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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtcgctatcttcaactttgcaaatcgcttcccacttcccactgcatggtgtttcatttctaatgaaatcaatgcgtcgttaactaaatgttatatttcttcatcatatacagGTGAGGGAGATGCCAAACGTCTTGATTCTTCCTCGCAGTGCTGACTACAGCGAGGAAGTGTGGGCCGAGATACGGTCCAAGGCCATCTCTGTGCTGTACT

Basic information

species Physcomitrella patens
transcript PP1S35_361V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S35_361V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os03g03460.1 (Oryza sativa), 3'ss of exon 2
gtacgtcgctatcttcaactttgcaaatcgcttcccacttcccactgcatggtgtttcatttctaatgaaatcaatgcgtcgtt-aactaaatgttatat-ttcttcatcatatacagGTGAGGGAGATGCCAAACGTCTTGATTCTTCCTCGCAGTGCTGACTACAGCGAGGAAGTGTGGGCCGAGATACGGTCCAAGGCCATCTCTGTGCTGTACT
                   |||    || |||       | |||||   |  |  | ||| |   |  |||  ||   || ||| | | ||||| |  ||  | || ||   | | |||| |||||||||||||| || || ||||||||||| ||||| |||||||| || |||||||||   || ||| |    || || ||| |  |  || | |
------------------ttttctgcattgctatggtggtgccacttgttcatcatccatcttataaaaaaagaacttgttgttcagcaaaatgatggatactatttatttgacatagGTAAGGGAGATGCCAAATGTTTTAATTCTTCCTCGAAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATCACGATATTGCAGT

upper sequence: PP1S35_361V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G476107_T02 (Zea mays), 3'ss of exon 4
gtacgtcgctatcttcaactttgcaaatcgcttcccacttcccactgcatggtgtttcatttctaatgaaatcaatgcgtcgttaactaaatgttatatttcttcatcatatacagGTGAGGGAGATGCCAAACGTCTTGATTCTTCCTCGCAGTGCTGACTACAGCGAGGAAGTGTGGGCCGAGATACGGTCCAAGGCCATCTCTGTGCTGTACT
    |||         ||     | | | |||      ||  ||| |  |  ||||||||| | | |    |||       | | ||| |          || |     | |||||||| ||||||||||||| || || |||||||| || ||||| ||||||||||| |||||||||   || ||| |    || || ||  || || |  | |
----gtcctcgcagataaggacacgagttgctgttattttaacaccgt-tattgtttcattac-attttgttcagcaaactggtgactga----------tcattgctgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGCGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT

upper sequence: PP1S35_361V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G460952_T01 (Zea mays), 3'ss of exon 1
------------------------------------------------------------------------gtacgtcgctatcttcaactttgcaaatcgcttcccacttccca------ctgcatggtgtttc---atttctaatgaaatcaatgcgtcgttaactaaat--gttatatttcttcatcatatacagGTGAGGGAGATGCCAAACGTCTTGATTCTTCCTCGCAGTGCTGACTACAGCGAGGAAGTGTGGGCCGAGATACGGTCCAAGGCCATCTCTGTGCTGTACT
                                                                            ||| | |    ||   |  |   |  |  | ||     ||      |  | |    ||||   || |  |    ||   |    | ||| |  |||   || |    || |  |  | |||||||| ||||||||||||| || || |||||||| || ||||| |||||||| || |||||||||   || ||| |    || || ||  || || |  | |
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctgggggtggtgaagtaccctcagtgtcaccactaccacaatcacctgtgacccctcaaaattcaagaactcaacctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT

upper sequence: PP1S35_361V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G418294_T01 (Zea mays), 3'ss of exon 3
gtacgtcgctatcttcaactttgcaaatcgcttcccacttcccactgcatggtgtttcatttctaatgaaatcaatgcgtcgttaactaaatgttatatttcttcatcatatacagGTGAGGGAGATGCCAAACGTCTTGATTCTTCCTCGCAGTGCTGACTACAGCGAGGAAGTGTGGGCCGAGATACGGTCCAAGGCCATCTCTGTGCTGTACT
            |||     |||  |   |||| |   | |  |    | | |  |  |    | |||     ||    |  || | ||  |||||| | |  ||||     ||||||| | ||||||||||| || || ||||||||||| ||||| |||||||| || |||||||||   |||||  |    || || ||| |  |  || | |
-----------actttgcacttgtga--tgcttgctg-tacttataatacgctaatagaaaagtcatgtttcaaacaaatgatttaatacttgttatgtgt--tcattgatcacagGTGCGTGAGATGCCAAATGTATTAATTCTTCCTCGAAGTGCAGACTACAGTGAAGAAGTGTGGATGGAGATCAGAGAGAAAGCAATCGCAATATTGCAGT

upper sequence: PP1S35_361V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G394945_T01 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------------gtacgtcgctatcttcaactttgcaaatcgcttcccacttccca------ctgcatggtgtttc---atttctaatgaaatcaatgcgtcgttaactaaat--gttatatttcttcatcatatacagGTGAGGGAGATGCCAAACGTCTTGATTCTTCCTCGCAGTGCTGACTACAGCGAGGAAGTGTGGGCCGAGATACGGTCCAAGGCCATCTCTGTGCTGTACT
                                                                            ||| | |    ||   |  |  ||  |  | ||     ||      |  | |    ||||   || |  |    ||   |    | ||| |  |||   || |    || |  |  | |||||||| ||||||||||||| || || |||||||| || ||||| ||||||||  | |||||||||   || ||| |    || || ||  || || |  | |
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctggtggtggtgaagtaccctcagtgtcaccactaccacaatcacctatgacccctcaaaattcaagaactcaacctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTAAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT

upper sequence: PP1S35_361V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT1G01510.1 (Arabidopsis thaliana), 3'ss of exon 3
gtacgtcgctatcttcaactttgcaaatcgcttcccacttcccactgcatggtgtttcatttctaatgaaatcaatgcgtcgttaa--ctaaat--gttatatttcttcatcatatacagGTGAGGGAGATGCCAAACGTCTTGATTCTTCCTCGCAGTGCTGACTACAGCGAGGAAGTGTGGGCCGAGATACGGTCCAAGGCCATCTCTGTGCTGTACT
||| | |  | | ||| | |    |||   |||| || || |  |||| |  | | |  ||||  || |  |   |  || ||| |  ||  ||   |||||| |  |  |||| | ||||||| ||| |||||||| || || ||||| ||||||||||| || ||||| |||||||| |||   |||||| ||   ||||| |||||| |  || | |
gtatgactttcttttccagtgactaaa---cttcacatttgcgcctgcctattctcttgtttc--atcatcttcttctgttgtttatcctgcatccattatatcttgttttcat-tgcagGTGAAGGAAATGCCAAATGTGTTAATTCTACCTCGCAGTGCAGATTACAGTGAGGAAGTATGGATGGAGATAAGGGAGAAGGCTATCTCTATCTTGCATT

upper sequence: PP1S35_361V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ07708 (Selaginella moellendorffii), 3'ss of exon 3
gtacgtcgctatcttcaactttgcaaatcgcttcccacttcccactgcatggtgtttcatttctaatgaaatcaatgcgtcgttaactaaatgttatatttcttcatcatatacagGTGAGGGAGATGCCAAACGTCTTGATTCTTCCTCGCAGTGCTGACTACAGCGAGGAAGTGTGGGCCGAGATACGGTCCAAGGCCATCTCTGTGCTGTACT
                                              | | |    |   ||| | |||    | |   ||    ||||  |  |  | |||||         |||||| ||||||||| ||||||| || ||||||||||| ||||| || ||||| || || | ||||  ||| || ||||  |||||  | ||| |||||   |
----------------------------------------------gtaagcacctggtttttttatg----cgacatgtttggaacttgac-tcgtgtttct---------acagGTCAGGGAGATGTCAAACGTGTTAATTCTTCCTCGGAGTGCCGATTACAGTGACGATGCGTGGAACGAAATCCGGTTAAAGGCATTTTCTCTGCTGAGGT

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: 16 (upstream exon), 20 (downstream exon)
Score: 2

CCTGCTGGATGACTGTGCGATGAAGGAAGCGCTCATCAATGGCACTGTTGCTAGCTGTGCCCTCGACGGCATCGAAGGCCCACAGTGGCTCGAAGCTTGGgtacgtcgct ... tcatatacagGTGAGGGAGATGCCAAACGTCTTGATTCTTCCTCGCAGTGCTGACTACAGCGAGGAAGTGTGGGCCGAGATACGGTCCAAGGCCATCTCTGTGCTGTACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaatgaaatcaatgcgtcgttaactaaatgttatatttcttcatcatatacagGTGAGGGAGATGCCAAACGTCTTGATTCTTCCTCGCAGTGCTGACTACAGCGAGGAAGTGTGGGCCGAGATACGGTCCAAGGCCATCTCTGTGCTGTACT
                       aactaaa  putative branch site (score: 2)
                                     tttcttcatc  putative PPT
                     ttaactaaatgttata  TA-rich tract