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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcacagtggcttttgtgctacatgttgatgaatcatacgaactacgttatactgcagcatatgtgtgctttttctttctcctcgtactgactaaggctagatattggtggtggcgatttcagGAGCATTTGTTCATAGTTTGTGAGTTACTTCGAGCTAATTTGTACGAGTTCCACAAATACAACAGAGAATCAGGTGGTGAGGTGTACTTTACGATGCCCC

Basic information

species Physcomitrella patens
transcript PP1S47_312V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S47_312V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G181002_T01 (Zea mays), 3'ss of exon 3
gtaatcacagtggcttttgtgctacatgttgatgaatcatacgaactacgttatactgcagcatatg-tgtgctttttctttctcctcgtactgactaaggctagatattggtggtggcgatttcagGAGCATTTGTTCATAGTTTGTGAGTTACTTCGAGCTAATTTGTACGAGTTCCACAAATACAACAGAGAATCAGGTGGTGAGGTGTACTTTACGATGCCCC
                 |     ||   |     || || |       ||    || ||| |||||  |    ||| |  |  |    ||||| ||| |   || | |||| | |         |||||||||||| | ||||| |||||  | ||    || ||| |||||||||| || |||| ||||||||||||||| |||||||| ||||| || |||||  
-----------------taaatgactcttctccaaaacaaattgctctcgagtcacagcatcatataataaagtttgttgtgtttgctgtact-acttattttaaacattgtttg---------cagGAGCATTTGCTGATAGTCTGTGAACTTCTGAAGGCAAATCTGTACGAGTTTCAGAAATTCAACAGAGAATCAGGGGGTGAGGTTTACTTCACAATGCCAA

upper sequence: PP1S47_312V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G015073_T01 (Zea mays), 3'ss of exon 3
gtaatcacagtggcttttgtgctacatgttgatgaatcatacgaa-ctacgttatactgcagcatatgtgtgctttttctttctcctcgtactgactaaggctagatattggtggtggcgatttcagGAGCATTTGTTCATAGTTTGTGAGTTACTTCGAGCTAATTTGTACGAGTTCCACAAATACAACAGAGAATCAGGTGGTGAGGTGTACTTTACGATGCCCC
         |    ||  | |||    |||||| | |  | |    | |    |   |||   | |         |||||||  |         ||| |    | ||| || | |         ||||| |||||| | ||||| |||||  | ||    || ||| |||| ||||| || |||| ||||||||||||||| |||||||| ||||| || |||||  
---------ggaatttcagagctcagggttgataattggttcttttccaaagcaatttgccttaaagtcacaacatttctttacc---------acttatttcaaatactgtttg---------cagGAACATTTGCTGATAGTCTGTGAACTTCTGAAGGCAAATCTGTATGAGTTTCAGAAATTCAACAGAGAATCAGGGGGTGAGGTTTACTTCACAATGCCAA

upper sequence: PP1S47_312V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA08G06160.1 (Glycine max), 3'ss of exon 5
gtaatcacagtggcttttgtgctacatgttgatgaatcatacgaactacgttatactgcagcatatgtgtgctttttctttctcctcgtactgactaaggctagatattggtggtggcgatttcagGAGCATTTGTTCATAGTTTGTGAGTTACTTCGAGCTAATTTGTACGAGTTCCACAAATACAACAGAGAATCAGGTGGTGAGGTGTACTTTACGATGCCCC
                   || |   |  || | | |  |     |   ||| || |     |||  ||| |      |||  | ||  | |   | |  ||   | ||     ||   ||  |||||||||||||| ||||| |||||| |||||  ||| || ||||| ||||| || ||||  || ||||||||||||||||| ||||||||||| |||||  
-------------------tgtttacttctgttaattttttaatgccttgtt-tatta----atagttgtacaccaaatttgccatctgatttcatcactctttcttttcccattgt--atggcagGAGCATTTGTTAATAGTATGTGAGCTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA

upper sequence: PP1S47_312V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA05G33560.1 (Glycine max), 3'ss of exon 3
gtaatcacagtggcttttgtgctacatgttgatgaatcatacgaactacgttatactgcagcatatgtgtgctttttctttctc-ctcgtactgactaaggctagatattggtggtggcgatttcagGAGCATTTGTTCATAGTTTGTGAGTTACTTCGAGCTAATTTGTACGAGTTCCACAAATACAACAGAGAATCAGGTGGTGAGGTGTACTTTACGATGCCCC
          |  ||| |||  ||  | ||||     | |    | |   |  | || || || || |||  | |  |||| || ||| | ||         |    ||||         ||  ||||| |||||||| ||||| |||||  |||||  ||| || ||||| ||||| || ||||  || ||||||||||||||||| ||||||||||| |||||  
--------gtttacttctgt--taatttttgaatggccttgtttatt-tatagttctacaccaaatttgtcatctaactttatcactctttct--------tttcccattgt--------atggcagGAACATTTGTTAATAGTATGTGAACTACTTAAAGCAAACTTGTATGAGTTTCATAAATTTAATAGAGAATCAGGTGGTGAAGTGTACTTTACAATGCCAA

upper sequence: PP1S47_312V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT1G73450.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------------gtaatca-cagtggcttt-tgtgctacatgttgatgaatcatacgaactacgt-tatactgcagcatatgtgtgctttttctttctcctcgtactgactaaggctagatattggtgg--tggcgatttcagGAGCATTTGTTCATAGTTTGTGAGTTACTTCGAGCTAATTTGTACGAGTTCCACAAATACAACAGAGAATCAGGTGGTGAGGTGTACTTTACGATGCCCC
                                                     || | ||   ||| |||| | | | |||  || |  |    |  |||| |  |   |  |     |||  | |||  | | | |||    | | ||  |   |  |   |||    |  ||    || |||||||| ||| | || || |||||  | |||   || ||| | ||||||||||||||||  |||||||||||||||||||| || || || ||||||||  
gtaagtgattacatcccttttgcaaaatttggttttgctactgtatatcaaaagtgaccaattgtgtctttctcttcaacaattttagcacaagtgtgaaccatatgccttttatttaatacctttgcaatatttctctttgtggattgtttggtgtaacggattccctgaatgttctttgcagGAGCACTTGCTAATTGTATGTGAACTTCTTAAGGCCAATCTATACGAGTTCCACAAATTTAACAGAGAATCAGGTGGTGAAGTTTATTTCACGATGCCAA

upper sequence: PP1S47_312V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT1G73460.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaatcacagtggcttttgtgctacatgttgatgaatcatacgaactacgttatactgcagcatatgtgtgct-ttttctttctcctcgtactgactaaggcta--gatattggtggtggcgatttcagGAGCATTTGTTCATAGTTTGTGAGTTACTTCGAGCTAATTTGTACGAGTTCCACAAATACAACAGAGAATCAGGTGGTGAGGTGTACTTTACGATGCCCC
                            ||||   || | | |    |   || |||  || |  | ||   | || | | |||    | | ||  |   |  |  |||        ||    || |||||||| ||| | || || |||||  | |||   || ||| | ||||| ||||||||||  |||||||||||||||||||| || || || ||||||||  
---------------------------attgaaatataa-aggggtcataataaacta-agtaggtttgcattattatatctctttgtggattgtttggtgtaacggattccctgaatgttctttgcagGAGCACTTGCTAATTGTATGTGAACTTCTTAAGGCCAATCTATACGAATTCCACAAATTTAACAGAGAATCAGGTGGTGAAGTTTATTTCACGATGCCAA

upper sequence: PP1S47_312V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ29918 (Selaginella moellendorffii), 3'ss of exon 1
gtaatcacagtggcttttgtgctacatgttgatgaatcatacgaactacgttatactgcagcatatgtgtgctttttctttctcctcgtactgactaaggctagatattggtggtggcgatttcagGAGCATTTGTTCATAGTTTGTGAGTTACTTCGAGCTAATTTGTACGAGTTCCACAAATACAACAGAGAATCAGGTGGTGAGGTGTACTTTACGATGCCCC
                                                                  ||  |   |||  | |   ||  |||| |        | || ||          |||||||||||  | || || || |||||| |||| ||||||||| |||||||||| ||||| |||||| |||| || || || ||||| || || ||||||||  
------------------------------------------------------------------gtaagacgttttgtgcaattctcactgtc--------ggtactgaaaccaaacttttcagGAGCACCTATTTATCGTCTGTGAGCTACTACGAGCTAATCTGTACGAGTTTCACAAGTACAACCGAGATTCGGGAGGGGAGGTCTATTTCACGATGCCTA

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|162162553|gb|FC338647.1|FC338647
EST:     GACTGTACGATTACTTTTACCACAAG                         GAGCATTTGTTCATAGTTTGTGAGTTACTTCGAGCTAATTTGTACGAGTTC
genomic: GACTGTACGATTACTTTTACCACAAGgtaatcacag ... gcgatttcagGAGCATTTGTTCATAGTTTGTGAGTTACTTCGAGCTAATTTGTACGAGTTC
EST: gi|162256790|gb|FC432684.1|FC432684
EST:     CGGGTGATAAACACCATCTGTTGCGACTGTACGATTACTTTTACCACAAG                         GAGCATTTGTTCATAGTTTGTGAGTTACTTCGAGCTAATTTGTACGAGTTC
genomic: CGGGTGATAAACACCATCTGTTGCGACTGTACGATTACTTTTACCACAAGgtaatcacag ... gcgatttcagGAGCATTTGTTCATAGTTTGTGAGTTACTTCGAGCTAATTTGTACGAGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttttctttctcctcgtactgactaaggctagatattggtggtggcgatttcagGAGCATTTGTTCATAGTTTGTGAGTTACTTCGAGCTAATTTGTACGAGTTCCACAAATACAACAGAGAATCAGGTGGTGAGGTGTACTTTACGATGCCCC
                 tactgac  putative branch site (score: 1)
                              tagatatt  TA-rich tract