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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactagccaccaaacaaagcatcatgtgatgggttcataagatggcttccttttttgagattcgtactcgtttgttggtcactgacggattgttcgatatcgcagGTTTGTTGAGATCATGGCACCCGTGTTTTCACGAAAAGCATGGCGTTGCGTCTGGTACATAATACAG

Basic information

species Physcomitrella patens
transcript PP1S448_20V6.3
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S448_20V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA05G30850.1 (Glycine max), 3'ss of exon 8
gtaactagccaccaaacaaagcatcatgtgatgggttcataagatggcttccttttttgagattcgtactcgtttgttggtcactgacggattgttcgatatcgcagGTTTGTTGAGATCATGGCACCCGTGTTTTCACGAAAAGCATGGCGTTGCGTCTGGTACATAATACAG
|||| || |    ||| ||    |  | |  |   ||   | |    |    ||||   |  ||   |   | |  ||   |||      ||| |   | || |||||||||||||||| ||||| || |||||||||||||| |||||||| || || ||| | || || |||
gtaagtaactgttaaagaat---ttttatttttttttggcaggggtacaatattttcccatcttta-atgagctgatt--ccacc-----attctgtaacat-gcagGTTTGTTGAGATAATGGCTCCAGTGTTTTCACGAAATGCATGGCGCTGTGTGTGGCATATGATTCAG

upper sequence: PP1S448_20V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA08G14050.1 (Glycine max), 3'ss of exon 8
gtaactagccaccaaacaaagcatcatgtgatgggttcataagatggcttccttttttgagattcgtactcgtttgttggtcactgacggattgttcgatatcgcagGTTTGTTGAGATCATGGCACCCGTGTTTTCACGAAAAGCATGGCGTTGCGTCTGGTACATAATACAG
|||| || |    |  || |   |  | ||  ||| | | || ||   ||||  | || ||        | | |  ||   |||      ||| |   | || |||||||||||||||| ||||| || |||||||||||||| |||||||| || || ||| | || || |||
gtaagtaactgtta--cagatttttttttgggggggttacaatat--tttcccatctttag-------ttagctgatt--ccacc-----attctgtaacat-gcagGTTTGTTGAGATTATGGCTCCAGTGTTTTCACGAAATGCATGGCGCTGTGTGTGGCATATGATTCAG

upper sequence: PP1S448_20V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA08G14040.1 (Glycine max), 3'ss of exon 10
gtaactagccaccaaacaaagcatcatgtgatgggttcataagatggcttccttttttgagattcgtactcgtttgttggtcactgacggattgttcgatat-cgcagGTTTGTTGAGATCATGGCACCCGTGTTTTCACGAAAAGCATGGCGTTGCGTCTGGTACATAATACAG
                                |    ||| || ||      | ||||   |||  | | |   |      |  |  |  ||| |   ||    |||| ||||||||||| ||||| || |||||||||||| | ||||||||||| |||||| | || || |||
--------------------------------gtaagcatcagttgaagcattatttttgtatt-atccacccataccaaactgtatccaattatgttatgcatgcagATTTGTTGAGATTATGGCTCCAGTGTTTTCACGAGATGCATGGCGTTGTGTCTGGCATATGATTCAG

upper sequence: PP1S448_20V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: AT1G08040.2 (Arabidopsis thaliana), 3'ss of exon 10
gtaactagccaccaaacaaagcatcatgtgatgggttcataagatggcttccttttttgagattcgtactcgtttgttggtcactgacggattgttcgatatcgcagGTTTGTTGAGATCATGGCACCCGTGTTTTCACGAAAAGCATGGCGTTGCGTCTGGTACATAATACAG
       | | |   ||      ||      |   |   |  ||         |         |  ||    ||| | | | || |  |  || | | |  | |||||||||||||||| |||||||| || |||||  || |||||||||| || || ||| | || || |||
---gtacggctctgtactctctttctctcattctctctctttgactaacctactgaagagtgcttatatcaattt-tcgataacaggtgtgttttcccac-ttgcagGTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAG

upper sequence: PP1S448_20V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv14s0066g00310.t01 (Vitis vinifera), 3'ss of exon 8
----------gtaactagccaccaaacaaagcatcatgtgatgggttcataagatggcttccttttttg-agattcgtactcgtttgttggtcactgacggattgttcgatatcgcagGTTTGTTGAGATCATGGCACCCGTGTTTTCACGAAAAGCATGGCGTTGCGTCTGGTACATAATACAG
            |  ||        ||| | |||  ||  |    ||  ||   |      || ||||   |||||  |    | |     | | |||    |  ||  |||| |||| |||||||||||||||||  | |||||||| ||||| ||||||||||| || ||| | || || |||
gtatgtgcacagatttaatttaagtacagaacattttgaaa---atttgtactgtaaggaactgttttatggattcaaataaatct-----ttattgattattacttaaatat-gcagCTTTGTTGAGATCATGGCTACTGTGTTTTCTCGAAATGCATGGCGTTGTGTTTGGCATATGATTCAG

upper sequence: PP1S448_20V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv00s0229g00150.t01 (Vitis vinifera), 3'ss of exon 7
gtaactagccaccaaacaaagcatcatgtgatgggttcataagat-ggcttccttttttgagattcgtactcgtttgttggtcactgacggattgttc--gatatcgcagGTTTGTTGAGATCATGGCACCCGTGTTTTCACGAAAAGCATGGCGTTGCGTCTGGTACATAATACAG
                 |  |   |||   ||    | |||| ||    ||   |      ||  | |      ||   |||  ||||     |  |   ||  | |||||||||||||||| |||||||| || || ||| || |||||||||| || || ||| | || || |||
---------------gtatggttacattaaatattgtaataaaatcaaattatctacactggaaacatgaggcattaaaggt-gctgagatcctacttatgaatttgcagGTTTGTTGAGATTATGGCACCAGTCTTCTCAAGAGAAGCATGGCGCTGTGTTTGGCATATGATCCAG

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|162277818|gb|FC454281.1|FC454281
EST:     GTGGAACATCCTGGTTGGTGCAAAGATCCGCTCAAGCCCCCCTGTGCAGG                         GTTTGTTGAGATCATGGCACCCGTGTTTTCACGAAAAGCATGGCGTTGCGT
genomic: GTGGAACATCCTGGTTGGTGCAAAGATCCGCTCAAGCCCCCCTGTGCAGGgtaactagcc ... gatatcgcagGTTTGTTGAGATCATGGCACCCGTGTTTTCACGAAAAGCATGGCGTTGCGT
EST: gi|37826494|gb|BJ584506.1|BJ584506
EST:     TGGTGCAAAGATCCGCTCAAGCCCCCCTGTGCAGG                         GTTTGTTGAGATCATGGCACCCGTGTTTTCACGAAAAGCATGGCGTTGCGT
genomic: TGGTGCAAAGATCCGCTCAAGCCCCCCTGTGCAGGgtaactagcc ... gatatcgcagGTTTGTTGAGATCATGGCACCCGTGTTTTCACGAAAAGCATGGCGTTGCGT
EST: gi|162277817|gb|FC454280.1|FC454280
EST:     GTGGAACATCCTGGTTGGTGCAAAGATCCGCTCAAGCCCCCCTGTGCAGG                         GTTTGTTGAGATCATGGCACCCGTGTTTTCACGAAAAGCATGGCGTTGCGT
genomic: GTGGAACATCCTGGTTGGTGCAAAGATCCGCTCAAGCCCCCCTGTGCAGGgtaactagcc ... gatatcgcagGTTTGTTGAGATCATGGCACCCGTGTTTTCACGAAAAGCATGGCGTTGCGT
EST: gi|162177786|gb|FC354620.1|FC354620
EST:     GTGGAACATCCTGGTTGGTGCAAAGATCCGCTCAAGCCCCCCTGTGCAGG                         GTTTGTTGAGATCATGGCACCCGTGTTT
genomic: GTGGAACATCCTGGTTGGTGCAAAGATCCGCTCAAGCCCCCCTGTGCAGGgtaactagcc ... gatatcgcagGTTTGTTGAGATCATGGCACCCGTGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttgagattcgtactcgtttgttggtcactgacggattgttcgatatcgcagGTTTGTTGAGATCATGGCACCCGTGTTTTCACGAAAAGCATGGCGTTGCGTCTGGTACATAATACAG
                             cactgac  putative branch site (score: 2)