|gb|CI645151.1|CI645151
EST:     TTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAG                         ATTTTGTTTGGTGTCCTGTACATTGTGAACCTTAGCCTTGTTCTGCTGATG
genomic: TTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAGgtcgccgatt ... gttgttgcagATTTTGTTTGGTGTCCTGTACATTGTGAACCTTAGCCTTGTTCTGCTGATG
EST: gi|88740960|gb|CI764468.1|CI764468
EST:     TTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAA                         ATTTTGTTTGGTGTCCTGTACAT
genomic: TTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAGgtcgccgatt ... gttgttgcagATTTTGTTTGGTGTCCTGTACAT
EST: gi|88765491|gb|CI774585.1|CI774585
EST:     TTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAG                         ATTTTGTTTGGTGTCCTGTACATTGTGAACCTTAGCC
genomic: TTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAGgtcgccgatt ... gttgttgcagATTTTGTTTGGTGTCCTGTACATTGTGAACCTTAGCC
EST: gi|88312323|gb|CI582661.1|CI582661
EST:     TTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAG                         ATTTTGTTTGGTGTCCTGTACATTGTGAACCTTAGCCTTGTTCTGCTGATG
genomic: TTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAGgtcgccgatt ... gttgttgcagATTTTGTTTGGTGTCCTGTACATTGTGAACCTTAGCCTTGTTCTGCTGATG
EST: gi|88576279|gb|CI670424.1|CI670424
EST:     TTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAG                         ATTTTGTTTGGTGTCCTGTACATTGTGAACCTTAGCCTTGTTCTGCTGATG
genomic: TTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAGgtcgccgatt ... gttgttgcagATTTTGTTTGGTGTCCTGTACATTGTGAACCTTAGCCTTGTTCTGCTGATG
EST: gi|88309854|gb|CI656988.1|CI656988
EST:     TTACTCCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAG                         ATTTTGTTTGGTGTCCTGTACATTGTGAACCTTAGCCTTGTTCT
genomic: TTACTCC-GCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAGgtcgccgatt ... gttgttgcagATTTTGTTTGGTGTCCTGTACATTGTGAACCTTAGCCTTGTTCT
EST: gi|88763364|gb|CI772825.1|CI772825
EST:     TTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAG                         ATTTTGTTTGGTGTCCTGTACATTGTGAACCTTAGCCTTGT
genomic: TTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAGgtcgccgatt ... gttgttgcagATTTTGTTTGGTGTCCTGTACATTGTGAACCTTAGCCTTGT
EST: gi|88592824|gb|CI710953.1|CI710953
EST:     TTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAG                         ATTTTGTTTGGTGTCCTGTACATTGTGAACCTT
genomic: TTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAGgtcgccgatt ... gttgttgcagATTTTGTTTGGTGTCCTGTACATTGTGAACCTT
EST: gi|88449328|gb|CI582200.1|CI582200
EST:     TTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAG                         ATTTTGTTTGGTGTCCTGTACATTGTGAACCTTAGCCTTGTTCTGGTGATG
genomic: TTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAGgtcgccgatt ... gttgttgcagATTTTGTTTGGTGTCCTGTACATTGTGAACCTTAGCCTTGTTCTGCTGATG
EST: gi|88327935|gb|CI648334.1|CI648334
EST:     TTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAG                         ATTTTGTTTGGTGTCCTGTACATTGTGAACCTTAGCCTTGTTCTGCT
genomic: TTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAGgtcgccgatt ... gttgttgcagATTTTGTTTGGTGTCCTGTACATTGTGAACCTTAGCCTTGTTCTGCT
EST: gi|88763578|gb|CI773025.1|CI773025
EST:     TTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAG                         ATTTTGTTTGGTGTCCTGTACATTGTGAACCTTAGCCTTGTTCT
genomic: TTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAGgtcgccgatt ... gttgttgcagATTTTGTTTGGTGTCCTGTACATTGTGAACCTTAGCCTTGTTCT
EST: gi|88741433|gb|CI764941.1|CI764941
EST:     TTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAG                         ATTTTGTTTGGTGTCCTGTACATTGTGAACCTTAGCCTTG
genomic: TTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAGgtcgccgatt ... gttgttgcagATTTTGTTTGGTGTCCTGTACATTGTGAACCTTAGCCTTG
EST: gi|88337341|gb|CI629631.1|CI629631
EST:     TTACTCCGCCATCAAGCTTCTCACCGCNCGGCCAAGTCTTCCCCGCGCAG                         ATTTTGTTTGGTGTC
genomic: TTACTCCGCCATCAAGCTTCTCACCGC-CGGCCAAGTCTTCCCCGCGCAGgtcgccgatt ... gttgttgcagATTTTGTTTGGTGTC

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: 48 (upstream exon), 46 (downstream exon)
Score: 9

GATCGAGGGCGACACGGGGCCGCTCGTCTACCCGGCCGGCTTCCTCTACGTTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAGgtcgccgatt ... gttgttgcagATTTTGTTTGGTGTCCTGTACATTGTGAACCTTAGCCTTGTTCTGCTGATGTACGTCAAGACTGAAGTGGTAGGGATGCCTGTGTTCTCTCCTGGTTTGC




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCGAGGGCGACACGGGGCCGCTCGTCTACCCGGCCGGCTTCCTCTACGTTTACTCCGCCATCAAGCTTCTCACCGCCGGCCAAGTCTTCCCCGCGCAGgtcgccgattgtcttcttgtctgctctgttctttccttggctcctcgccttcttcatgtgctcagttgtgctaaattttgatgagttgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT