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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGTTTCTGCGCCAGCCACACTTTATTGTGTGGGATAATCCTGACATTGTCACACATGAGGTCATGGGTGGTCTTAAGAATGTGTACGCCATTGGTGCCGgtgagccactgtcacgatcctctgtgttagtcttctatgcattgagaatgtaatcatctaatgttttctcattctagcctttagagttaaatcactgaat...

Basic information

species Physcomitrella patens
transcript PP1S114_190V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S114_190V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os01g71280.1 (Oryza sativa), 5'ss of exon 3
AAGTTTCTGCGCCAGCCACACTTTATTGTGTGGGATAATCCTGACATTGTCACACATGAGGTCATGGGTGGTCTTAAGAATGTGTACGCCATTGGTGCCGgtgagc-cactgtcacgatcctctgtgttagtcttctatgcattgagaatgtaatcatctaatgttttctcattctagcctttagagttaaatcactgaat
||||||||| | || ||||| || ||||| ||||||||   |||  |||| ||||||||||| ||||||||| | |||||||| |||||||| ||||| ||| ||   | | | |  |   ||||| ||  | | | |   ||| |  || |    | |        |      |||  | |   |   ||   |  || |
AAGTTTCTGAGACAACCACATTTCATTGTCTGGGATAACAGTGATCTTGTTACACATGAGGTGATGGGTGGTTTGAAGAATGTCTACGCCATCGGTGCTGgtaagaatattttaaatacgttctgt-ttgttttccaaaatattaactatctttataacagtaaaaataattaactaatcctactaacaaacgaatggagt

upper sequence: PP1S114_190V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os01g58740.1 (Oryza sativa), 5'ss of exon 3
AAGTTTCTGCGCCAGCCACACTTTATTGTGTGGGATAATCCTGACATTGTCACACATGAGGTCATGGGTGGTCTTAAGAATGTGTACGCCATTGGTGCCGgtga--gccactgtcacgatcctctgtgttagtcttcta-tgcattgagaatgtaatcatctaatgttttctcattctagcctttag--agttaaatcactgaat
|| ||| || | ||||| || |||||||| |||||||||  |||  |  | |||||||| |||||||| ||| | || |||||||| ||||||||||||||| |   | | |  | |  |    ||| || |   |||  || | | |   |  |  ||| || |||| |   ||| |||| |   |   |||  |   |     
AAATTTTTGAGGCAGCCTCATTTTATTGTATGGGATAATAGTGATCTCATTACACATGAAGTCATGGGAGGTTTGAAAAATGTGTATGCCATTGGTGCCGgtaatttctatttcctctcttgattgtttttgctatcttctgtaatcacggtagag-catatactgttgtgatatt-tagcatggggtatgttggaatgcac---

upper sequence: PP1S114_190V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA19G31730.1 (Glycine max), 5'ss of exon 2
AAGTTTCTGCGCCAGCCACACTTTATTGTGTGGGATAATCCTGACATTGTCACACATGAGGTCATGGGTGGTCTTAAGAATGTGTACGCCATTGGTGCCGgtgagccactgtcacgatcctctgtgttagtcttctatgcattgagaatgtaatcatctaatgttttctcattctagcctttagagt-taaatcactgaat--
|||||| ||||||| |||||||||||||| ||||||||   |||  | ||||| |||||||||||||||||  | || ||||| || || ||||| || ||| ||| |||       |  | | | ||    | | |||  |  |   || | | ||| | | |  ||   || | |  | |  | | |     | |  |   
AAGTTTTTGCGCCAACCACACTTTATTGTCTGGGATAACAGTGATCTCGTCACTCATGAGGTCATGGGTGGCTTGAAAAATGTCTATGCAATTGGAGCTGgtaagctactaattaattgttatatctttacatgccatg--tcaaacttgcagtaatcca-tatcatcatgttttggtttgtgtaatgttgtctatttcactt

upper sequence: PP1S114_190V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA10G15900.1 (Glycine max), 5'ss of exon 2
AAGTTTCTGCGCCAGCCACACTTTATTGTGTGGGATAATCCTGACATTGTCACACATGAGGTCATGGGTGGTCTTAAGAATGTGTACGCCATTGGTGCCGgtgagccactgtcacgatcctctgtgttagtcttctatgcattgagaatgtaatcatctaatgttttctcat-tctagcctttagagttaaatcactgaat
|||||||| || || ||||| |||||||| ||||| ||   |||| ||||||| |||||| |||||||||| || || ||||| || || |||||||||||| |||  |        |   | |  | ||| ||  |   | || |||  |  |  |    ||| ||  ||| |||    | |   || |      ||| |
AAGTTTCTACGACAACCACATTTTATTGTCTGGGACAACAGTGACCTTGTCACCCATGAGATCATGGGTGGCCTGAAAAATGTCTATGCAATTGGTGCCGgtaagcttcaaat-tagttaacagcataagttttacagctaatgtgaaacttgtagtaatctgtattgccatgtcttttatatgttgtaatggttgtgact

upper sequence: PP1S114_190V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA03G28970.1 (Glycine max), 5'ss of exon 2
AAGTTTCTGCGCCAGCCACACTTTATTGTGTGGGATAATCCTGACATTGTCACACATGAGGTCATGGGTGGTCTTAAGAATGTGTACGCCATTGGTGCCGgtgagccactgtcacgatcctctgtgttagtcttctatgca---ttgagaatgtaatcatctaatgttttctcattctagcctttagagttaaatca--ctgaat--
|||||| | || || |||||||||||||| ||||||||   |||| | ||||| |||||||||||||||||  | || ||||| || || || || || ||| |||  ||      ||    |||  ||   ||  |||||   |  |   || | | ||   || |  ||   || | |  | |  | |    |||   | | |  
AAGTTTTTACGACAACCACACTTTATTGTCTGGGATAACAGTGACCTCGTCACGCATGAGGTCATGGGTGGCTTGAAAAATGTCTATGCAATAGGAGCTGgtaagcttcta-----attaattgttataactttacatgcaaggtcaaacttgcagtaatt--atatcatcgtgttttggtttgtgtaatgttgtcaatttcactag

upper sequence: PP1S114_190V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA02G33340.1 (Glycine max), 5'ss of exon 2
AAGTTTCTGCGCCAGCCACACTTTATTGTGTGGGATAATCCTGACATTGTCACACATGAGGTCATGGGTGGTCTTAAGAATGTGTACGCCATTGGTGCCGgtgagccactgtcacgatcctctgtgttagtcttctatgcattgagaatgtaatcatctaatgttttctcattctagcctttaga-gtta-aatcactg-aat-
|||||||| || || ||||| |||||||| ||||| ||   |||| ||||||| |||||||||||||||||  | || ||||| || || |||||||| ||| ||   ||       |     |    ||  ||  |     | ||||   | |  |   |   | | |     || | |||| | |||| |||   ||  || 
AAGTTTCTACGACAACCACATTTTATTGTCTGGGACAACAGTGACCTTGTCACCCATGAGGTCATGGGTGGCTTGAAAAATGTCTATGCAATTGGTGCAGgtaagattctaat-tagttaatagcacaagctttaca---gctaagaagtaacttgttctaatctgtattgccatatcttttatatgttataatggttgcgatt

upper sequence: PP1S114_190V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: AT2G41540.2 (Arabidopsis thaliana), 5'ss of exon 3
AAGTTTCTGCGCCAGCCACACTTTATTGTGTGGGATAATCCTGACATTGTCACACATGAGGTCATGGGTGGTCTTAAGAATGTGTACGCCATTGGTGCCGgtgagccactgtcacgatcctctgtgttagtcttctatgcattgagaatgtaatcatctaatgttttctcattctagcctttagagttaaatcactgaat
|||||  |  | || || || || ||||| ||||| |||  |||  |||| |||||||| || ||||| ||||| |||||||| ||||||||||| || ||| ||   ||||            |||         | | |||       |||| ||| |  |||||| || | |   | ||   |||   |  | |   
AAGTTCTTAAGACAACCTCATTTCATTGTTTGGGACAATAGTGATCTTGTGACACATGAAGTAATGGGAGGTCTCAAGAATGTCTACGCCATTGGAGCTGgtaagtttctgt-----------atgtagac-----acggatttgagtgataattatcaa--gttttcacactttgatccttcttgttgtgtt-cag---

upper sequence: PP1S114_190V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv08s0007g09000.t01 (Vitis vinifera), 5'ss of exon 2
AAGTTTCTGCGCCAGCCACACTTTATTGTGTGGGATAATCCTGACATTGTCACACATGAGGTCATGGGTGGTCTTAAGAATGTGTACGCCATTGGTGCCGgtgagccactgtcacgatcctctgtgttagtcttctatgcattgagaatgtaatcatctaatgttttctcattc-tagcctttagagttaaatcactg-aat-------------------------------------------------------------------------------------------------------
||||||||| | || || || || || || ||||| ||   |||| ||||||| ||||| || ||||||||  | ||||||||||| |||||||| |||||| ||    | |     | || | || | ||  | ||   |  | ||   |  |  |  ||  ||     ||    | ||||   || ||||   | | |||                                                                                                       
AAGTTTCTGAGGCAACCCCATTTCATCGTATGGGACAACAGTGACCTTGTCACTCATGAAGTTATGGGTGGCTTAAAGAATGTGTATGCCATTGGAGCCGgtaagttgttat-----ttctttatgatggtaatata-atagagggatcattgtgcttgaagtttcatatatgagcatccttgtcagataaacttcagcaatgatctggttctcattttgacctactaggagaagaaaaccaaaatttaaaaatgttgttattggatttaatcaagagtctcacattttcactttgattttccag

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|67726206|gb|BJ976465.1|BJ976465
EST:     CACACATGAGGTCATGGGTGGTCTTAAGAATGTGTACGCCATTGGTGCCG                         GAATGGTGGGAGCTTTGACCAACGAGTCAGCTACAAGCAAGGCCGTGTATT
genomic: CACACATGAGGTCATGGGTGGTCTTAAGAATGTGTACGCCATTGGTGCCGgtgagccact ... gcatatgcagGAATGGTGGGAGCTTTGACCAACGAGTCAGCTACAAGCAAGGCCGTGTATT
EST: gi|162199433|gb|FC374060.1|FC374060
EST:     CACACATGAGGTCATGGGTGGTCTTAAGAATGTGTACGCCATTGGTGCCG                         GAATGGTGGGAGCTTTGACCAACGAGTCAGCTACAAGCAAGGCCGTGTATT
genomic: CACACATGAGGTCATGGGTGGTCTTAAGAATGTGTACGCCATTGGTGCCGgtgagccact ... gcatatgcagGAATGGTGGGAGCTTTGACCAACGAGTCAGCTACAAGCAAGGCCGTGTATT
EST: gi|162240949|gb|FC415228.1|FC415228
EST:     CACACATGAGGTCATGGGTGGTCTTAAGAATGTGTACGCCATTGGTGCCG                         GAATGGTGGGAGCTTTGACCAACGAGTCAGCTACAAGCAAGGCCGTGTATT
genomic: CACACATGAGGTCATGGGTGGTCTTAAGAATGTGTACGCCATTGGTGCCGgtgagccact ... gcatatgcagGAATGGTGGGAGCTTTGACCAACGAGTCAGCTACAAGCAAGGCCGTGTATT
EST: gi|162251559|gb|FC427746.1|FC427746
EST:     CACACATGAGGTCATGGGTGGTCTTAAGAATGTGTACGCCATTGGTGCCG                         GAATGGTGGGAGCTTTGACCAACGAGTCAGCTACAAGCAAGGCCGTGTATT
genomic: CACACATGAGGTCATGGGTGGTCTTAAGAATGTGTACGCCATTGGTGCCGgtgagccact ... gcatatgcagGAATGGTGGGAGCTTTGACCAACGAGTCAGCTACAAGCAAGGCCGTGTATT

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: 29 (upstream exon), 32 (downstream exon)
Score: 10

AAGTTTCTGCGCCAGCCACACTTTATTGTGTGGGATAATCCTGACATTGTCACACATGAGGTCATGGGTGGTCTTAAGAATGTGTACGCCATTGGTGCCGgtgagccact ... gcatatgcagGAATGGTGGGAGCTTTGACCAACGAGTCAGCTACAAGCAAGGCCGTGTATTTTTCACATTCAACATCAGAGATGATTTATATCACACGTTTGCTGGCAGA




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