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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttttagacacggaaattcaacaacacgatggaattctctgtttttcaatggattgaattgtgtgggtttctgattgtaggttaagcaacacaagagctgaatggaaaatatggtgcacgtttggcagGTCATAGACAAATCATTTGGTTTTGATACCGCAGTTGAAGAAGCACAGCGTGCAATTAATGCTGCGCACGTGGAAGCTGAGAGTGTTCATAATGGCATTG

Basic information

species Physcomitrella patens
transcript PP1S81_165V6.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 8
gtacgttttagacacggaaattcaacaacacgatggaattctctgtttttcaatggattgaattgtgtgggtttctgattgtaggttaagcaacacaagagctgaatggaaaatatggtgcacgtttggcagGTCATAGACAAATCATTTGGTTTTGATACCGCAGTTGAAGAAGCACAGCGTGCAATTAATGCTGCGCACGTGGAAGCTGAGAGTGTTCATAATGGCATTG
                                  | |||  ||| |||  || |  |||||  |   | || |    ||| | |  ||    |  ||  |  ||  |  |   ||||           |||||| || |||| |||||||||||| || || |||||||| || || || |||||||| |||||||| || || |||||||  || |   | ||||| || |
----------------------------------gtaatgatctttttcacattatattgacat---tagggtatgaattatggtgtat---atgcataatttgtttctaccctatgt----------gcagGTAATTGACAGATCATTTGGTTTCGACACTGCAGTTGAGGAGGCCCAACGTGCAATAAATGCTGCTCATGTAGAAGCTGGAAGCGCCGAGAATGGTATAG

upper sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os05g44922.2 (Oryza sativa), 3'ss of exon 8
gtacgttttagacacggaaattcaacaacacgatggaat--tctctgtttttcaatggattgaattgtgtgggtttctgattgtaggttaagcaacacaagagctgaatggaaa----atatggtgcacgtttggcagGTCATAGACAAATCATTTGGTTTTGATACCGCAGTTGAAGAAGCACAGCGTGCAATTAATGCTGCGCACGTGGAAGCTGAGAGTGTTCATAATGGCATTG
                | | ||        |||||      | | ||| |   |||   ||| |  |  ||   ||| | |    | | |  | | |  |   || | ||   |    |  |  | |  | ||   || |||| ||||| ||||||||||||||||| || || ||||| || |||||||| ||| || | || || |||||||||   |||| | | ||||| || |
----------------gtattttttttgtgcgatgtgtctatttttgtgtagaaatttgttgtac-gcatgctgttcagttgacggttcatacgagattatgacttattgcttatgttacctttttcttgattcttagATCATTGACAAGTCATTTGGTTTTGATACGGCCGTAGAAGAGGCCCAGCGTGCCATTGATTCAGCTCATGTGGAAGCTTGCAGTGCTGAGAATGGAATAG

upper sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM5G879882_T01 (Zea mays), 3'ss of exon 1
gtacgttttagacacggaaattcaacaacacgatggaattctctgtttttcaatggattgaattgtgtgggtttctgattgtaggttaagca-acacaagagctgaatggaaaatatggtgcacgtttggc-agGTCATAGACAAATCATTTGGTTTTGATACCGCAGTTGAAGAAGCACAGCGTGCAATTAATGCTGCGCACGTGGAAGCTGAGAGTGTTCATAATGGCATTG------------------------------
                                                                                         ||| | ||  |  ||     ||  || || |  |  | |||  |||| |||||||| ||||||||||||||||| || || |||||||| |||||||| |||||||| || || |||||||||   |||| | | ||||| || |                              
-----------------------------------------------------------------------------------------gcagagacctgtactatgctgattatttg-tatatatatggttaggttatagacaagtcatttggttttgatactgctgtagaagaagcccagcgtgccatTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAGGTTTAGTGAAGCTTATGGGTCGCTATAGTG

upper sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM5G879882_T03 (Zea mays), 3'ss of exon 8
gtacgttttagacacggaaattcaacaacacgatggaattctctgtt--tttcaatggattgaattgtgtgggtttctgattgtaggttaagcaacacaagagctgaatggaaaatatggtgcacgtttggc-agGTCATAGACAAATCATTTGGTTTTGATACCGCAGTTGAAGAAGCACAGCGTGCAATTAATGCTGCGCACGTGGAAGCTGAGAGTGTTCATAATGGCATTG
|||  |||| | |||    | |      |      |  | |   | |  |||   || ||  |  | |     |    || |||||   |    | ||  |  ||     ||  || || |  |  | |||  |||| |||||||| ||||||||||||||||| || || |||||||| |||||||| |||||||| || || |||||||||   |||| | | ||||| || |
gtaatttttggccacttctacttgttctcttttcagcttgcatagatgcttttgctgcat--acctcttgatttggaagactgtagtgcag---agacctgtactatgctgattatttg-tatatatatggttagGTTATAGACAAGTCATTTGGTTTTGATACTGCTGTAGAAGAAGCCCAGCGTGCCATTAATGCAGCTCATGTGGAAGCTTCAAGTGCTGAAAATGGAATAG

upper sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM5G816636_T02 (Zea mays), 3'ss of exon 8
gtacgttttagacacggaaattcaacaacacgatggaattctctg-tttttcaatggattgaattgtgtgggtttctgattgtaggttaagcaacacaagagctgaatggaaaatatggtgcacgtttggcagGTCATAGACAAATCATTTGGTTTTGATACCGCAGTTGAAGAAGCACAGCGTGCAATTAATGCTGCGCACGTGGAAGCTGAGAGTGTTCATAATGGCATTG
                    |   |     |     | ||   || | |||   ||||   ||| |     |    |     | | | |    |  |  | | || | | |     || | | | | |  ||||| || ||||| ||||||||||| || || |||||||| || || || |||||||| |||||||| || ||||||||||  |||| | | ||||| || |
-------------------gtaatatgtttctccacattttagtgatattttggtggaaaaaatggaagatgacatttgacat-gatcacatgaaccttgtg-tgcacgaactcactgttacccatgtttcagGTAATTGACAAGTCATTTGGTTTCGACACAGCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAG

upper sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 7
gtacgttt-tagaca----cggaaattcaacaacacgatggaattctctgtttttcaatggattgaattgtgtgggtttctgattgtaggttaagcaacacaagagctgaatggaaaatatggtgcacgtttggcagGTCATAGACAAATCATTTGGTTTTGATACCGCAGTTGAAGAAGCACAGCGTGCAATTAATGCTGCGCACGTGGAAGCTGAGAGTGTTCATAATGGCATTG
||| | || |  |||    |  |  ||      | |  ||||| |||    || ||| |  | |  |||   ||   |  || || |   | ||| |||   |     | || |         | |   ||    |||| || |||||||| |||||||||||||| || ||||| || || || ||||| |||||||| || || || |||||||| ||| || | ||||||||||
gtatgcttgttcacaatgtcatattttttgttcctccctggaactctaatcttatcattaaaatacatt---tgaagtgttggttatctatgaagaaacttcatgttcggattgcc-------ttctttttctttagGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGCATTG

upper sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA10G33820.1 (Glycine max), 3'ss of exon 8
gtacgttttagacacggaaattcaacaacacgatggaattctctgtttttcaatggattgaattgtgtgggtttctgattgtaggttaagcaacacaagagctgaatggaaaatatggtgcacgtttggc---agGTCATAGACAAATCATTTGGTTTTGATACCGCAGTTGAAGAAGCACAGCGTGCAATTAATGCTGCGCACGTGGAAGCTGAGAGTGTTCATAATGGCATTG
                     || ||    | |||| ||||| | | |||      ||| ||    ||   |   ||     |  | |||||          |  |||  |    | ||    |||||||   |||| ||||||||||| ||||| |||||||| || || |||||||| ||| | || ||||| ||||| || ||||| | ||| |||||| | |||||  |||
-------------------tgtctacttt-caatggcattctttatattt------attaaaacaagtatatccttgg--acaaatgaagcatt-------ttttatgttattacttgtttgtgtttggctccagGTGATAGACAAATCTTTTGGATTTGATACTGCTGTGGAAGAAGCCCAGAGAGCCATTAACGCTGCACATGTGGAGGTTGAAAGTGTTGAAAATGGAGTTG

upper sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 8
----gtacgttttagacacggaaattcaacaacacgatggaattctctgtttttcaatggattgaattgtgtgggtttctgattgtaggttaagcaacacaagagctgaatggaaaatatggtgcacgtttggcagGTCATAGACAAATCATTTGGTTTTGATACCGCAGTTGAAGAAGCACAGCGTGCAATTAATGCTGCGCACGTGGAAGCTGAGAGTGTTCATAATGGCATTG
    |   |||    |      | ||      | |  ||||| |||    || ||| |  | |  ||    ||   |  |  || |   | | | |||   |    ||   |||   | |  |     |||   |||| || |||||||| |||||||||||||| || ||||| || || || ||||| |||||||| || || || |||||||| ||| || | ||||| ||||
gtatgcttgttcacaatgtcatatttttgtttctccctggaactctaatcttatcattaaaatatatc---tgaagtgttagttctctatgaggaaacttcatca-tgttcggattgtcttctttttcttt---agGTTATTGACAAATCTTTTGGTTTTGATACTGCGGTTGAGGAGGCTCAACGTGCCATTAATGCAGCTCATGTTGAAGCTGAAAGTATTGAGAATGGTATTG

upper sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 9
lower sequence: AT5G61580.1 (Arabidopsis thaliana), 3'ss of exon 7
gtacgttttagacacggaaattcaacaacacgatggaattctctgtttttcaatggattgaattgtgtgggtttctgattgtaggttaagcaacacaagagctgaatggaaaatatggtgcacgtttggcagGTCATAGACAAATCATTTGGTTTTGATACCGCAGTTGAAGAAGCACAGCGTGCAATTAATGCTGCGCACGTGGAAGCTGAGAGTGTTCATAATGGCATTG
                               |     |  |  || |  |       || |  | |     | ||| || || |  |     | |||    ||  ||       || || |         |||| || |||||||||||||| |||||||| || ||||| |||||||| || || ||||||||||| || || || |  ||||| ||  | |||||  |||
-------------------------------gtaaatacccattgataattttcaacttaaggtctacttttctctcat-gtggagtttcttatacatcttcttcatc-----cattgttc--------tagGTGATTGACAAATCATTTGGCTTTGATACGGCGGTTGAGGAAGCACAACGAGCTATTAATGCTGCACATGTAGAGGTCGAGAGCGTGGAAAATGGAGTTG

upper sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv04s0008g00520.t01 (Vitis vinifera), 3'ss of exon 8
gtacgttttagacacggaaattcaac-aacacgatggaattctctgt--ttttcaatggattgaattgtgtgggtttctgattgtaggttaagcaacacaagagctgaatggaaaatatggtgcacgtttggcagGTCATAGACAAATCATTTGGTTTTGATACCGCAGTTGAAGAAGCACAGCGTGCAATTAATGCTGCGCACGTGGAAGCTGAGAGTGTTCATAATGGCATTG
|||| | ||    |  | |  | ||  ||     |    |||||  |  ||||||||  |     |||  |  |  | | || ||   || | |               | ||     |  |     ||   ||||| || |||||||| |||||||||||||| || |||||||||||||||||||| |||||||| || || || ||| |||| ||| || | ||||| ||||
gtacttcttgcctattgcacctgaattaattttgttcttttctccatctttttcaataaacc---ttgcattagcctgtaat-gtgtcttcacct--------------tagactgccttctcttgatt---cagGTTATTGACAAATCGTTTGGTTTTGATACTGCTGTTGAAGAAGCACAGCGTGCCATTAATGCGGCACATGTTGAATCTGAAAGTATTGAGAATGGTATTG

upper sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv16s0013g01140.t01 (Vitis vinifera), 3'ss of exon 8
gtacgttttagacacggaaattcaacaacacgatggaattctctgtttttcaatggattgaattgtgtgggtttctgattgtaggttaagcaacacaagagctgaatggaaaatatggtgcacgtttggcagGTCATAGACAAATCATTTGGTTTTGATACCGCAGTTGAAGAAGCACAGCGTGCAATTAATGCTGCGCACGTGGAAGCTGAGAGTGTTCATAATGGCATTG
        ||   | |  || |     |   | || | | || |||| | |||        ||| |||     | | | | ||  ||   | |   ||      |||   | |     | |  ||||  ||||| |||||||| || |||||||||||||| || ||||| ||||| ||| | ||||| |||||||| || ||||||| ||| |||||  | |||||  |||
--------tatttatgtgaact-----attaggtgaagt-ctatgttctccaa--------attctgt-----tatcaatatacttt---ccatttaattttctaatatgataataacttcttgttt--cagGTGATAGACAAGTCTTTTGGTTTTGATACTGCTGTTGAGGAAGCTCAGAGAGCAATCAATGCTGCACATGTGGAAGTTGAAAGTGTAGAAAATGGAGTTG

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|162199151|gb|FC374597.1|FC374597
EST:     TGAAGGTTGCGGTTGCGGGCATTCCCAAAACAATCGATAATGATCTCGAT                         GTCATAGACAAATCATTTGGTTTTGATACCGCAGTTGAAGAAGCACAGCGT
genomic: TGAAGGTTGCGGTTGCGGGCATTCCCAAAACAATCGATAATGATCTCGATgtacgtttta ... cgtttggcagGTCATAGACAAATCATTTGGTTTTGATACCGCAGTTGAAGAAGCACAGCGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtaggttaagcaacacaagagctgaatggaaaatatggtgcacgtttggcagGTCATAGACAAATCATTTGGTTTTGATACCGCAGTTGAAGAAGCACAGCGTGCAATTAATGCTGCGCACGTGGAAGCTGAGAGTGTTCATAATGGCATTG
 ttctgat  putative branch site (score: 3)
                                aaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttttagacacggaaattcaacaacacgatggaattctctgtttttcaatggattgaattgtgtgggtttctgattgtaggttaagcaacacaagagctgaatggaaaatatggtgcacgtttggcagGTCATAGACAAATCATTTGGTTTTGATACCGCAGTTGAAGAAGCACAGCGTGCAATTAATGCTGCGCACGTGGAAGCTGAGAGTGTTCATAATGGCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA