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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTAACCGGAAAACCTCTTTTCCCTGGGAAGAATGTGGTTCATCAACTTGATATAATTACAGATCTACTAGGAACACCTTCTCCAGAAACAATATCTAGGgtcagtatggattgacttcaaaaaattgcttattacttagttccaataaaatcctataatgcttatatctacattcacttatgcaacag

Basic information

species Oryza sativa
transcript LOC_Os05g05160.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g05160.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G089484_T01 (Zea mays), 5'ss of exon 5
TTTAACCGGAAAACCTCTTTTCCCTGGGAAGAATGTGGTTCATCAACTTGATATAATTACAGATCTACTAGGAACACCTTCTCCAGAAACAATATCTAGGgtcagtatggattgacttcaaaaaattgcttattacttagttccaataaaatcctataatgcttatatctacattcacttatgcaacag
 ||||| ||||||||||||||||| ||||| |||||||| |||||||||||||||||||||||||| || |||||||||||||| ||| ||||||| |||||  |||    ||  | |||| |   || || ||   || | | |  ||| |    |||||||| ||  || |||  | | |       
GTTAACTGGAAAACCTCTTTTCCCGGGGAAAAATGTGGTACATCAACTTGATATAATTACAGATCTCCTTGGAACACCTTCTCCCGAAGCAATATCAAGGgtaggtacattttagcatcaata---tgtttgttg--tactgcaacaaaagtggagtaatgcttctacata-attgccctgtag-----

upper sequence: LOC_Os05g05160.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G017351_T01 (Zea mays), 5'ss of exon 4
TTTAACCGGAAAACCTCTTTTCCCTGGGAAGAATGTGGTTCATCAACTTGATATAATTACAGATCTACTAGGAACACCTTCTCCAGAAACAATATCTAGGgtcagtatggattgacttcaaaaaattgcttattacttagttccaataaaatcctataatgcttatatctacattcacttatgcaacag
 ||||| |||||||| |||||||| ||||| |||||||| ||||||||||||||||||||||||||  | |||||||||||||||||| ||||||| |||||  |||  | ||  | |||   | ||| ||||||  || | | |  |||||  | |||||||| || ||| ||  | |||  |   ||
ATTAACTGGAAAACCGCTTTTCCCGGGGAAAAATGTGGTACATCAACTTGATATAATTACAGATCTCATGGGAACACCTTCTCCAGAAGCAATATCGAGGgtaggtacagtttagcatca---atttgtttatta--tattgctatgaaaatgatctaatgcttctagctatatgtaattaccctgtag

upper sequence: LOC_Os05g05160.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA07G38510.1 (Glycine max), 5'ss of exon 4
TTTAACCGGAAAACCTCTTTTCCCTGGGAAGAATGTGGTTCATCAACTTGATATAATTACAGATCTACTAGGAACACCTTCTCCAGAAACAATATCTAGGgtcagtatggattgacttcaaaaaattgcttattacttagttccaataaaatcctataatgcttatatctacattcacttatgcaacag
|||||| ||||||||||||||||| ||||||||||| || |||||| | ||  | || || ||| | || |||||||| ||||| ||| | ||  |||||||| ||     || | ||   ||   | ||    | || ||  |  | |  |  | || |   |||| |          |||  |||||
TTTAACTGGAAAACCTCTTTTCCCAGGGAAGAATGTTGTCCATCAATTGGACCTCATGACTGATTTTCTTGGAACACCATCTCCTGAAGCCATTGCTAGGgtctgtt---gttcatttgccaatccttctagcaaatttgtgtcctttattttgt-tacttaatataaccttggcagtatat-taacag

upper sequence: LOC_Os05g05160.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA13G28120.1 (Glycine max), 5'ss of exon 5
TTTAACCGGAAAACCTCTTTTCCCTGGGAAGAATGTGGTTCATCAACTTGATATAATTACAGATCTACTAGGAACACCTTCTCCAGAAACAATATCTAGGgtcagtatggattgacttcaaaaaattgcttattacttagttccaataaaatcctataatgcttatatctacattcac-ttatgcaacag-
||| || ||||||||||||||||||||||||||||| || |||||||| ||  | || || ||||| || ||||| || ||||  ||| | ||  ||||||||  | | | |    |||       | | | ||    | ||    |    |  | |  | || |   | || ||    |||  | | |  
TTTGACGGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTCCATCAACTAGACCTTATGACTGATCTTCTTGGAACTCCATCTCTTGAAGCCATTGCTAGGgtc--tgttgttcagtttcc-----cttccttttggcaattttgtttgttctattttgttactcaatgcaaccttggtattacactaaaag

upper sequence: LOC_Os05g05160.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA17G02220.1 (Glycine max), 5'ss of exon 5
TTTAACCGGAAAACCTCTTTTCCCTGGGAAGAATGTGGTTCATCAACTTGATATAATTACAGATCTACTAGGAACACCTTCTCCAGAAACAATATCTAGGgtcagtatggattgacttcaaaaaattgcttattacttagttccaataaaatcctataatgcttatatctacattcacttatgcaacag
|||||| ||||||||||||||||| ||||||||||| || |||||| | ||  | || || ||| | || |||||||| ||||| ||| | ||  |||||||| ||     || | ||   ||   ||||    | || ||  |  | |  |  | || |   |||| |          |||  |||||
TTTAACTGGAAAACCTCTTTTCCCAGGGAAGAATGTTGTCCATCAATTGGACCTCATGACTGATTTTCTTGGAACACCGTCTCCTGAAGCCATTGCTAGGgtctgtt---gttcatttgccaatcctgctagcaaatttgtgtcctttattttgt-tacttaatataaccttgggagtatat-taacag

upper sequence: LOC_Os05g05160.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA15G10940.4 (Glycine max), 5'ss of exon 5
TTTAACCGGAAAACCTCTTTTCCCTGGGAAGAATGTGGTTCATCAACTTGATATAATTACAGATCTACTAGGAACACCTTCTCCAGAAACAATATCTAGGgtcagtatggattgacttcaaaaaattgcttattacttagttccaataaaatcctataatgcttatatctacattcacttatgc-aacag
||| |||||||||||||||||||||||||||||||| ||||||||||| ||  | || || ||||| || ||||| || ||||  ||| | ||  ||||||||  | | | |    |||       | | | |||   | ||    |    |  | |  | ||||     || ||    ||| | || ||
TTTGACCGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTTCATCAACTAGACCTTATGACTGATCTTCTTGGAACTCCATCTCTTGAAGCCATTGCTAGGgtc--tgttgttcagtttcc-----cttccttttagcaattttgtttgttctattttgttacttaatgaaaccttggtatatactaatag

upper sequence: LOC_Os05g05160.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT5G19010.1 (Arabidopsis thaliana), 5'ss of exon 5
TTTAACCGGAAAACCTCTTTTCCCTGGGAAGAATGTGGTTCATCAACTTGATATAATTACAGATCTACTAGGAACACCTTCTCCAGAAACAATATCTAGGgtcagtatggattgacttcaaaaaattgcttattacttagttccaataaaatcctataatgcttatatctacattcacttatgcaacag
 ||||| || |||||||||||||| ||||| |||||||| |||||| | ||| | || || ||| | || ||||| || ||| | ||| | ||     ||    |||||  ||   ||| | ||  ||||||   | | ||| |  |      ||  | | |||| |   | |                
CTTAACAGGGAAACCTCTTTTCCCCGGGAAAAATGTGGTCCATCAATTGGATCTGATGACGGATATGCTGGGAACTCCATCTGCTGAAGCCATT----GGAAGGgtatgtgttcctttccacaa--tgcttaa-gcattgtttctttttttggctgaatttcttacactgaaacag-------------

upper sequence: LOC_Os05g05160.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S87_157V6.2 (Physcomitrella patens), 5'ss of exon 5
TTTAACCGGAAAACCTCTTTTCCCTGGGAAGAATGTGGTTCATCAACTTGATATAATTACAGATCTACTAGGAACACCTTCTCCAGAAACAATATCTAGGgtcagtatggattgacttcaaaaaatt--gcttatta---cttagttccaataaaa---tcctat--aatgcttatatctacattcacttatgcaacag---
 || |||||||| || |||||||||||||||||||| |||||||| || ||| | || |||||  | || ||||  || ||| |||||||  |    ||||| ||     |  | | | ||| | ||   |||  |    || | | | | | |||   ||||||  |  | ||  | |  |||  | |  ||   | |   
GTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGGATCTTATGACAGACATGCTTGGAAGTCCATCTTCAGAAACCGTTCAAAGGgtaagagcaca--gtcctgaaatactttaacttggtgaggctcaatgcaagtgaaagaatcctatggagagttttaagcggcataaattcctgattctgtct

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|25798100|gb|CA754061.1|CA754061
EST:     ATATAATTACAGATCTACTAGGAACACCTTCTCCAGAAACAATATCTAGG                         ATTAGAAATGAGAAGGCAAGACGTTACTTGAACAGTATGAGGCGGAAAAAA
genomic: ATATAATTACAGATCTACTAGGAACACCTTCTCCAGAAACAATATCTAGGgtcagtatgg ... tatgcaacagATTAGAAATGAGAAGGCAAGACGTTACTTGAACAGTATGAGGCGGAAAAAA
EST: gi|58611987|gb|CK039699.1|CK039699
EST:     ATATAATTACAGATCTACTAGGAACACCTTCTCCAGAAACAATATCTGGG                         ATTAGAAATGAGAAGGCAAGACGTTACTTGAACAGTATGAGGCGGAAAAAA
genomic: ATATAATTACAGATCTACTAGGAACACCTTCTCCAGAAACAATATCTAGGgtcagtatgg ... tatgcaacagATTAGAAATGAGAAGGCAAGACGTTACTTGAACAGTATGAGGCGGAAAAAA
EST: gi|44669193|gb|CR282627.1|CR282627
EST:     ATATAATTACAGATCTACTAGGAACACCTTCTCCAGAAACAATATCTAGG                         ATTAGAAATGAGAGGGCAAGACGTTACTTGAACAGTATGAGGCGGAAAAAA
genomic: ATATAATTACAGATCTACTAGGAACACCTTCTCCAGAAACAATATCTAGGgtcagtatgg ... tatgcaacagATTAGAAATGAGAAGGCAAGACGTTACTTGAACAGTATGAGGCGGAAAAAA
EST: gi|58665648|gb|CK054334.1|CK054334
EST:     CAGATCTACTAGGAACACCTTCTCCAGAAACAATATCTAGG                         ATTAGAAATGAGAAGGCAAGACGTTACTTGAACAGTATGAGTGCGGAAAAA
genomic: CAGATCTACTAGGAACACCTTCTCCAGAAACAATATCTAGGgtcagtatgg ... tatgcaacagATTAGAAATGAGAAGGCAAGACGTTACTTGAACAGTATGAG-GCGGAAAAA
EST: gi|313081129|gb|HO213715.1|HO213715
EST:     GAAACAATATCTAGG                         ATTAGAAATGAGAAGGCAAGACGTTACTTGAACAGTATGAGGCGGAAAAAA
genomic: GAAACAATATCTAGGgtcagtatgg ... tatgcaacagATTAGAAATGAGAAGGCAAGACGTTACTTGAACAGTATGAGGCGGAAAAAA
EST: gi|58664632|gb|CK053318.1|CK053318
EST:     ATATAATTACAGATCTACTAGGAACACCTTCTCCAGAAACAATATCTAGG                         ATTAGAAATGAGAAGGCAAGACGTTACTTGAACAGTATGAGGCGGAAAAAA
genomic: ATATAATTACAGATCTACTAGGAACACCTTCTCCAGAAACAATATCTAGGgtcagtatgg ... tatgcaacagATTAGAAATGAGAAGGCAAGACGTTACTTGAACAGTATGAGGCGGAAAAAA
EST: gi|58684336|gb|CK073023.1|CK073023
EST:     ATATAATTACAGATCTACTAGGAACACCTTCTCCAGAAACAATATCTAGG                         ATTAGAAATGAGAAGGCAAGACGTTACTTGAACAGTATGAGGCGGAAAAAA
genomic: ATATAATTACAGATCTACTAGGAACACCTTCTCCAGAAACAATATCTAGGgtcagtatgg ... tatgcaacagATTAGAAATGAGAAGGCAAGACGTTACTTGAACAGTATGAGGCGGAAAAAA

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: 65 (upstream exon), 71 (downstream exon)
Score: 37

TTTAACCGGAAAACCTCTTTTCCCTGGGAAGAATGTGGTTCATCAACTTGATATAATTACAGATCTACTAGGAACACCTTCTCCAGAAACAATATCTAGGgtcagtatgg ... tatgcaacagATTAGAAATGAGAAGGCAAGACGTTACTTGAACAGTATGAGGCGGAAAAAACCTATACCATTTACACAGAAGTTCCCAAATGCAGATCCACTTGCAATGC




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