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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtcttgcctcaggtttatcatagtatagtttcccaatttacagtatacccttttctgataaatgttgaatttgactgaaaagtggagcatttgttttttttttctttatgatgcagAAGCAAGGCAAGAATTTAAAGATTCTTGTTCAGTTCAAGTGTACAGTATCCAGGCTTGTATTCCAAAAGATACTGCTGTACTTTGGAATCCTGAATTTGT

Basic information

species Oryza sativa
transcript LOC_Os01g10690.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10690.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G481471_T01 (Zea mays), 3'ss of exon 1
-------------gtaatgtcttgcctcaggtttatcatagtatagtttcccaatttacagtatacc-cttttctgataaatgttgaatttgactgaaaagtggagcatttgttttttttttctttatgatgcagAAGCAAGGCAAGAATTTAAAGATTCTTGTTCAGTTCAAGTGTACAGTATCCAGGCTTGTATTCCAAAAGATACTGCTGTACTTTGGAATCCTGAATTTGT
| | | | |||| | || || | || | | | | |||| || | || ||| |||||||| || |||| |||| | || | ||| | | ||| | | || | |||||| || | || | | | || | || |
caaattttcaaagattcttgttcggttcagatctacagta-tccaggcctgtattccaaaagatacagctatactttggaatcatgaatttgtgcatgcagAGGAG-ATTTTCAACCAGCCTTTTGACTATG--AGAACTGTTTGAGAGATAATAGGTA-TTGTTCTCTTAGCCCATTTGGTTTTC---TCCCAAGTCTCAGGCATGC---------------------------

upper sequence: LOC_Os01g10690.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G043623_T02 (Zea mays), 3'ss of exon 1
------------------gtaatgtcttgcctcaggtttatcatagtatagtttcccaatttacagtatacccttttctgataaatgttgaatttgactgaaaagtggagcatttgttttttttttctttatgatgcagAAGCAAGGCAAGAATTTAAAGATTCTTGTTCAGTTCAAGTGTACAGTATCCAGGCTTGTATTCCAAAAGATACTGCTGTACTTTGGAATCCTGAATTTGT
| | | | |||| | || || | || | | | | |||| || || ||| |||||||| | ||||| ||| | || |||| ||| | || ||| | |||||| || | || | | | | ||
caaggcaaattttcaaagattcttgttcggttcagatctacagta-tccaggcctgtattccaaaagatacagcttactttggaatcatgaatttgtgcagGCAAAGGAGCTTTT----CAACCAGCCTTTTGATTATGAAAACTGTTTGAGATATAATAGGTATTGTTCTCTTAGCCCATTTGGTTTTCT--CCCAAGTCTCAGGC--------------------------------

upper sequence: LOC_Os01g10690.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G435338_T01 (Zea mays), 3'ss of exon 8
----------------gtaatgtcttgcctcaggtttatcatagtatagtttcccaatttacagtatacccttttctgataaatgt-tgaatttgactgaaaagtggagcatttgttt------tttttttctttatgatgcagAAGCAAGGCAAGAATTTAAAGATTCTTGTTCAGTTCAAGTGTACAGTATCCAGGCTTGTATTCCAAAAGATACTGCTGTACTTTGGAATCCTGAATTTGT
| || | | | | ||| | | ||| | || | | ||| | || | | ||| | | | || | | || | | | | ||||||||||||||||| || |||||||||||||||||||| | |||||||||||||| ||||||||||||||||| ||||||||||||||||||||||||||
gtaacgcacgaattttctgatcctctaggatgaatattttgctaactagatcgaaattttcctgtgtcttcacttcccagtgatatgtttcttttatctagtgtcaaatttcttatgtgaaaagttaatctgtcttccatgcagAAGCAAGGCAAATTTTCAAAGATTCTTGTTCAGTTCAGATCTACAGTATCCAGGCCTGTATTCCAAAAGATACAGCTGTACTTTGGAATCCTGAATTTGT

upper sequence: LOC_Os01g10690.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G005536_T02 (Zea mays), 3'ss of exon 2
-----------------------------------------------gtaatgtcttgcctcaggtttatc---atagtatagtttcccaatttacagtatacccttttctgataaatgttgaatttgactgaaaagtggagcattt--gttt-----tttttttctttatgatgcagAAGCAAGGCAAGAATTTAAAGATTCTTGTTCAGTTCAAGTGTACAGTATCCAGGCTTGTATTCCAAAAGATACTGCTGTACTTTGGAATCCTGAATTTGT
|| || | || | | ||| ||| | | | ||| | || | | || | || | ||| | || | || | ||| | | | | | |||||||||||||||| | || |||||||||||||||||||| | ||||| |||||||| ||||||||||||||||| ||||| |||||||||| |||||||||
gtaatgcatgaatttctgttcttatttatggtacagtttcctgatttgtggtgcttcatctaggatatatttggataactagatctaaaattttcctgtgttttcgctttccagtgatttgctttttttttcttgtgtcaaatatcttagttgaaaggtcaatctgtcttctatgcagAAGCAAGGCATGGTTTCAAAGATTCTTGTTCAGTTCAGATCTACAGCATCCAGGCCTGTATTCCAAAAGATACAGCTGTGCTTTGGAATCATGAATTTGT

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|88294789|gb|CI604661.1|CI604661
EST:     GAACCCCACAAATTATTGTGTAAAACTCACTTCAGGCCATAAACTTGAAG                         AAGCAAGGCAAGAATTTAAAGATTCTTGTTCAGTTCA
genomic: GAACCCCACAAATTATTGTGTAAAACTCACTTCAGGCCATAAACTTGAAGgtaatgtctt ... tatgatgcagAAGCAAGGCAAGAATTTAAAGATTCTTGTTCAGTTCA
EST: gi|88731234|gb|CI754847.1|CI754847
EST:     GAACCCCACAAATTATTGTGTAAAACTCACTTCAGGCCATAAACTTGAAG                         AAGCAAGGCAAGAATTTAAAGATTCTTGTTCAGTTCAAGTGTACAGTATCC
genomic: GAACCCCACAAATTATTGTGTAAAACTCACTTCAGGCCATAAACTTGAAGgtaatgtctt ... tatgatgcagAAGCAAGGCAAGAATTTAAAGATTCTTGTTCAGTTCAAGTGTACAGTATCC
EST: gi|88717869|gb|CI739381.1|CI739381
EST:     GAACCCCACAAATTATTGTGTAAAACTCACTTCAGGCCATAAACTTGAAG                         AAGCAAGGCAAGAATTTAAAGATTCTTGTTCAGTTCAA
genomic: GAACCCCACAAATTATTGTGTAAAACTCACTTCAGGCCATAAACTTGAAGgtaatgtctt ... tatgatgcagAAGCAAGGCAAGAATTTAAAGATTCTTGTTCAGTTCAA
EST: gi|58687559|gb|CK076246.1|CK076246
EST:     GAACCCCACAAATTATTGTGTAAAACTCACTTCAGGCCATAAACTTGAAG                         AAGCAAGGCAAGAATTTAAAGATTCTTGTTCAGTTCAAGTGTACAGTATCC
genomic: GAACCCCACAAATTATTGTGTAAAACTCACTTCAGGCCATAAACTTGAAGgtaatgtctt ... tatgatgcagAAGCAAGGCAAGAATTTAAAGATTCTTGTTCAGTTCAAGTGTACAGTATCC
EST: gi|88725034|gb|CI748293.1|CI748293
EST:     GAACCCCACAAATTATTGTGTAAAACTCACTTCAGGCCATAAACTTGAAG                         AAGCAAGGCAAGAATTTAAAGAT
genomic: GAACCCCACAAATTATTGTGTAAAACTCACTTCAGGCCATAAACTTGAAGgtaatgtctt ... tatgatgcagAAGCAAGGCAAGAATTTAAAGAT
EST: gi|66917469|gb|CX104317.1|CX104317
EST:     GAACCCCACAAATTATTGTGTAAAACTCACTTCAGGCCATAAACTTGAAG                         AAGCAAGGCAAGAATTTAAAGATTCTTGTTCAGTTCAAGTGTACAGTATCC
genomic: GAACCCCACAAATTATTGTGTAAAACTCACTTCAGGCCATAAACTTGAAGgtaatgtctt ... tatgatgcagAAGCAAGGCAAGAATTTAAAGATTCTTGTTCAGTTCAAGTGTACAGTATCC
EST: gi|88724862|gb|CI748121.1|CI748121
EST:     GAACCCCACAAATTATTGTGTAAAACTCACTTCAGGCCATAAACTTGAAG                         AAGCAAGGCAAG
genomic: GAACCCCACAAATTATTGTGTAAAACTCACTTCAGGCCATAAACTTGAAGgtaatgtctt ... tatgatgcagAAGCAAGGCAAG

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: 75 (upstream exon), 47 (downstream exon)
Score: 4

CATGGGGCTGATCTTAAAGTGATTTACAGTGTGTCTGGATGGTTAAAGAAGAACCCCACAAATTATTGTGTAAAACTCACTTCAGGCCATAAACTTGAAGgtaatgtctt ... tatgatgcagAAGCAAGGCAAGAATTTAAAGATTCTTGTTCAGTTCAAGTGTACAGTATCCAGGCTTGTATTCCAAAAGATACTGCTGTACTTTGGAATCCTGAATTTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttgaatttgactgaaaagtggagcatttgttttttttttctttatgatgcagAAGCAAGGCAAGAATTTAAAGATTCTTGTTCAGTTCAAGTGTACAGTATCCAGGCTTGTATTCCAAAAGATACTGCTGTACTTTGGAATCCTGAATTTGT
       atttgac  putative branch site (score: 4)
 catttgtttttttttt  putative PPT
 atttgttttttttttc  TA-rich tract