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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTACCCAGTCTTCGAGGTGTTGTACTTCACAGTCCAATCCTTTCCGGACTTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAGgtatgctgatgaactattccttattgcagcaacacgtaatgcaggtttcacaaattcacacggaatctcttccaaagcttttattttatatgagcagacc...

Basic information

species Physcomitrella patens
transcript PP1S123_154V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S123_154V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G039214_T01 (Zea mays), 5'ss of exon 3
GCTACCCAGTCTTCGAGGTGTTGTACTTCACAGTCCAATCCTTTCCGGACTTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAGgtatgctgatgaactattccttattgcag-caacac-gtaatgcaggtttcacaaattcacacggaatctcttccaaagcttttattttatatgagcagacc
  || |    || |||| |||||| || || ||||| ||  | || || ||  |||||||||| || ||||| ||||| || ||||||||||| |||||||| ||  | | | || ||  ||   |||  ||| |  |   |    | |||   |  |||   |     | ||       |        ||   |       
TTTATCTCAGCTGCGAGCTGTTGTCCTGCATAGTCCTATATTGTCAGGGCTGAGAGTTATGTATCCTGTGAAGCGCACATATTGGTTTGACATCTACAAGgtttgtcg-tcatctgttaattgcggcattcaatattgagttatccgcttctatatctcaggtgcctgattttttgttattcaggcgacatgcaattttgt-

upper sequence: PP1S123_154V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA05G02840.1 (Glycine max), 5'ss of exon 3
GCTACCCAGTCTTCGAGGTGTTGTACTTCACAGTCCAATCCTTTCCGGACTTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAGgt---atgctgatgaactattccttattgcagcaacacgtaatgcaggtttcacaaattcacacggaatctcttccaaagcttttattttatatgagcagacc
  ||||| | ||  | | |||||| || |||||||| || || || ||| |  |||| |||||||| |||||||| || |||||||||||||||||||||||   || ||     | | | |  |||          | |  | |       |   ||| ||| |||  |     || || || | || |   || ||||   
TTTACCCCGACTAAGGGCTGTTGTTCTCCACAGTCCTATACTATCAGGATTGAGAGTCATGTACCCTGTGAAACGGACATACTGGTTTGACATTTACAAGgtcagatactttgtcattgtcctatatgctttggtttcctttttctcaagaaaactatttacatgga--cctgaacatag-ttgtgttattcttgcgcag---

upper sequence: PP1S123_154V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA17G13510.1 (Glycine max), 5'ss of exon 3
GCTACCCAGTCTTCGAGGTGTTGTACTTCACAGTCCAATCCTTTCCGGACTTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAGgtatgctgatgaactattccttattgcagcaacacgtaatgcaggtttcacaa---attcacacggaatctcttccaaagcttttattttatatgagcagacc
  ||||| | ||  | | |||||| || |||||||| || || || ||| |  |||| |||||||| |||||||| || || ||||||||||||||||||||  | |  |     |||      |          ||  |     | |   ||   ||| ||| |||  |     ||||| || | || |   ||  |||   
TTTACCCCGACTAAGGGCTGTTGTTCTCCACAGTCCTATACTATCAGGATTGAGAGTCATGTACCCTGTGAAACGGACATATTGGTTTGACATTTACAAGgtcagatactttgtcattgtcctatatgctttggtgtcctttttctctagaaaactatttacatgga--cctgaacaaag-ttgtgttattcttgcacag---

upper sequence: PP1S123_154V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA06G18400.1 (Glycine max), 5'ss of exon 3
GCTACCCAGTCTTCGAGGTGTTGTACTTCACAGTCCAATCCTTTCCGGACTTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAGgtatgctgatgaactattccttattgcagcaacacgtaatgcaggtttcacaaattcacacggaatctcttccaaa--gcttttattttata--tgagcagacc
  ||||| ||||  | | |||||| || |||||||| || || || || ||  |||| |||||||| |||||||| || ||||||||||||||||| ||||| |    ||    |||| | ||||   ||   | || ||   | ||| | || |    | |  || | |   ||     ||  |||||||   |  ||||   
TTTACCCCGTCTAAGGGCTGTTGTTCTCCACAGTCCTATACTATCAGGGCTGAGAGTCATGTACCCTGTGAAACGGACATACTGGTTTGACATTTATAAGgttta--aattttttatttcctattt--gcttgatgtcattt-gatttgaaaattatgtatgtgatgtatctgaacttagttccattttattgttttgcag---

upper sequence: PP1S123_154V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA04G36460.1 (Glycine max), 5'ss of exon 3
GCTACCCAGTCTTCGAGGTGTTGTACTTCACAGTCCAATCCTTTCCGGACTTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAGgtatgctgatgaactattccttattgcagcaacacgtaatgcaggtttcacaaattcacacggaatctcttccaaagctt----ttattttata--tgagcagacc
  ||||| ||||  | | |||||| || |||||||| || || || || ||  |||| |||||||| |||||||| || ||||||||||||||||| |||||      ||    |||| | | ||   ||   | || ||   | ||| | || |    | |   | | |  |  | |||      |||||||   |  ||||   
TTTACCCCGTCTAAGGGCTGTTGTTCTCCACAGTCCTATACTATCAGGGCTGAGAGTCATGTACCCTGTGAAACGGACATACTGGTTTGACATTTATAAGgt---taaattttttatttcctgttt--gcttgatgtcattt-gatttgaaaattatgtaagtggtgtgtatctgaacttagttccattttattgttttgcag---

upper sequence: PP1S123_154V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA19G04900.1 (Glycine max), 5'ss of exon 3
GCTACCCAGTCTTCGAGGTGTTGTACTTCACAGTCCAATCCTTTCCGGACTTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAGgtatgctgatgaactattccttattgcagcaacacgtaatgcaggtttcacaaatt-cacacggaatctcttccaaagcttttattttatatgagcagacc
  || | |  ||| | | |||  | || |||||||||||| | || || ||||| || ||||| || || || ||||| ||||||||||||||||| ||||| |     | | | || |   ||||  |  |  | |||| ||   |   ||| || ||  |    |    |     |  ||  ||| ||           
TTTATCAAACCTTAGGGCTGTGATTCTCCACAGTCCAATCTTATCTGGCCTTCGTGTCATGTATCCTGTAAAGCGCACATACTGGTTTGACATTTATAAGgttttacctttatcaatgctgaattg--gtgaatcataattcataatgttcaattttcattcattttaatattattggtcttcttttgatgcag-------

upper sequence: PP1S123_154V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA13G06890.1 (Glycine max), 5'ss of exon 3
GCTACCCAGTCTTCGAGGTGTTGTACTTCACAGTCCAATCCTTTCCGGACTTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAGgtatgctgatgaactattccttattgcagcaacacgtaatgcaggtttcacaa-attcacacggaatctcttccaaagctttta-ttttatatgagcagacc
  |||| |  ||| | | |||  | || |||||||||||| | || || ||||| || |||||  | ||||| ||||| ||||||||||||||||| ||||| |       | ||||  |  | |||   ||   || |  ||   |||| ||  |||||     |||  ||  ||   | ||  | || | |   |  |  
TTTACCAAACCTTAGGGCTGTGATTCTCCACAGTCCAATCTTATCGGGCCTTCGTGTCATGTATTCTGTGAAGCGCACATACTGGTTTGACATTTATAAGgtttt------acctatatc--aatgcta-aattggtgaatcataattcataatgttcacttttcatccattttaatattattggtcttcttttgacgcag-

upper sequence: PP1S123_154V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT4G24760.1 (Arabidopsis thaliana), 5'ss of exon 3
GCTACCCAGTCTTCGAGGTGTTGTACTTCACAGTCCAATCCTTTCCGGACTTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAGgtatgctgatgaactattccttattgcagcaacacgtaatgcaggtttcacaaattcacacggaatctcttccaaagcttttattttatatgagcagacc
  | ||  | ||  ||| |    | ||||| |||||||| ||||| || ||| |||||||||| || || || || || || ||||||||||| ||||||||   |  || |     |  | ||| |   |   | | |||  | |   | | ||||   |      ||||   |   |||| ||| || |         
TTTGCCTCGACTAAGAGCTTCCATTCTTCATAGTCCAATTCTTTCTGGGCTTAGAGTTATGTATCCCGTTAAGCGAACTTATTGGTTTGACATATACAAGgtgaac--ataatacccttttgatttctcta---catgatgttgctgataaacattcctcc-----ttcttgacaccgttttgtttgatcttcttcag--

upper sequence: PP1S123_154V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv01s0010g00670.t01 (Vitis vinifera), 5'ss of exon 3
GCTACCCAGTCTTCGAGGTGTTGTACTTCACAGTCCAATCCTTTCCGGACTTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAGgtatgctgatgaactattccttattgcagcaacacgtaatgcaggtttcacaaattcacacggaatctcttccaaagcttttattttatatgagcagacc
  |  |  |  |  | | |||| | ||||||||||||||||| || || |||||||| ||||| || ||||| || || |  |||||||| || ||||||||||         || ||   | |||         | | ||   || |   || ||    |     ||| | ||  | | ||  ||| |    ||||   
TTTCGCTCGATTGAGGGCTGTTATTCTTCACAGTCCAATCCTATCTGGGCTTCGAGTCATGTATCCTGTGAAGCGAACATTTTGGTTTGATATCTACAAGgtatttc------cttttttcttttg----gttgtgcattgtcagtgtttaaattttgtcc-----ctcattcatgggtgtttgtttctgct-gcag---

upper sequence: PP1S123_154V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv14s0006g02620.t01 (Vitis vinifera), 5'ss of exon 3
GCTACCCAGTCTTCGAGGTGTTGTACTTCACAGTCCAATCCTTTCCGGACTTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAGgtatgctgatgaactattccttattgcagcaa-cacgtaatgcaggt---ttcacaaattcacacggaat--------ctcttccaaagcttttattttatatgagcagacc------------------------------
  || | |   |  ||||||| ||  | || || |||||  | || ||  |  | ||  ||||||| || ||||| || ||||||||||| |||||||||||||    || |     || |   |  |  |  ||  || || ||     ||   |  || |     |||        || | |    | ||||||||| |||| |                                    
TGTATCAAACTTGAGAGGTGTGGTCTTACATAGCCCAATTTTGTCTGGGTTGAGGGTCTTGTACCCTGTCAAACGGACATACTGGTTTGATATTTACAAGgtatttccatcatactatcgtggctagattagtcagatagtggagtcatatttttatttttatttttaattcttttctctttacttttgtttttattttttatgggtgattggggctcacttctttgctttgttcttttcag

upper sequence: PP1S123_154V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv14s0083g00800.t01 (Vitis vinifera), 5'ss of exon 3
GCTACCCAGTCTTCGAGGTGTTGTACTTCACAGTCCAATCCTTTCCGGACTTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAGgtatgctgatgaactattccttattgcagcaacacgtaatgcaggtttcacaaattcacacggaatctcttccaaagcttttattttatatgagcagacc
| || | ||  |  | | ||| || || |||||  ||||| | || |||||| ||||  |||| ||||||||||| || || ||||||||||||| |||||| ||||       |     ||| || |   |   || ||| | ||||    |||| |     | |  |  | || |   |   |||||  | ||||   
GTTATCAAGATTGAGGGCTGTAGTTCTCCACAGCGCAATCTTGTCTGGACTTAGAGTCCTGTATCCAGTGAAACGGACATATTGGTTTGACATTTTCAAGgtttgct-------tgccttttaatgaattcaatggttatgtaagttt---gaattta-----acttaccactaatggccta--tttatg-gtgcag---

upper sequence: PP1S123_154V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ19908 (Selaginella moellendorffii), 5'ss of exon 3
GCTACCCAGTCTTCGAGGTGTTGTACTTCACAGTCCAATCCTTTCCGGACTTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAGgtatgctgatgaactattccttattgcagcaacacgtaatgcaggtttcacaaattcacacggaatctcttccaaagcttttattttatatgagcagacc
 || || || || || | ||| || |||||||| || || || || ||||| ||||| ||||| || ||||| |||||||||||||||||||| |||||||||   || ||   | |||  | ||                ||  |||| ||    ||| |  |    |   ||  |||||| || | |  | ||||   
ACTGCCAAGGCTCCGGGCTGTAGTTCTTCACAGCCCGATTCTATCTGGACTGCGAGTAATGTATCCCGTGAAGCGCACGTACTGGTTTGACATCTACAAGgtactttgttg---ttttctctttt----------------cacttttcccag---cacgca-agctccgctcactgctttttttgttttcgcgcag---

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|162158593|gb|FC335506.1|FC335506
EST:     TTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAG                         AACATTGACAAAATTGGTCAAATCTCCTGTCCCGTACTCGTGATGCAT
genomic: TTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAGgtatgctgat ... aattttgcagAACATTGACAAAATTGGTCAAATCTCCTGTCCCGTACTCGTGATGCAT
EST: gi|208369768|gb|DC944190.1|DC944190
EST:     TTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAG                         AACATTGACAAAATTGGTCAAATCTCCTGTCCCGTACTCGTGATGCAT
genomic: TTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAGgtatgctgat ... aattttgcagAACATTGACAAAATTGGTCAAATCTCCTGTCCCGTACTCGTGATGCAT
EST: gi|67725568|gb|BJ975827.1|BJ975827
EST:     TTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAG                         AACATTGACAAAATTGGTCAAATCTCCTGTCCCGTACTCGTGATGCAT
genomic: TTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAGgtatgctgat ... aattttgcagAACATTGACAAAATTGGTCAAATCTCCTGTCCCGTACTCGTGATGCAT
EST: gi|162245814|gb|FC420780.1|FC420780
EST:     TTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAG                         AACATTGACAAAATTGGTCAAATCTCCTGTCCCGTACTCGTGATGCAT
genomic: TTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAGgtatgctgat ... aattttgcagAACATTGACAAAATTGGTCAAATCTCCTGTCCCGTACTCGTGATGCAT
EST: gi|37848196|gb|BJ606204.1|BJ606204
EST:     TCGAGTTAATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAG                         AACATTGACAAAATTGGTCAAATCTCCTGTCCCGTACTCGTGATGCAT
genomic: TCGAGTT-ATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAGgtatgctgat ... aattttgcagAACATTGACAAAATTGGTCAAATCTCCTGTCCCGTACTCGTGATGCAT
EST: gi|208361618|gb|DC950320.1|DC950320
EST:     TTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAG                         AACATTGACAAAATTGGTCAAATCTCCTGTCCCGTACTCGTGATGCAT
genomic: TTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAGgtatgctgat ... aattttgcagAACATTGACAAAATTGGTCAAATCTCCTGTCCCGTACTCGTGATGCAT
EST: gi|67726537|gb|BJ976796.1|BJ976796
EST:     TTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAG                         AACATTGACAAAATTGGTCAAATCTCCTGTCCCGTACTCGTGATGCAT
genomic: TTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAGgtatgctgat ... aattttgcagAACATTGACAAAATTGGTCAAATCTCCTGTCCCGTACTCGTGATGCAT
EST: gi|208393539|gb|DC949701.1|DC949701
EST:     TTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAG                         AACATTGACAAAATTGGTCAAATCTCCTGTCCCGTACTCGTGATGCAT
genomic: TTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAGgtatgctgat ... aattttgcagAACATTGACAAAATTGGTCAAATCTCCTGTCCCGTACTCGTGATGCAT
EST: gi|208357448|gb|DC953772.1|DC953772
EST:     TTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAG                         AACATTGACAAAATTGGTCAAATCTCCTGTCCCGTACTCGTGATGCAT
genomic: TTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAGgtatgctgat ... aattttgcagAACATTGACAAAATTGGTCAAATCTCCTGTCCCGTACTCGTGATGCAT
EST: gi|162158592|gb|FC335505.1|FC335505
EST:     TTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAG                         AACATTGACAAAATTGGTCAAATCTCCTGTCCCGTACTCGTGATGCAT
genomic: TTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAGgtatgctgat ... aattttgcagAACATTGACAAAATTGGTCAAATCTCCTGTCCCGTACTCGTGATGCAT

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: 18 (upstream exon), 27 (downstream exon)
Score: 3

GCTACCCAGTCTTCGAGGTGTTGTACTTCACAGTCCAATCCTTTCCGGACTTCGAGTTATGTACCCAGTGAAACGCACGTACTGGTTTGACATTTACAAGgtatgctgat ... aattttgcagAACATTGACAAAATTGGTCAAATCTCCTGTCCCGTACTCGTGATGCAT




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