Sequence
atgc intronic sequence ATGC exonic sequencegtatgctgcattaaccagttgtgacttttcagacgtgtcacttatcatttctgtttgctttttgttctatatattgacaatcattttggttatacagAGGATATCGGCAAAAGATGCACTTGACGCGGAGTATTTCTGGACTGATCCCTTACCGTGTGATCCAAAGAG
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-----------------------------
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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
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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
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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
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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
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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
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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
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----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
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gtgagtgtgatcatttgttacgcattgggatattgcttcacacttcagtatgctacgcttaaacatcctcgttacatcgaaacctcttatctgtgcattaattcatggttttgtctgtgcagCGAATCTGTGCTAAAGATGCACTCGACGCCGAATATTTCTGGACTGAACCCTTTCCCTGCCAACCAAGCAGMapped 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|CI288959EST: AGCACGCGCTGGATCTTTTAGAGAAGATGTTAACTTTGGATCCATCACAG AGGATATCGGCAAAAGATGCACTTGACGCGGAGTATTTCTGGACTGATCCC
genomic: AGCACGCGCTGGATCTTTTAGAGAAGATGTTAACTTTGGATCCATCACAGgtatgctgca ... ggttatacagAGGATATCGGCAAAAGATGCACTTGACGCGGAGTATTTCTGGACTGATCCC
EST:
gi|38471575|gb|CF955706.1|CF955706EST: 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:
30CTTTGATCAGCACGCGCTGGATCTTTTAGAGAAGATGTTAACTTTGGATCCATCACAGgtatgctgca ... ggttatacagAGGATATCGGCAAAAGATGCACTTGACGCGGAGTATTTCTGGACTGATCCCTTACCGTGTGATCCAAAGAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcatttctgtttgctttttgttctatatattgacaatcattttggttatacagAGGATATCGGCAAAAGATGCACTTGACGCGGAGTATTTCTGGACTGATCCCTTACCGTGTGATCCAAAGAG
tattgac putative branch site (score: 30)
tttttgttctatatat TA-rich tract