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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttccccttacactacccacattctactcattagccgcaggctcttggaaccttcggaaaattttgaagtaaatatgtttaatattatattcgatctgatcacagGTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAACAGGAATATCTACGATTGATGTCATGAACTCTATTGCTCGAGGGCAAAA

Basic information

species Physcomitrella patens
transcript PP1S85_75V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 6
-----------gtacttccccttacactacc-cacattctactcattagccgcaggctcttggaacctt-cggaaaattttgaagtaaatatgtt--------taatatta-------tattcgat-ctgatcacagGTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAACAGGAATATCTACGATTGATGTCATGAACTCTATTGCTCGAGGGCAAAA
            |   | |   | |||| |     |   |  |  |||   ||| | ||||  | |  | ||||   |    ||    |||| |         ||||||||         | ||||  | ||  ||||    || || ||||| |||||  | || || ||||| |||||||| |||||||| ||||| || ||||||||||||||||| ||||||||||| |||||
gtaagtttttgctcaattcaggtgcactgctatggaaattcatagttaagtgcatgttcttttatcagtacggatggtggctaaacttatatttctcttctgataatattaataatgtcttccgatgtttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAACAGGGATATCAACCATTGATGTCATGAACTCCATTGCTCGAGGCCAAAA

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 6
--------------------gtacttccccttacactacccacattc---tactcatt------agccgcaggctcttggaacctt-------------cggaaaattttgaag-------taaatatgtttaatattatattc-gatctgatcacagGTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAACAGGAATATCTACGATTGATGTCATGAACTCTATTGCTCGAGGGCAAAA
                    | ||    |  |||| | | ||   |    | |   ||      ||  | ||| | | | |   ||             |   ||||     ||       | ||  | | ||||  | || || ||| |  |  ||||    || || ||||| |||||| | || || |||||||||||||| ||||| || ||||| || |||||||| |||||||| |||||||| ||||||||
gtaagtaatttctggttcaagcacgctgctctacaatgctcatggtgaagtgcatgttgtggagagtagtaggttttagaagtattgattgattagcggcattaaatcaatgagtccatctttaaagtttgtaatcatgtactctgattttgttgcagGAAGTTCTATTAATCCCAGTGAGAGAACCTATCCAGAGGAGATGATCCAAACTGGGATATCCACCATTGATGTGATGAACTCCATTGCTCGTGGGCAAAA

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 5
-----------------------------------------gtacttccccttacactacc-cacattctactcattagccgca--ggctcttggaacc--ttcggaaaattttgaagtaaatatgtttaatattatattcgatctgatcacagGTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAACAGGAATATCTACGATTGATGTCATGAACTCTATTGCTCGAGGGCAAAA
                                          |  ||      |  ||  |   ||   ||    |||| || |  || |  | ||      ||    | |       ||||| |  | |||||    |  ||| |     ||||    || || || || |||||| | || || |||||||||||||| ||||| || ||||| || |||||||||||||| || |||||||| || |||||
gtaagtaatttctggttctagcatgctgctctacaatactcatggttaagtgcatgctgtcgtgcagagtaggttttagacgtattggttaattgagttaaatcaatgagtccatctttaaattttgtaaatatgtactctgattttgctgcagGAAGTTCTATTAACCCCAGTGAGAGAACCTATCCAGAGGAGATGATCCAAACTGGGATATCCACCATTGATGTCATGAATTCCATTGCTCGTGGACAAAA

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 6
gtacttccccttacactacccacattctactcattagccgcaggctcttggaaccttcggaaaat-tttgaagtaaatatgtttaatattatattcgatctgatcacagGTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAACAGGAATATCTACGATTGATGTCATGAACTCTATTGCTCGAGGGCAAAA
                       |||  |||   |    ||||  |  |  ||   |  |   || | |||| |         ||||||  |   | || ||     | ||   || ||||||||||||||||| || ||||| ||||||||||| || || ||||||||||| |||||||||||||| ||||||||| |||| |||||
---------------------gtatttaacttcct--ttgcagtgttctacaattgtatgttgatgtgtgaatttttaccccctaatatctt-cccaatatgtcagGAAGT---TCCATCAATCCTAGTGAGCGAACCTACCCTGAGGAGATGATACAGACTGGAATATCTACAATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 7
gtacttccccttacactacccacattctactcattagccgcaggctcttggaaccttcggaaaat-tttgaagtaaatatgtttaatattatattcgatctgatcacagGTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAACAGGAATATCTACGATTGATGTCATGAACTCTATTGCTCGAGGGCAAAA
                       |||  | |   |    ||||  |  |  ||   |  |   || | |||  |   |     ||||||  |   | ||   ||  ||||    || ||||||||||||||| | || || || ||||||||||| || |||||||||||||| |||||||||||||| ||||||||| |||| |||||
---------------------gtatttaaattcct--ttgcagtgttctacaattgtatgttgatgtgtgagttttttccccctaatatctt-cccaat---atttcagGAAGTTCCATCAATCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGACAGGAATATCTACAATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 6
gtacttccccttacactacccacattctactcattagccgcaggctcttggaaccttcggaaaattttgaagtaaatatgtttaatattatattcgatctg-atcacagGTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAACAGGAATATCTACGATTGATGTCATGAACTCTATTGCTCGAGGGCAAAA-
                                  ||        ||  |||     || ||| ||       |   | ||  |  |   |||||    ||| |   ||||    || ||||| ||||||||| | || || |||||||||||||| || |||||||||||||| |||||||||||||| ||||||||| |||| ||||| 
----------------------------------tatataatttcttctggggaggtctgaatatgcatgtttttctttgcctttttaaatattttccctgtaattcaggAAGTTCCATCAACCCTAGTGAGAGAACCTATCCAGAGGAGATGATACAGACAGGAATATCTACCATTGATGTCATGAATTCTATTGCTAGAGGTCAAAAG

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 6
gtacttccccttacactacccacattctactcattagccgcaggctcttggaaccttcggaaaattttgaagtaaatatg--tttaatattatattcgatctgatcacagGTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAACAGGAATATCTACGATTGATGTCATGAACTCTATTGCTCGAGGGCAAAA
                                  ||        ||  |||     |  ||| || |     ||  | ||  |||  || ||||| |    | ||  ||||    || ||||| ||||||||| | || || || ||||||||||| || ||||| |||||||| |||||||||||||| ||||||||| |||| |||||
---------------------------------gtataaaatttcttctggggaggtatgaatatgtatgtttatctttgccttttttaatatatcccccataatt-cagGAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGACAGGGATATCTACCATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 6
gtacttccccttacactacccacattctactcattagccgcaggctcttggaaccttcggaaaattttgaagtaaatatgtttaatattatat---tcgatc-tgatcacagGTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAACAGGAATATCTACGATTGATGTCATGAACTCTATTGCTCGAGGGCAAAA
                          | | | | |  |   || |  ||| |  ||   || ||    | |  |||| ||||| | ||| | |   |||||  |  | | |||    || ||||| || |||||  | || ||||| || |||||||| ||||| || || ||||| ||||||||||||||||| |||||||| || || ||
---------------------gtgagc-attgactgcctcaagtcaattgtactctgaagagaa----ggaaaaaatctgttttaaattgtttcggtcgataatttttatagGAAGTTCAATCAACCCCAGTGAAAGAACCTACCCTGAAGAGATGATACAAACGGGGATTTCTACCATTGATGTCATGAACTCCATTGCTCGTGGACAGAA

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 7
gtacttccccttacactacccacattctactcattagccgcaggctcttggaaccttcggaaaattttgaagtaaatatgtttaatattatattcgatctgatcacagGTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAACAGGAATATCTACGATTGATGTCATGAACTCTATTGCTCGAGGGCAAAA
                          || ||  |||||| |  | ||    ||          ||  | ||  | | |  | ||||  || | |     |  || ||||    || |||||||| |||||| | || || || || ||||||||||| || || ||||| || |||||||||||||||||||| ||  |||| || ||
---------------------gtgagctgct--ttagcctcttg-tcacataattactatctcataataaaacacacagatataattctagacttttgtttctc-cagGAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGACGGGTATATCCACCATTGATGTCATGAACTCTATCGCCAGAGGACAGAA

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 6
gtacttccccttacactacccacattctactcattagccgcaggctcttggaaccttcggaaaattttgaagtaaatatgtttaatattatattcgatctgatcacagGTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAACAGGAATATCTACGATTGATGTCATGAACTCTATTGCTCGAGGGCAAAA
       |  | |  |||   | ||  |  |   |  ||  | |||   | ||   |   |   | |     || |||    |||  |  |  | |   |  ||| |||    || ||||| || |||||| | || || || || |||||||| |||||||| || ||||| ||||||||||||||||| ||||||||||| |||||
-----gtcagtaatgctaggaagataatgatttattaccaaaagctagggaaaagattttatgttatctggatatataa---taaactcttccttgtctt--tcatagGAAGTTCTATCAACCCCAGTGAGAGAACCTATCCTGAAGAGATGATACAAACAGGGATTTCTACTATTGATGTCATGAACTCCATTGCTCGAGGTCAAAA

upper sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 6
gtacttccccttacactacccacattctactcattagccgcaggctcttggaaccttcggaaaattttgaagtaa-atatgtttaatattatattcgatctgatcacagGTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAACAGGAATATCTACGATTGATGTCATGAACTCTATTGCTCGAGGGCAAAA
||   |    |   |      |   | ||  |||||        ||||    | |||  ||   |     |||   | ||  |  |   | | |     ||  |  ||||    || ||||||||||||||| | || || || || |||||||| || ||||| || ||||| |||||||||||||| ||||||||  |||| || ||
gtgagttttttaggaggtggtattatttaaccattaaaactcacctct---gaactttagagtttacaacagtggcagatcctgtactctttttctttccttttttcagGGAGTTCCATCAATCCTAGTGAGAGAACATATCCTGAAGAGATGATCCAGACAGGGATTTCTACAATTGATGTCATGAATTCTATTGCCAGAGGACAGAA

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|100417322|gb|BY957275.1|BY957275
EST:     TATTGACAACGGCCCTCCAATTCTTGCAGAAGCTTATCTGGACATTTCAG                         GTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAA
genomic: TATTGACAACGGCCCTCCAATTCTTGCAGAAGCTTATCTGGACATTTCAGgtacttcccc ... ctgatcacagGTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAA
EST: gi|67575005|gb|BJ947829.1|BJ947829
EST:     TATTGACAACGGCCCTCCAATTCTTGCAGAAGCTTATCTGGACATTTCAG                         GTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAA
genomic: TATTGACAACGGCCCTCCAATTCTTGCAGAAGCTTATCTGGACATTTCAGgtacttcccc ... ctgatcacagGTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAA
EST: gi|162190700|gb|FC367586.1|FC367586
EST:     TATTGACAACGGCCCTCCAATTCTTGCAGAAGCTTATCTGGACATTTCAG                         GTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAA
genomic: TATTGACAACGGCCCTCCAATTCTTGCAGAAGCTTATCTGGACATTTCAGgtacttcccc ... ctgatcacagGTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAA
EST: gi|18367548|gb|BJ199631.1|BJ199631
EST:     TATTGACAACGGCCCTCCAATTCTTGCAGAAGCTTATCTGGACATTTCAG                         GTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAA
genomic: TATTGACAACGGCCCTCCAATTCTTGCAGAAGCTTATCTGGACATTTCAGgtacttcccc ... ctgatcacagGTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttcggaaaattttgaagtaaatatgtttaatattatattcgatctgatcacagGTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAACAGGAATATCTACGATTGATGTCATGAACTCTATTGCTCGAGGGCAAAA
                                           atctgat  putative branch site (score: 4)
       aaaattttgaagtaaa  TA-rich tract