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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtttcaaattcatgactgaagtatatttatatgttacttacatgtgtgctgtgaatatctcaagtattttctctttgttgattgttgtcccctttgcagCGTATACTGGATGCTCTATTCCCTTCTGTTCTTGGAGGTACTTGCGCCATTCCTGGTGCATTTGGATGTGGAAAGACTGTCATTAGTCAAGCGCTCTCTA

Basic information

species Physcomitrella patens
transcript PP1S44_102V6.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 9
-------------------------ggtttca-aattcatgactgaagtatatttatatgttacttacatg----tgtgctgtgaatatctcaagtattttctctttgttgat-tgttgtc--ccctttgcagCGTATACTGGATGCTCTATTCCCTTCTGTTCTTGGAGGTACTTGCGCCATTCCTGGTGCATTTGGATGTGGAAAGACTGTCATTAGTCAAGCGCTCTCTA
                            |||| |||   | | |  | ||   | | |  ||| | |  ||    | | ||||     |||    ||||||  | |   | || |  |||   |  ||| |||||| |||| ||||| ||||| || || ||||||||||| ||||| || |||||||| |||||||| |||||||| |||||||||||||| || || || |
gtacacgaagcttgctactcccagctccttcataatgtgttattttattagtgtcaaaatttaatgaagtgatgctttcctgtcctgttctatcatattttgccgtgtctcatatcctgtgaactgttttcagCGTGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAA

upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 9
-------------------------------------------------------------------ggtttcaaattcatgactgaagtatatttata-tgttacttacatgtgtgctgtgaatatctcaagtattttctctttgttgattgttgtcccctttgcagCGTATACTGGATGCTCTATTCCCTTCTGTTCTTGGAGGTACTTGCGCCATTCCTGGTGCATTTGGATGTGGAAAGACTGTCATTAGTCAAGCGCTCTCTA
                                                                   ||||||    |    ||      ||  | | | |  |  || |     |  | |   ||    |   || |  |  || |  | | ||   |  |   |||||| |||| |||||  | ||||| || ||||||||||| || || ||||||||||| || ||||| ||||||||||||||||||||||| || || || |
gtttgtacagaacctaccatggttctcactcataataatatgtgcttttcctccccatttttattaaggtttctgtgttg-aaccactaaatgctcaaagtactgttttccccc-tcttttttctactcaactaatctaattcttatatacttttaaacgatcc-cagCGTGTACTTGATGCATTGTTCCCCTCAGTTCTTGGAGGAACATGTGCCATTCCTGGAGCTTTTGGTTGTGGAAAGACTGTCATTAGTCAGGCACTTTCCA

upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 9
----------------------------------------------ggtttc---aaattcatgactg--aagtatatttatatgttacttacatgtgtgctg-tgaat--atctcaagtattttctctttgttgattgttgtcccctttgcagCGTATACTGGATGCTCTATTCCCTTCTGTTCTTGGAGGTACTTGCGCCATTCCTGGTGCATTTGGATGTGGAAAGACTGTCATTAGTCAAGCGCTCTCTA
                                              | ||||   ||| |    | ||  ||| || || | ||| |  ||   |   |  |  |||||  | || |||| || | |  ||    || ||||         |||||| |||||||||| |||||||| || ||||| ||||| ||||| || ||||| || |||||||| ||||| || |||||||||||||| || || || |
gtttgtctataagttgccttgagcttggttgtcaataattatcaatgttttctaaaaacttgaaattgccaagcattttcagatgatgtttcacttcatcttactgaattaaccttaagtcttgtttgcttacaaatggttg---------cagCGTGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATTCCAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA

upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 6
------------------------------------------ggtttc-----aaattcatgactg--aagtatatttatatgttacttacatgtgtgctgtgaatatctcaagtattttctctttgttgattgttgtcccctttgcagCGTATACTGGATGCTCTATTCCCTTCTGTTCTTGGAGGTACTTGCGCCATTCCTGGTGCATTTGGATGTGGAAAGACTGTCATTAGTCAAGCGCTCTCTA
                                           ||||      ||| |    |  |  ||| || || | | | |  || | | | |  |     |   | || | ||      ||||    | |       ||| |||||| |||||||||| |||||||| || ||||| ||||| ||||| || ||||| || |||||||| ||||| || |||||||||||||| || || || |
gtttgtctataagttgccttagcttggttgtctataattgtcagtttttgctaaaacttgaaatcgccaagcattttcagacgatgtttccctttatcttac---tccattaaatcttgaagtcttgtatgctttcaaatggttt-cagCGTGTACTGGATGCACTATTCCCCTCAGTTCTGGGAGGCACTTGTGCTATTCCAGGGGCATTTGGTTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCA

upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 9
ggtttcaaattcatgactgaagtatatttatatgttacttacatgtgtgctgtgaatatctcaagtattttctctttgttgattgttgtcccct-----ttgcagCGTATACTGGATGCTCTATTCCCTTCTGTTCTTGGAGGTACTTGCGCCATTCCTGGTGCATTTGGATGTGGAAAGACTGTCATTAGTCAAGCGCTCTCTA
                     ||| | | |  ||||||   || ||||    |  ||     || | |  |  | ||  || ||  || |  ||     || |||||| | || ||||| || ||||| || |||||||| || ||||| |||||||||||||| ||||| ||||| || || ||||||||||| || || ||||
---------------------gtaaactcagttgttac---caagtgtctcctccatgatctaattgtgatagccttcatgcttaatgacttctgttttttacagCGTGTTCTTGATGCCCTTTTCCCCTCAGTTCTTGGCGGGACTTGTGCCATTCCTGGTGCTTTTGGTTGTGGTAAAACAGTCATTAGTCAGGCTCTTTCTA

upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 9
ggtttcaaattcatgactgaagtatatttatatgttacttacatgtgtgctgtgaatatctcaagtattttctctttgttgattg-----ttgtcccctttgcagCGTATACTGGATGCTCTATTCCCTTCTGTTCTTGGAGGTACTTGCGCCATTCCTGGTGCATTTGGATGTGGAAAGACTGTCATTAGTCAAGCGCTCTCTA
                     ||| | | |  |||||    || ||||    |  |||    || | |  |  ||||  ||  |      || | |  ||| |||||| | || ||||| || ||||| || |||||||| || ||||| ||||| ||||| || ||||| ||||| || |||||||||||||| || || ||||
---------------------gtaaactcagttgttat---caagtgtctcatccataatctaattgtgatagctttcatgcgtaatgacttctgctttttacagCGTGTTCTTGATGCCCTTTTCCCCTCAGTTCTTGGCGGGACTTGTGCCATACCTGGAGCTTTTGGTTGTGGTAAAACTGTCATTAGTCAGGCTCTTTCTA

upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 9
ggtttcaaattcatgactgaagtatatttatatgttacttacatgtgtgctgtgaatatctcaagtattttctctttgttgattgttgtcccctttgcagCGTATACTGGATGCTCTATTCCCTTCTGTTCTTGGAGGTACTTGCGCCATTCCTGGTGCATTTGGATGTGGAAAGACTGTCATTAGTCAAGCGCTCTCTA
          | || |||  | || |||  | |   | |       ||  | ||||||   || || ||  ||  ||| |  || || |||  ||  |||||| | || ||||| || ||||||||||||||||| || || || |||||||||||||| ||||| ||||| || ||||| || ||||| || || || |
---------gtgattactcgatta-attcttcttacagtggtgatagtcatttgaata---catgtgttg-ctgattgct--ttcttttcctgttgtcagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATTCCTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCA

upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 9
ggtttcaaattcatgactgaagtatatttatatgttacttacatgtgtgctgtgaatatctcaagtattttctctttgttgattgttgtcccctttgcagCGTATACTGGATGCTCTATTCCCTTCTGTTCTTGGAGGTACTTGCGCCATTCCTGGTGCATTTGGATGTGGAAAGACTGTCATTAGTCAAGCGCTCTCTA
 ||    |    |  |   || | ||||   |   | || |  | ||     || |    | |||| | |||       ||||| ||||  | | | |||||| | || ||||| || |||||||||||||| || || ||||| ||||| ||||| |||||||| |||||||| || ||||| |||||||| || ||||
-gtaattagcatacaaactaaatgtattatcagtattctcatctatggctgctgtaagcttgaagtgtgttcc------tgatttttgtttcatct-cagCGTGTTCTTGATGCCCTTTTCCCTTCTGTTCTCGGTGGAACTTGTGCCATACCTGGGGCATTTGGTTGTGGAAAAACAGTCATCAGTCAAGCTCTTTCTA

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|162186097|gb|FC361301.1|FC361301
EST:     GACCTGTTGCTGAGAAGCTGGCAGCTGATACTCCGTTGCTCACTGGTCAG                         CGTATACTGGATGCTCTATTCCCTTCT
genomic: GACCTGTTGCTGAGAAGCTGGCAGCTGATACTCCGTTGCTCACTGGTCAGgtatgttgta ... ccctttgcagCGTATACTGGATGCTCTATTCCCTTCT
EST: gi|162179503|gb|FC356543.1|FC356543
EST:     GACCTGTTGCTGAGAAGCTGGCAGCTGATACTCCGTTGCTCACTGGTCAG                         CGTATACTGGATGCTCTATTCCCTTCTGTTCTTGGAGGTACTTGCGCCATT
genomic: GACCTGTTGCTGAGAAGCTGGCAGCTGATACTCCGTTGCTCACTGGTCAGgtatgttgta ... ccctttgcagCGTATACTGGATGCTCTATTCCCTTCTGTTCTTGGAGGTACTTGCGCCATT

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: 35 (upstream exon), 35 (downstream exon)
Score: 33

GCCTGGCCTGTGCGCACACCAAGACCTGTTGCTGAGAAGCTGGCAGCTGATACTCCGTTGCTCACTGGTCAGgtatgttgta ... ccctttgcagCGTATACTGGATGCTCTATTCCCTTCTGTTCTTGGAGGTACTTGCGCCATTCCTGGTGCATTTGGATGTGGAAAGACTGTCATTAGTCAAGCGCTCTCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgctgtgaatatctcaagtattttctctttgttgattgttgtcccctttgcagCGTATACTGGATGCTCTATTCCCTTCTGTTCTTGGAGGTACTTGCGCCATTCCTGGTGCATTTGGATGTGGAAAGACTGTCATTAGTCAAGCGCTCTCTA
                               tgttgat  putative branch site (score: 33)
                                     ttgttgtccccttt  CT-rich tract
                 aagtatttt  TA-rich tract