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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctgcattaaccagttgtgacttttcagacgtgtcacttatcatttctgtttgctttttgttctatatattgacaatcattttggttatacagAGGATATCGGCAAAAGATGCACTTGACGCGGAGTATTTCTGGACTGATCCCTTACCGTGTGATCCAAAGAG

Basic information

species Oryza sativa
transcript LOC_Os01g72790.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g72790.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G028452_T02 (Zea mays), 3'ss of exon 9
-------------------------------gtatgctgcattaaccagtt-gtgacttttcag----acgtgtcacttatcatttctgttt-gctttttgttctatatattgacaa----tcatttt-----ggttatacagAGGATATCGGCAAAAGATGCACTTGACGCGGAGTATTTCTGGACTGATCCCTTACCGTGTGATCCAAAGAG-----------------------------
| | | || ||| || || |||| | | || || | | || ||| | | | | || || | |||| ||| ||| |||| ||||||||||| ||||||||||||||||| || || |||||||||||| | | | | | ||
gtatactacattgtgtgaattttacagaaaattttatttgtttggccattttatgtttttttggtgctatttgctgtctacaaatactatttagatctgtttttcatgcctcaacaagttttcacttttttaaaattattcagAGGATATCAGCAAAAGATGCACTTGATGCAGAATATTTCTGGACTTCACGAGCGATGAGCGCGGCCGTGAACACCATGAGGATACGGGCCCCCAGATGGC

upper sequence: LOC_Os01g72790.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G019267_T01 (Zea mays), 3'ss of exon 10
----------------------------------------------gtatgctgcattaaccagttgtgacttttcagacgtgtcacttatcatttctgtttgctttttgttctatatattgacaatcattttggttatacagAGGATATCGGCAAAAGATGCACTTGACGCGGAGTATTTCTGGACTGATCCCTTACCGTGTGATCCAAAGAG
||| | || || ||| || | | || || |||| | | ||||| | | || ||||||||||| ||||||||||||||||| ||||| ||||||||||||||||||||||| || |||||||| ||
gtatgctacattgcgtgaattactgtaagtttaatttgtttagtcaaaatggttagttcctattccgtacttttctttggctgctgtgtgttgttcacacctgtcatttgggtcttcttttgacgcctctacaaatcattcagAGGATATCAGCAAAAGATGCACTTGATGCGGAATATTTCTGGACTGATCCCTTACCATGCGATCCAAAAAG

upper sequence: LOC_Os01g72790.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA20G10960.1 (Glycine max), 3'ss of exon 9
-----gtatgctgcattaaccagttgtgacttttca-gacgtgtcacttatcatttctgtttgctttttgttctatatattgacaatcattttggttatacagAGGATATCGGCAAAAGATGCACTTGACGCGGAGTATTTCTGGACTGATCCCTTACCGTGTGATCCAAAGAG
||| || || | || | ||| | || | ||| || | | | | || || | | | | | | ||| ||| | |||||| || | || || ||||||||||| || |||||||||||||| ||||| ||||| |||||||| |||||
caataatattactcactactgggagatgtccttttatgatgaatca-ttctgttcttgatctgtattctaatatttgtttgccaaattgattt--ctcgacagAGAATTACTGCCAAGGATGCACTTGATGCTGAGTATTTCTGGACGGATCCATTACCATGTGATCCTAAGAG

upper sequence: LOC_Os01g72790.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA14G04410.1 (Glycine max), 3'ss of exon 10
-------gtatgctgcattaaccagttgtgacttttcagacgtgtcacttatcatttctgtttgctttttgttctatatattgacaatcattttggttatacagAGGATATCGGCAAAAGATGCACTTGACGCGGAGTATTTCTGGACTGATCCCTTACCGTGTGATCCAAAGAG
||| | | | || ||| | | | || | || | ||| | || | | | | ||| |||| ||| || ||||||| || | || |||||||||||||| || |||||||||||||| ||||| |||||||| ||||| |||||
aagaaaattattatctgccacttggctgcatggttttatgataattaattttgtttatgatctgcatcctgatatttgt-ttgtcaat---tttatttctacagAGAATTACTGCGAAAGATGCACTTGATGCTGAGTATTTCTGGACAGATCCATTACCGTGCGATCCCAAGAG

upper sequence: LOC_Os01g72790.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA02G44400.1 (Glycine max), 3'ss of exon 11
----gtatgctgcattaaccagttgtgacttttcagacgtgtcacttatcatttctgtttgctttttgttctatatattgacaatcattttggtta-tacagAGGATATCGGCAAAAGATGCACTTGACGCGGAGTATTTCTGGACTGATCCCTTACCGTGTGATCCAAAGAG
| ||| ||| ||| |||| | | | | |||| || | | || || | ||| ||| |||| || ||||||| || | || |||||||||||||| || |||||||||||||| ||||| ||||| || ||||| |||||
aaaaaaaaatattatttgccacttg--gctttatgattttatgataattaattttctcatgatctgcgtcttaatttttgtttgtcaatttgatttctacagAGAATTACTGCGAAAGATGCACTTGATGCTGAGTATTTCTGGACAGATCCATTACCATGCGATCCCAAGAG

upper sequence: LOC_Os01g72790.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT5G10270.1 (Arabidopsis thaliana), 3'ss of exon 10
------------------------------------------------------gtatgctgcatt---aaccagttgtgacttttcagacgtgtcacttatcatttctgtttgctttttgttctatatattgacaatcattttggttatacagAGGATATCGGCAAAAGATGCACTTGACGCGGAGTATTTCTGGACTGATCCCTTACCGTGTGATCCAAAGAG
| | ||| || | | | || |||| | || | | | ||| | || | | | | | || ||| | | |||| ||||||||||| ||||| ||||| || ||||| || ||||||||||| || || ||||| ||||||||
gtatcagagacctttattcttattcccagcgaattatctttcttaaaaactgtcttttactgttttttggatgaaacatacctcttcaagtcaggacattgttaacaccatttagatatt-taatgtctcctttttttc-tttcccctgtgtagAGAATATCGGCAAAGGATGCTCTTGATGCCGAGTACTTTTGGACTGATCCGTTGCCATGTGACCCAAAGAG

upper sequence: LOC_Os01g72790.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv06s0009g01800.t01 (Vitis vinifera), 3'ss of exon 11
gtatgctgcattaaccagttgtgacttttcagacgtgt-cacttatcatttctgtttgctttttgttctatatattgacaatcattttgg--ttata-----cagAGGATATCGGCAAAAGATGCACTTGACGCGGAGTATTTCTGGACTGATCCCTTACCGTGTGATCCAAAGAG
|| | || ||||| || || | | ||||||| || || | | | | ||| || | | |||| ||| | |||| ||||| || || ||||||||||| || ||||||||||||||||| || || || |||||||| |||||
----tttgtttaaaggagttg-attttagcatatatacacacttatatttctctttctccctctctaatatcctatgtccctttttttaaaattacaaaatgtagAGAATATCTGCCAAGGATGCACTTGATGCTGAGTATTTCTGGACTGACCCTTTGCCTTGTGATCCCAAGAG

upper sequence: LOC_Os01g72790.1 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S121_162V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------gtatgctgcattaaccagttg--tgacttttcag-acgtgtcacttatcatttctgtttgctt-------tttgttctatatattgaca-atcattttggttatacagAGGATATCGGCAAAAGATGCACTTGACGCGGAGTATTTCTGGACTGATCCCTTACCGTGTGATCCAAAGAG
| | ||||| ||| | || ||||| | | | |||| | || || | | | | ||| | ||| | || ||||| | | ||| | || | || ||||||||||| ||||| || |||||||||||||| ||||| || || | |||| ||
gtgagtgtgatcatttgttacgcattgggatattgcttcacacttcagtatgctacgcttaaacatcctcgttacatcgaaacctcttatctgtgcattaattcatggttttgtctgtgcagCGAATCTGTGCTAAAGATGCACTCGACGCCGAATATTTCTGGACTGAACCCTTTCCCTGCCAACCAAGCAG

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|86897633|gb|CI288959.1|CI288959
EST:     AGCACGCGCTGGATCTTTTAGAGAAGATGTTAACTTTGGATCCATCACAG                         AGGATATCGGCAAAAGATGCACTTGACGCGGAGTATTTCTGGACTGATCCC
genomic: AGCACGCGCTGGATCTTTTAGAGAAGATGTTAACTTTGGATCCATCACAGgtatgctgca ... ggttatacagAGGATATCGGCAAAAGATGCACTTGACGCGGAGTATTTCTGGACTGATCCC
EST: gi|38471575|gb|CF955706.1|CF955706
EST:     AGCACGCGCTGGATCTTTTAGAGAAGATGTTAACTTTGGATCCATCACAG                         AGGATATCGGCAAAAGATGCACTTGACGCGGAGTATTTCTGGACTGATCCC
genomic: AGCACGCGCTGGATCTTTTAGAGAAGATGTTAACTTTGGATCCATCACAGgtatgctgca ... ggttatacagAGGATATCGGCAAAAGATGCACTTGACGCGGAGTATTTCTGGACTGATCCC

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: 58 (upstream exon), 71 (downstream exon)
Score: 30

CTTTGATCAGCACGCGCTGGATCTTTTAGAGAAGATGTTAACTTTGGATCCATCACAGgtatgctgca ... ggttatacagAGGATATCGGCAAAAGATGCACTTGACGCGGAGTATTTCTGGACTGATCCCTTACCGTGTGATCCAAAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcatttctgtttgctttttgttctatatattgacaatcattttggttatacagAGGATATCGGCAAAAGATGCACTTGACGCGGAGTATTTCTGGACTGATCCCTTACCGTGTGATCCAAAGAG
                             tattgac  putative branch site (score: 30)
 tttttgttctatatat  TA-rich tract