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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagcaaatttgtaatctattcagttggtttttaattaagaccttcagtgtgctacaaattttttccactctcaattcttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG

Basic information

species Physcomitrella patens
transcript PP1S425_12V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os01g51380.2 (Oryza sativa), 3'ss of exon 9
gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagcaaatttgtaatctat-tcagttggtttttaattaagaccttcagtgtgctacaaatt--ttttccactctcaattcttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG
                                                                                               |  ||||  ||    ||        | |||     ||  ||    ||||   | ||||     |  | | ||   ||| | || ||  | ||   |  |||||||||| ||||| || ||||| ||||| || ||||| ||||||||||| |||||||||||| |||| || || ||||| |||||||| || || ||||
---------------------------------------------------------------------------------------------aaatctagtccttt--taataccacggtttatgctgatttcttaagtattatatcattcaagtcacctctacttaccttttctctgtctttcctcacatcagGTTTCTGCAGCTCGAGAGGAAGTACCTGGACGGCGTGGTTATCCTGGTTATATGTATACTGATTTGGCAACTATCTATGAGCGTGCTGGTCGCATAGAAG

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 9
gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagca-aatttgtaatctattcagttggtttttaattaagaccttcagtgtgctacaaattttttccactctcaattctt-caaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG
                                                                                          ||||    |  | ||  |    |||   | ||  |||  | ||   ||| ||| |    ||  |  ||  || |||      |  |     | |||  |  ||||| || || || || ||||||||||| ||  | ||||| |||||||| || ||||||||||||||||| ||||| ||||| || ||||| || || ||||
----------------------------------------------------------------------------------------acatctccttttatgttcgactgcaataaatgataaatt--gctgaaattttattta----ttgtgattggcactaatacaacacggtaattgtgcttatatgtagGTATCAGCAGCCCGAGAAGAAGTGCCAGGTAGGCGTGGGTATCCTGGATATATGTATACTGATCTGGCAACCATATATGAGCGAGCTGGGCGTATTGAAG

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 9
gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagcaaatttgtaatctattcagttggtttttaattaagaccttcagtgtgctacaaattttttccactctcaattcttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG
                                                                                 | | ||   |||     | || |||| | ||     |  |  ||| | ||  | ||| ||   |    | |   |||||||      ||   || |   |         |||||||||| || || ||||| ||||| ||  | ||||| |||||||| || ||||||||||||||||| || || ||||| |||||||| || || ||||
--------------------------------------------------------------------------------agtatttaagatcaacctttgtatttaggtaatcaaatggtaaattgatttcatgtttgat---gtttctaataatgctacatgggcattgtgctttttgt---------agGTTTCTGCAGCCCGAGAAGAGGTGCCAGGTAGGCGTGGTTATCCTGGATATATGTATACTGATCTGGCAACAATATATGAGCGTGCTGGGCGTATTGAAG

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 9
gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagcaaatttgtaatctattcagttggtttttaattaagaccttcagtgtgctacaaattttttccactctcaattcttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG
                                                                                           | | | ||| ||   |   |  |||   ||    | | |   |    |||| |   | |  || |   | ||   |         |      ||    ||||||||||| || || ||||| ||||| ||  | ||||| |||||||| || |||||||||||| |||| || || ||||| |||||||| || || ||||
-------------------------------------------------------------------------------------------ttttatatatttaagattaaccttttctattagctaattaaatgacaaattgatgtcgtt-gtttctaataatgctacatgggcattgtgcttttttgtagGTTTCTGCAGCCCGAGAAGAGGTGCCAGGTAGGCGTGGTTATCCTGGATATATGTATACTGATTTGGCAACAATATATGAGCGTGCTGGGCGTATTGAAG

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 10
gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagcaaatttgtaatctattcagttggtttttaattaagaccttca-gtgtgctacaaattttttccactctcaattcttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG
                                                                                         | |  ||  | | ||||   |||   | | |  ||||   ||||  | | |  || | ||  |  | |    ||||   ||| || |  || ||  ||  |||||| |||||||| || ||||||||||| ||  | ||||| |||||||| || |||||||| ||||| || || ||||||||||| |||||  |||| || |
---------------------------------------------------------------------------------------aatgtgggacttgggttttttccaa---tatgacttattt--ttggagtatgagaaataactgaacatatttctcaaacaatttgca-tgacacttgatcccatagGTATCTGCTGCCCGAGAAGAAGTGCCGGGTAGACGTGGTTATCCTGGATATATGTATACAGATCTTGCAACAATTTATGAACGAGCTGGGAGAATTGAGG

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 9
gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagcaaatttgtaatctattcagttggtttttaattaagaccttcag-tgtgctacaaattttttccactctcaattcttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG
         || |  | ||    | || | |||||          | ||| |||      |||||   |  ||    ||     | || | |   || |    ||     |    | |  | |||||  ||||  | | |  || | ||  |  | |      ||   ||| || |  || ||  ||   ||||| |||||||| || ||||||||||| ||  | ||||| |||||||| || |||||||| ||||| || || ||||||||||| |||||  |||| || |
----gtaatttaccttcaactgttattagtttggaagaagcaacaaaaagataggggacttgaaaccttttatag-gctttaatgatgat-ttaaaattgacattcttttatgcctttggtttattc--ttggagtatgagaaataactgaaaatatttctataacaatttgca-tgacacttgatcccgtagGTATCTGCTGCCCGAGAAGAAGTGCCAGGAAGACGTGGTTATCCTGGATATATGTATACAGATCTTGCAACAATTTATGAACGAGCTGGGAGAATTGAGG

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 9
gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagcaaatttgtaatctattcagttggtttttaattaag-accttcagtgtgctacaaattttttccactctcaattcttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG
                                                                                         | | |  |    |||||   | | | |  ||  ||   |  |  |||  ||  ||  |  || |   ||  || |  ||   ||  |||  || ||     ||||| |||||||| || |||||||| |||||  | ||||| || || |||||||||||||| ||||| || || || || |||||||||||| |||| || |
---------------------------------------------------------------------------------------catttatttatctctttttctccgactataaaaagtaactaagtattttgcaaacaattagattgacaatggaacta--ttgaccccttctggatcct----gtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTACCCCGGTTACATGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGG

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 9
gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagcaaatttgtaatctattcagttggtttttaattaagaccttcagtgtgctacaaattttttccactctcaattcttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG
                                                                                        |||| |  |    ||| | ||   ||| | | |  |   |  |  |||  ||  ||     |        |  || | ||  || ||      ||||    ||||| |||||||| || |||||||| |||||  | ||||| ||||| || ||||||||||| ||||| || || || || |||||||||||| |||| || |
-------------------------------------------------------------------------------------catgtatttatatctttttctcagagtattagaagt--aacaaagtattttgcaaacaattagattgacaa--tggaactattaaccccttctggatctt---gtagGTATCTGCTGCCCGAGAAGAAGTACCTGGTAGACGTGGGTATCCCGGCTACATGTATACAGATCTTGCAACAATATACGAACGTGCTGGAAGAATTGAGG

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 9
gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagcaaatttgtaatctattcagttggtttttaattaagaccttcagtgtgctacaaattttttccactctcaattcttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG
                                                                                              | |||   ||| |      |||||  | | | |  | | ||   ||||      || ||  |   | ||| ||     ||  | || |||      |||||||||||||||| |||||||| |||||  | ||||||||||| || || |||||||| ||||| || || ||||||||||| || ||||| || ||||
----------------------------------------------------------------------------------------------gtaatgagtttcactgtcctttgtg-tatgtcccat-gattcaaaatttga--tttaagctttgaataaaattaacaaacg-tgaactct------agGTTTCTGCTGCTCGAGAAGAAGTTCCTGGAAGACGTGGATATCCGGGGTATATGTATACAGATCTTGCAACTATTTATGAACGCGCGGGACGTATTGAAG

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 9
gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagcaaatttgtaatctattcagttggtttttaattaagaccttcagtgtgctacaaattttttccactctcaattcttcaaa----tagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG
                                                                                                      |   | | | |||||  | |     ||||    |||| || | ||| |  || |  | |   |  | |    |   ||   |   ||    |||||||| ||||| || ||||| || || ||  | ||||||||||| ||||| ||||| |||||||| || || ||||||||||||||||| || || ||||
-----------------------------------------------------------------------------------------------------gtaaaatgaatatttgataccggagtagtt--cctttatttcataccat--gttttttcctcttcatgtttgataataagattgagaaactgtagGTTTCCGCTGCCCGAGAAGAGGTTCCCGGAAGACGTGGATATCCAGGTTATATGTACACTGATCTTGCAACTATTTATGAACGTGCTGGGCGTATAGAAG

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 10
gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagcaaatttgtaatctattcagttggtttttaa---ttaagaccttcagtgtgctacaaattttttccactctcaattcttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG
                                                                                                    ||  | |   | ||||| |  || |        || || |   || |||   |  |    ||  ||   | ||  ||  | | |  | |   ||||| |||||||| |||||||||||||||||  | ||||| || || ||||||||||| || ||  |||| ||||| || ||  | || || ||||| ||||
----------------------------------------------------------------------------------------------------gtgataaccgatatttgcatgctctgttcacaattcttgaactttgagatgataggaagcctgaaatagtgtttaacgttgactaatacccttagGTCTCTGCTGCCCGTGAAGAAGTGCCTGGAAGGCGTGGTTACCCAGGTTACATGTACACCGACTTGGCTACCATATACGAGAGAGCAGGGCGAATTGAAG

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 9
gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagcaaatttg-taatctattcagttggtttttaattaagaccttcagtg-tgctacaaattttttccactctcaattcttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG
                                                                                           ||| |  | ||| || || |  |||  | |  ||  |  |||  || |  | ||   | ||| || ||||    ||     | |||    |||        |||| |||||||| || |||||||| || ||| | ||||| |||||||| || ||||||||||||||||| || |||||||||||||||||||| || ||||
-----------------------------------------------------------------------------------------cttctaattttgttcttgagtatttttaatcaagtaccccattgaattct--tcaaactcatcactgatgcttgtgatgcaaactactt---attgcaactgcagGTATCTGCTGCCCGAGAAGAAGTTCCCGGGAGGCGTGGGTATCCTGGGTATATGTATACTGATCTGGCGACGATTTATGAACGTGCTGGACGTATTGAAG

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 9
gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagcaaatttgtaatctattcagttggtttttaattaagaccttcagtgtgctacaaattttttccactctcaattcttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG
                                                                                             | | |   |||  || || |    ||||| | |    |  |     |||   ||  | | | |     |  |   |   | | ||  || |      |||| ||||| || || || ||||| |||||  | ||||| |||||||| || |||||||||||||| || || |||||||| ||||||||||| || ||||
-------------------------------------------------------------------------------------------cttcataggttttaaaatcatacggataatcgaattt-ctattgcaccattcccacacttactttcacctacttgactggaaatgtctgttttgactgcagGTATCTGCAGCCCGGGAGGAAGTACCTGGAAGGCGTGGGTATCCTGGGTATATGTATACTGATCTTGCAACAATTTATGAGCGTGCTGGACGTATAGAAG

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 8
gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagcaaatttgtaatctattcagttggtttttaattaagaccttcagtgtgctacaaattttttccactctcaattcttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG
                                                                                                                                         ||    |    |  ||| ||  |  |    | |  |    ||   |||    ||||| ||||| |||||||| || |||||||| |||||||||||||||||||| |||||||| ||| |||| || ||||| || |||||||||||||| ||||
----------------------------------------------------------------------------------------------------------------------------------------gtatggtatgtttcaagtttgtcatgagagctatg-ataaccagggctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG

upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ13375 (Selaginella moellendorffii), 3'ss of exon 8
gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagcaaatttgtaatctattcagttggtttttaattaagaccttcagtgtgctacaaattttttccactctcaattcttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG
                                                                                                                                       | | ||       ||||   |  |    |   ||   |    ||   |||    ||||| ||||| |||||||| || |||||||| |||||||||||||||||||| |||||||| ||| |||| || ||||| || |||||||||||||| ||||
--------------------------------------------------------------------------------------------------------------------------------------gtatgatcgtatgtttcaagtttttcatgagagttatgataaccatggctttgtgtagGTGTCTGCCGCTCGTGAGGAGGTGCCTGGTCGTCGTGGATATCCTGGTTATATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAG

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|208363000|gb|DC946897.1|DC946897
EST:     ATCCTGACGGATATGAGTTCATATGCAGATGCGCTGCGTGAG                         GTTTNTGCTGCTCGTGAAGNAGTGCCTGGGCGTCGTGGATATCCTGGTTAC
genomic: ATCCTGACGGATATGAGTTCATATGCAGATGCGCTGCGTGAGgtacaagtgt ... cttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTAC
EST: gi|67700014|gb|BJ960247.1|BJ960247
EST:     TCCTGGTCATCCTGACGGATATGAGTTCATATGCAGATGCGCTGCGTGAG                         GTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTAC
genomic: TCCTGGTCATCCTGACGGATATGAGTTCATATGCAGATGCGCTGCGTGAGgtacaagtgt ... cttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattaagaccttcagtgtgctacaaattttttccactctcaattcttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG
 ttttaat  putative branch site (score: 3)
                           ttttttccactctcaa  putative PPT
                     tacaaatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaagtgtttctcttaaagacttttcgcttggactcctttttcagaagttagctcctgtgaaattctacatgctactccgcagttggtatctgaaatagtttttaagcaaatttgtaatctattcagttggtttttaattaagaccttcagtgtgctacaaattttttccactctcaattcttcaaatagGTTTCTGCTGCTCGTGAAGAAGTGCCTGGGCGTCGTGGATATCCTGGTTACATGTATACTGATCTGGCCACCATTTATGAACGTGCTGGACGAATCGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA