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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatatctccgaactgtatttttcagtgtgcttatctgtgtctggtctctgaaaagcaatgtattctgttggcttacgaccaatgttgtaaaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGACACGTACATTATCTTTGGCGAAGCCAAGATTGAGGACTTGAGTTCTCAAC

Basic information

species Physcomitrella patens
transcript PP1S10_319V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S10_319V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA19G30550.1 (Glycine max), 3'ss of exon 3
aaatatc-tccgaactgtatttttcagtgtgcttatctgtgtctggtctctgaaaagcaatgtattctgttggc--ttacgaccaatgttgtaaaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGACACGTACATTATCTTTGGCGAAGCCAAGATTGAGGACTTGAGTTCTCAAC
   || | |  ||    | ||||||  | | |    |  | | |  | | | | |   | | |  | || |     ||   ||    |   |    | |  ||||||| ||||| |||||    || || || |||||||| ||  |||| |||||||||||||| ||||| |||||||||||||| |||||||| || || |
-gttagcatttgactcatctttttcgcttttcaccaccctttttcatttgtcagatctattttgctttggtaaaaattgaaactttggactttgtttgtttagATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGACACGTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGC

upper sequence: PP1S10_319V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA03G27580.2 (Glycine max), 3'ss of exon 3
--aaatatctccgaactgtatttttcagtgtgcttatctgtgtctggtctctgaaaagcaatgtattctgttggcttacgaccaatgttgtaaaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGACACGTACATTATCTTTGGCGAAGCCAAGATTGAGGACTTGAGTTCTCAAC
   |  || |   | || | | |||    |  ||| ||  ||| |  ||| |     | | |      | |||  ||     |    ||||    ||   ||||||| || || || ||    || ||||| |||||||||||  | || ||||| |||||||| || ||||||||||||||||| |||||||| || || |
gttagcatttgacatctatttattttgaagaacttttcattgtttcatctatttc--gtacttgtcaatattgaatttatttctcctttgtttgttt---agATCCTGTTTGTTATATCAAAACCAGATGTTTTCAAGAGCCCGACTTCTGACACATACATTATATTCGGCGAAGCCAAGATTGAAGACTTGAGCTCACAGC

upper sequence: PP1S10_319V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA03G27570.1 (Glycine max), 3'ss of exon 3
--aaatatc-tccgaactgtatttttcagtgtgcttatctgtgtctggtctctgaaaagcaatgtattctg-ttggcttacgaccaatgttgtaaaattt-------gcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGACACGTACATTATCTTTGGCGAAGCCAAGATTGAGGACTTGAGTTCTCAAC
   | || | |  ||   || |||||   | | |    || | | | |  | ||  |    || |||| || || | | |  |   |   | |  | |||         ||||||| ||||| |||||    || || || |||||||| ||  | || |||||||||||||| ||||| |||||||||||||| |||||||| || || |
gttagtagcatttgacacgtctttttagcttttcaccactcttttttgcatttgtcag---atttattttgctttggtaaaaattgaaactttggacttttgtttgtttagATCCTGTTCGTCATCTCAAAACCAGACGTTTTCAAGAGTCCAACGTCTGACACGTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGC

upper sequence: PP1S10_319V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA19G30540.1 (Glycine max), 3'ss of exon 3
aaatatc-tccgaactgtatttttcagtgtgcttatctgtgtctggtctctgaaaagcaatgtattctgttggc--ttacgaccaatgttgtaaaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGACACGTACATTATCTTTGGCGAAGCCAAGATTGAGGACTTGAGTTCTCAAC
   || | |  ||    | ||||||| | | |    || | | |  | | | | |   | | |  | || |     ||   ||    |   |    | |  ||||||| ||||| |||||    || ||||| |||||||| ||  |||| || || |||||||| ||||| |||||||||||||| |||||||| || ||  
-gttagcatttgactcatctttttcacttttcaccactctttttcatttgtcagatctattttgctttggtaaaaattgaaactttggactttgtttgtttagATCCTGTTCGTTATCTCAAAACCAGATGTTTTCAAGAGTCCAACATCTGAAACTTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGT

upper sequence: PP1S10_319V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT3G12390.1 (Arabidopsis thaliana), 3'ss of exon 3
aaatatctccgaactgtatttttcagt-gtgcttatctgtgtctggtctctgaaaagcaatgtattctg--ttggcttacgaccaat-gttgtaaaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGACACGTACATTATCTTTGGCGAAGCCAAGATTGAGGACTTGAGTTCTCAAC
   | | |     || || | ||||||    ||||  |   | |  || |  |  ||   |  ||  ||   ||  ||  |  || | | | |  ||    |||||| | || || || ||    ||||||||||||||||| || ||||||||||| ||  | |||||||| || || ||||| ||||| ||||| |||||  
gtttgtgttttctctttaatattcagtcaatcttaatttcttttattcacacatcaggctttaatattgatctgttttggggacatttgctttggaac--acagATCTTGTTTGTCATATCAAAGCCTGATGTGTTCAAGAGTCCAGCATCAGACACATATGTGATCTTTGGAGAGGCGAAGATCGAGGATTTGAGCTCTCAGA

upper sequence: PP1S10_319V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv08s0040g00600.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------aaatatctccgaactgtatttttcagtgtgcttatctgtgtctggtctctgaaaagcaatgtattctgttggcttacgacca--atgttgtaaaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGACACGTACATTATCTTTGGCGAAGCCAAGATTGAGGACTTGAGTTCTCAAC
                                  ||| |   |  |      |   ||   ||  |   | || ||| |||    |    |  | ||| |||      |   |  ||| | |  | | | ||||| ||||| || |||||    || |||||||||||||||||  | |||||||| ||  | || |||||||| || ||||||||||| |||||||| ||||
gtcagtttctctttgcccactgttgattactttttatttttcatgttgggcctattgtcacctctttaatatcaggtttctttctattt-tacaatctattgaaagcagtttactatggtttttattattcagATTCTCTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCAACTTCAGACACTTATGTAATATTTGGCGAGGCAAAGATTGAGGATTTGAGTTCACAAC

upper sequence: PP1S10_319V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 3
aaatatctccgaactgtatttttcagtgtgcttatctgtgtctggtctctgaaaagcaatgtattctgttggcttacgaccaatgttgtaaaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGACACGTACATTATCTTTGGCGAAGCCAAGATTGAGGACTTGAGTTCTCAAC
                             |      || || ||||   |  ||   |||  |       | || ||  |   | | ||    ||| ||||| || || |||||||||   || || |||||||||||||| ||||| |||||  |||| ||||||||||| |||||||| |||||||||||||| || |
-----------------------------gtaagcttgcgt-tggtagatcgaagagaataga-------gactaacttcgcttctggttc--tttccagATACTGTTTGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC

upper sequence: PP1S10_319V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ21445 (Selaginella moellendorffii), 3'ss of exon 1
aaatatctccgaactgtatttttcagtgtgcttatctgtgtctggtctctgaaaagcaatgtattctgttggcttacgaccaatgttgtaaaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGACACGTACATTATCTTTGGCGAAGCCAAGATTGAGGACTTGAGTTCTCAAC
                                ||    ||  | ||   |||||   |||  | |||     ||| ||  |  ||||      ||| ||||| || ||||||||||||   || || |||||||||||||| ||||| |||||  |||| ||||||||||| |||||||| |||||||||||||| || |
-------------------------------gtaagcttgcgtagtagatgaaagagaatagagtcta---actt-cgctccttgttc-----tttccagATACTGTTCGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC

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|162210245|gb|FC386730.1|FC386730
EST:     TGAAGCCCGTGACCGATGTCACCCGAGTTACCATCAAGAAGAGCAAAAAT                         ATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGAC
genomic: TGAAGCCCGTGACCGATGTCACCCGAGTTACCATCAAGAAGAGCAAAAATgtatgcctcg ... aaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGAC
EST: gi|37847320|gb|BJ605328.1|BJ605328
EST:     TGAAGCCCGTGACCGATGTCACCCGAGTTACCATCAAGAAGAGCAAAAAT                         ATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGAC
genomic: TGAAGCCCGTGACCGATGTCACCCGAGTTACCATCAAGAAGAGCAAAAATgtatgcctcg ... aaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGAC
EST: gi|67694196|gb|BJ954429.1|BJ954429
EST:     TGAAGCCCGTGACCGATGTCACCCGAGTTACCATCAAGAAGAGCAAAAAT                         ATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGAC
genomic: TGAAGCCCGTGACCGATGTCACCCGAGTTACCATCAAGAAGAGCAAAAATgtatgcctcg ... aaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGAC
EST: gi|67570895|gb|BJ943719.1|BJ943719
EST:     TGAAGCCCGTGACCGATGTCACCCGAGTTACCATCAAGAAGAGCAAAAAT                         ATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGAC
genomic: TGAAGCCCGTGACCGATGTCACCCGAGTTACCATCAAGAAGAGCAAAAATgtatgcctcg ... aaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGAC
EST: gi|7286954|gb|AW599441.1|AW599441
EST:     TGAAGCCCGTGACCGATGTCACCCGAGTTACCATCAAGAAGAGCAAAAAT                         ATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGAC
genomic: TGAAGCCCGTGACCGATGTCACCCGAGTTACCATCAAGAAGAGCAAAAATgtatgcctcg ... aaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGAC
EST: gi|162200867|gb|FC377062.1|FC377062
EST:     TGAAGCCCGTGACCGATGTCACCCGAGTTACCATCAAGAAGAGCAAAAAT                         ATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGAC
genomic: TGAAGCCCGTGACCGATGTCACCCGAGTTACCATCAAGAAGAGCAAAAATgtatgcctcg ... aaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGAC
EST: gi|19778194|gb|BQ039278.1|BQ039278
EST:     AAGAGCAAAAAT                         ATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGAC
genomic: AAGAGCAAAAATgtatgcctcg ... aaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGAC
EST: gi|37840258|gb|BJ598266.1|BJ598266
EST:     TGAAGCCCGTGACCGATGTCACCCGAGTTACCATCAAGAAGAGCAAAAAT                         ATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGAC
genomic: TGAAGCCCGTGACCGATGTCACCCGAGTTACCATCAAGAAGAGCAAAAATgtatgcctcg ... aaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGAC
EST: gi|7067581|gb|AW497436.1|AW497436
EST:     TGAAGCCCGTGACCGATGTCACCCGAGTTACCATCAAGAAGAGCAAAAAT                         ATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGAC
genomic: TGAAGCCCGTGACCGATGTCACCCGAGTTACCATCAAGAAGAGCAAAAATgtatgcctcg ... aaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGAC

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), 32 (downstream exon)
Score: 99

GCAGAGCCGTGGTGAGAAGAAAAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAGCCCGTGACCGATGTCACCCGAGTTACCATCAAGAAGAGCAAAAATgtatgcctcg ... aaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGACACGTACATTATCTTTGGCGAAGCCAAGATTGAGGACTTGAGTTCTCAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctgaaaagcaatgtattctgttggcttacgaccaatgttgtaaaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGACACGTACATTATCTTTGGCGAAGCCAAGATTGAGGACTTGAGTTCTCAAC
                         ggcttac  putative branch site (score: 99)
                                    aatgttgtaaaattt  TA-rich tract