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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtacacgcaactatgtttatgcagcagtttaaggtcctgcgtactttgtgaaggaattttagcgaacacttagtctgagtttattgtttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA

Basic information

species Physcomitrella patens
transcript PP1S85_168V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S85_168V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os02g52140.2 (Oryza sativa), 3'ss of exon 3
--gtacacgcaactatgtttatgcagcagtttaaggtcctgcgtactttgtgaaggaattttagcgaacacttagtctgagtttattgtttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA
   |  |  | | ||    | ||||      |  | |  |   || | ||  | | |  |||||    || | |   |     ||    |  |    |||||||||||||||| || || ||||||||||| || |||||||||||  ||||||| ||||| ||| | || || || || |||||||||||||||   || |
tttttaattctattaccagtctgcaagcacatctgat--tatctaatctgacatgtacatttagttttcattcatcttagtgatacaaatcatttaccgcagGTTGATTATGCATGTACCCCAGAAGAAGTGCAGCAGCATTTTCAAGCGTGTGGCACAGTCAATAGAGTGACGATCTTAACTGACAAGTTTGGACAGCCAA

upper sequence: PP1S85_168V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM5G862331_T04 (Zea mays), 3'ss of exon 3
gtacacgcaac-tatgtttatgcagcagtttaaggtcctgcgtactttgtgaagg--aattttagcgaacacttagtctgagtttat-tgtttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA
 |  | |  ||  ||  || |  |||  |  |      ||  |||   | | ||   |   | ||  |||||    | |||  | ||    |  ||    |||||| |||||||| ||||| ||||||||||| ||||||||||| ||  | ||||| || || ||  | || ||||| ||||||||||||||||||   || |
-ttaatgggacacatagtt-tctagccttacatttctgtgtctacccagagcagtccacactaagttaacacc--atttgaactgatacaatcatgtactgcagGTGGATTATGCTTGCACCCCAGAAGAAGTGCAACAGCATTTCCAAGCTTGTGGAACTGTCAACAGGGTGACAATCTTGACTGACAAGTTTGGACAGCCAA

upper sequence: PP1S85_168V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G108919_T06 (Zea mays), 3'ss of exon 1
-----gtacacgcaactatgtttatgcagcagtttaaggtcctgcgtactttgtgaaggaatt-ttagcgaacacttagtctgagtttattgtttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA
     ||       | |    | | |||   ||||  || | | | |  | ||| |   | || | ||  | || ||   ||||    ||  | |       ||||||||||||||| ||||| ||||||||||| || |||||||| ||  | ||||| || || ||  | || ||||| |||||||||||||||||    || |
taggcgtgttgcttaatgacataacgca-tggtttgtggccttacat-ttctgttatccatttgtcagtcagcattttaactgatgcaatcatatac----tgcagGTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGTGGAACTGTCAACAGGGTGACAATCTTGACTGACAAGTTTGGGCAGCCAA

upper sequence: PP1S85_168V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G082198_T01 (Zea mays), 3'ss of exon 3
--------gtacacgcaactatgtttatgcagcagtttaaggtcctgcgtactttgtgaaggaattttagcgaacacttagtctgagtttattgtttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA
         ||   | |  ||||| |||    ||| |    |      | | | ||| |    |||  |  | |  || ||| |  || || ||   |  ||   |||||||| ||||| ||||||||||||||||| || ||||||||  | || ||||| || |||||  | || |||||  ||||||||||||||||   ||| |
tcgaagttttatttgtatatatgtctatttgtcagctgtttggttattgaaatatgtaac---attacaa-gtatgctcagtttcggtgtaatgg--caact--acagGTTGACTATGCATGCACTCCAGAAGAAGTGCAGCAGCATTTCAATTCTTGTGGAACTGTTAACAGAGTGACAATCCTGACTGACAAGTTTGGGCAACCAA

upper sequence: PP1S85_168V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA05G31030.1 (Glycine max), 3'ss of exon 2
gtacacgcaactatgttta-tgcagcagtttaaggtcctgcgtactttgtgaaggaatt-ttagcgaacacttagtctgagtttattgtttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA
 |  |      |||| | | || | ||| || | | ||    |   ||   | |  ||| || |||   |       |||  ||    ||| || ||  |||||||||||||| ||||| ||||||||||| || || || |||||||| |||||||| || ||  | ||||| ||  ||||||||||||||||    || |
atctaatttcttatgataactgaatcaggtttaagccccttttggattaacatgatattattggcgtcaaaaccccttgaaattg--atttgtgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACTGACAAGTTTGGCCAGCCTA

upper sequence: PP1S85_168V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA15G06030.1 (Glycine max), 3'ss of exon 3
gtacacgcaactatgtttatgcagcagtttaaggtcctgcgta-ctttgtgaaggaattttagcgaacacttagtctgagtttattgtttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA
 |    |  |  |  |   ||||    |   |  |  | | || |  | |    |     | ||   ||  || ||| | |  |||   | | || | ||||| || ||| | |||||||| |||||||| ||||||||||||||||| ||||| ||||| ||  | ||||| |||   ||||| ||||||||   |||||
tttggtgttaacagatacttgcaaacatagtacttttttcatatcactttacttgttgcattgctctcatataatctca-tggatttgatgttctccacagGTGGACTATTCATGCACTCCTGAAGAAGTGCAACAGCATTTTCAGTCTTGTGGAACAGTAAACAGAGTCACCATTCGAACTGATAAGTTTGGCCAACCCA

upper sequence: PP1S85_168V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA08G14240.1 (Glycine max), 3'ss of exon 2
gtacacgcaactatgttta-tgcagcagtttaaggtcctgcgtactttgtgaaggaattttagcgaacacttagtctgagtttattg-tttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA
     |     |||| | | || | ||  || | | ||  | |      | |    || |||  |    |  |  |       |||| ||| || ||  |||||||||||||| ||||| ||||||||||| || || || |||||||| |||||||| || ||  | ||||| ||  |||| |||||||||||    || |
--tttctttcttatgataactgaatcaagtttaagccccccttttggattaacatgatattattggcatcaaaaccccttgaaattgatttgtgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACAGACAAGTTTGGCCAGCCTA

upper sequence: PP1S85_168V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA08G18970.1 (Glycine max), 3'ss of exon 3
gtacacgcaactatgtttatgcagcagtttaaggtcctgcgtactttg--tgaaggaatttta--gcgaacacttagtctgagtttattgtttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA
       ||  ||  |  |  ||  ||| | | ||  ||  | |||||  |  |    ||  |  ||   ||| || |||  ||  |||   | | || | ||||| || ||| | |||||||| || ||||| ||||||||||||||||| ||||| ||||| ||  |  |||| |||   ||||| ||||||||   |||||
--gttaacagatacttgaaaaca-tagtatcatgtggtgaatgctttggctttacttgttgcattgctctcacataatctt-gtggatttgatattctccacagGTGGACTATTCATGCACTCCTGAGGAAGTGCAACAGCATTTTCAGTCTTGTGGAACAGTAAACAGAATCACCATTCGAACTGATAAGTTTGGCCAACCCA

upper sequence: PP1S85_168V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ10007 (Selaginella moellendorffii), 3'ss of exon 2
gtacacgcaactatgtttatgcagcagtttaaggtcctgcgtactttgtgaaggaattttagcgaacacttagt-ctgagtttattgtttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA
                                      |     ||| |       | ||  ||    ||| |  || |||   | || | | |||   |||| |||||| | ||||| ||||| ||||| |||||||| ||||| || ||||| || ||||| || || || ||||| ||||||||||| |||   ||||
--------------------------------------gtaagttttcttttcttctcttctcgttgccttggaacttagtgagtggtatgttctt---agGTGGATTATTCGTGCACACCAGAGGAAGTCCAACAGCACTTTCAATCCTGTGGCACTGTTAACCGGGTTACTATTTTAACTGACAAGTTCGGACAGCCCA

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|18363019|gb|BJ195091.1|BJ195091
EST:     ATCAAGCGAACCGAGAGGAGGCTGATGCGCGTTCAGTTTTTGTTGGGAAT                         GTTGATTATGCCTGCACT
genomic: ATCAAGCGAACCGAGAGGAGGCTGATGCGCGTTCAGTTTTTGTTGGGAATgtaaacactc ... tgcttcgcagGTTGATTATGCCTGCACT
EST: gi|67507705|gb|BJ940585.1|BJ940585
EST:     ATCAAGCGAACCGAGAGGAGGCTGATGCGCGTTCAGTTTTTGTTGGGAAT                         GTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGT
genomic: ATCAAGCGAACCGAGAGGAGGCTGATGCGCGTTCAGTTTTTGTTGGGAATgtaaacactc ... tgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGT
EST: gi|67578551|gb|BJ950718.1|BJ950718
EST:     ATCAAGCGAACCGAGAGGAGGCTGATGCGCGTTCAGTTTTTGTTGGGAAT                         GTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGT
genomic: ATCAAGCGAACCGAGAGGAGGCTGATGCGCGTTCAGTTTTTGTTGGGAATgtaaacactc ... tgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgaaggaattttagcgaacacttagtctgagtttattgtttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA
                                         tttctgcttc  CT-rich tract
                                  tttattgttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacgcaactatgtttatgcagcagtttaaggtcctgcgtactttgtgaaggaattttagcgaacacttagtctgagtttattgtttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA

- - - - - - - - - -tgcagca