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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcacgtgtggacattttttgtctaatggtggctgtttcttcatgctagagacctattacacttctacaacgtttcatgtttttaatgctacatcattttctacagaaatatgagacttgtcagttgtcttccttactgtgcagGGAGTATTGGGTATCAAGGTGAAGATTATGCTCGACTGGGACCCCAAGGTCAAGCAAGGATCTGTGACTCTACTTCCAGATGTGGTGACCATTCACATGC

Basic information

species Physcomitrella patens
transcript PP1S487_22V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S487_22V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os03g38000.2 (Oryza sativa), 3'ss of exon 3
gcacgtgtggacattttttgtctaatggtggctgtttcttcatgctagagacctattacactt--ctacaacgtttcatgtttttaatgctacatcattttctacagaaatatgagacttgtcagttgtcttccttactgtgcagGGAGTATTGGGTATCAAGGTGAAGATTATGCTCGACTGGGACCCCAAGGTCAAGCAAGGATCTGTGACTCTACTTCCAGATGTGGTGACCATTCACATGC
                                                     | ||    |   ||  | | |   |   ||| ||  |  ||| || || |   |    |    ||||||   || ||||        ||||||| ||  | || |||||||||||||| |||||||||||||||||||||| ||||   ||  |    || |  || || ||| | || ||||| ||    |
--------------------------------------------------gtttgtttggttcaactcaagcatcgtagtatttaaaaacctcatgatcttttt--ggctcaacgcacttgttcattatcttt-------tgcagGGTGTTCTTGGCATCAAGGTGAAGATCATGCTCGACTGGGACCCCAAGGGCAAGGTTGGCCCGACCACCCCTCTGCCGGATCTTGTAACCATCCATGCTC

upper sequence: PP1S487_22V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os07g41750.1 (Oryza sativa), 3'ss of exon 5
gcacgtgtggacattttttgtctaatggtggctgtttcttcatgctagagacctattacacttctacaacgtttcatgtttttaatgctacatcattttctacagaaatatgagacttgtcagttgtcttccttactgtgcagGGAGTATTGGGTATCAAGGTGAAGATTATGCTCGACTGGGACCCCAAGGTCAAGCAAGGATCTGTGACTCTACTTCCAGATGTGGTGACCATTCACATGC
                                      ||  | |   | | | ||  |  ||  | ||  | |     | |   ||  | | | |          ||| |    |||   || ||  |  |||  | | ||||| ||  ||||||| ||||| ||||||||||| || ||||| || |||| |||||||||| |  ||||||   | || ||| | || ||||| ||    |
-------------------------------------gtttgtacataaaatccatc-cgtttgaataaaatgttgctgtctccttgtgatagctt---------gaatttttttcttagaagctgctt--cttgtttt-cagGGTGTGCTGGGTATTAAGGTCAAGATTATGCTTGATTGGGATCCGAAGGGCAAGCAAGGACCAATGACTCCTTTACCGGATCTTGTTACCATCCATGCCC

upper sequence: PP1S487_22V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G074300_T03 (Zea mays), 3'ss of exon 3
gcacgtgtggacattttttgtctaatggtggctgtttcttcatgctagagacctattacacttctacaacgtttcatgtttttaatgctacatcattttctacag---aaatatgaga-cttgtcagttgtcttcct-tactgtgcagGGAGTATTGGGTATCAAGGTGAAGATTATGCTCGACTGGGACCCCAAGGTCAAGCAAGGATCTGTGACTCTACTTCCAGATGTGGTGACCATTCACATGC
                                 |||| ||  ||||| |    |    |  |   |   |  ||  | | |        || |||||||| ||     |||| | |   ||   ||    ||||  | |   |||||||| ||  ||||||||||||||||||| ||||| ||||||||||| |||| ||||   ||  |  | || |  ||||| ||  |||||||||| || |  |
---------------------------------gtttgttt-tgctacaa---ttgcccgttgtaatgtctgtttgtctctgggtaagcacttcattttcgacgttccaaatgtaatttctcaacaaacatctttttctgtcgtgcagGGTGTTCTGGGTATCAAGGTGAAGATCATGCTTGACTGGGACCCGAAGGGCAAGGTTGGCCCGATCACCCCTCTTCCGGACCTGGTGACCATCCATACCC

upper sequence: PP1S487_22V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G093902_T02 (Zea mays), 3'ss of exon 5
gcacgtgtggacattttttgtctaatggtggctgtttcttcatgctagagacctattacacttctacaacgtttcatgtttttaatgctacatcattttctacagaaatatgagacttgtcagttgtcttccttactgtgcagGGAGTATTGGGTATCAAGGTGAAGATTATGCTCGACTGGGACCCCAAGGTCAAGCAAGGATCTGTGACTCTACTTCCAGATGTGGTGACCATTCACATGC
                                                     |  | |  |  ||  |  | | || || |||     ||||        | ||   |  |  |      ||||| |||   | |     |||| ||  | ||||||||||| ||||||||||| |||||||| || |||| |||||||||  |    |  |   | || ||| |||| || |||||| |||
--------------------------------------------------gtttggtgc-ttggtatcagatgttatcttattatgcaaacatataacaaaatagctgttagtaatactctagttgacttggcttc-----agGGTGTGCTTGGTATCAAGGTTAAGATTATGCTGGACTGGGATCCAAAGGGCAAGCAAGGGCCAACCATGCCTTTACCTGATTTGGTTACAATTCACGTGC

upper sequence: PP1S487_22V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G099352_T01 (Zea mays), 3'ss of exon 3
gcacgtgtggacattttttgtctaatggtggctgtttcttcatgctagagacctattacacttctacaacgtttcatgtttttaatgctacatcattttc-tacagaaatatgagacttgtcagttgtcttc--cttactgtgcagGGAGTATTGGGTATCAAGGTGAAGATTATGCTCGACTGGGACCCCAAGGTCAAGCAAGGATCTGTGACTCTACTTCCAGATGTGGTGACCATTCACATGC
                                 |||| ||  ||||  |  |   | |   ||        | ||| |         |||| |  |   | | |   ||| | |   |   ||  |  ||||    |   | |||||| ||  | || |||||||||||||| ||||| ||||||||||| |||| ||||   ||  |  | ||||  ||||| ||  |||||||||| ||||  |
---------------------------------gtttgtt--tgctgtaatctcctcaatgtttggtcgtctctcaagagcaggg-actacgttttccacgtgcttcaatttaa--ttacccaactaacttcaatctgtcgcgcagGGTGTTCTTGGCATCAAGGTGAAGATCATGCTTGACTGGGACCCGAAGGGCAAGGTTGGCCCGATCACTCCTCTTCCGGACCTGGTGACCATCCACACCC

upper sequence: PP1S487_22V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT5G35530.1 (Arabidopsis thaliana), 3'ss of exon 5
gcacgtgtggacattttttgtctaatggtggctgtttcttcatgctagagacctattacacttctacaacgtttcatgtttttaatgctacatcattttctacagaaatatgagacttgtcagttgtcttccttactgtgcagGGAGTATTGGGTATCAAGGTGAAGATTATGCTCGACTGGGACCCCAAGGTCAAGCAAGGATCTGTGACTCTACTTCCAGATGTGGTGACCATTCACATGC
                              |    |||||||   | || |||| || |  ||  |  || ||  |      || ||  |  |  | |        ||  |||  || || | |    |        |||||||| ||  | ||| ||||||||||||| ||||| |||||||||||||||| ||| |||||| |  |||| | | | || ||||| |||| ||| || |  |
------------------------------gtcagttcttcacagtggaaacctgtttc--ttgaatcacattctac----ctagtgagatcttgtgt--------aacctgaatctggttaatcacat--------gtgcagGGTGTGCTTGGTCTCAAGGTGAAGATCATGCTTGACTGGGACCCCAAGGGCAAACAAGGACCGATGACACCATTGCCTGATGTTGTGATCATCCATACAC

upper sequence: PP1S487_22V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT2G31610.1 (Arabidopsis thaliana), 3'ss of exon 4
gcacgtgtggacattttttgtctaatggtggctgtttcttcatgctagagacctattacactt-ctacaacgtttcatgtttttaatgctacatcattttctacagaaata--tgagacttgtcagttgtcttccttactgtgcagGGAGTATTGGGTATCAAGGTGAAGATTATGCTCGACTGGGACCCCAAGGTCAAGCAAGGATCTGTGACTCTACTTCCAGATGTGGTGACCATTCACATGC
                                                        ||  ||| |||    || || | | |   ||            | ||| |   |     |  |||||  |||    ||| || | ||||||| || ||||| |||||||||||||| ||||| ||||||||||| | || |||   |||| |   ||| | | | || ||||| |||| ||||||    |
-------------------------------------------------------gtatgctttctaatgagtctcttatctaccatttagtgagtaagtataccggctttgtctaatcttgttggtt-caatccgtatt-tgcagGGGGTGTTGGGAATCAAGGTGAAGATCATGCTTGACTGGGACCCTACGGGCAAATCAGGACCAAAGACACCATTGCCTGATGTTGTGATCATTCATGCTC

upper sequence: PP1S487_22V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv09s0002g01460.t01 (Vitis vinifera), 3'ss of exon 5
gcacgtgtggacattttttgtctaatggtggctgtttcttcatgctagagacctattacacttctacaacgtttcatgtttttaatgctacatcattttctacagaaatatgagacttgtcagttgtcttccttactgtgcagGGAGTATTGGGTATCAAGGTGAAGATTATGCTCGACTGGGACCCCAAGGTCAAGCAAGGATCTGTGACTCTACTTCCAGATGTGGTGACCATTCACATGC
                                  | || |  |||  |   |||      |||  |     |||||   ||||| |  |  || | || | ||     | |   |||| |  ||   |||  ||   |  ||||| || |||||||||||||||||||| ||||| |||||||| ||||||| |||||| ||  ||   || |  || || ||| | || ||||| ||||  |
--------------------------------aatctcctattgcatggttccttacctgctttga-----tttcaatgttttagttgtctattacttcccacc----ttttttacttttttgtgaacttaattg--gcacagGGTGTTTTGGGTATCAAGGTGAAGATCATGCTTGACTGGGATCCCAAGGGCAAGCAGGGCCCTAAAACACCTCTACCTGATCTTGTCACCATCCACACCC

upper sequence: PP1S487_22V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv04s0008g01750.t01 (Vitis vinifera), 3'ss of exon 5
gcacgtgtggacattttttgtctaatggtggctgtttcttcatgctagagacctattacacttctacaacgtttcatgtttttaatgctacatcattttctacagaaatatgagacttgtcagttgtcttccttactgtgcagGGAGTATTGGGTATCAAGGTGAAGATTATGCTCGACTGGGACCCCAAGGTCAAGCAAGGATCTGTGACTCTACTTCCAGATGTGGTGACCATTCACATGC
                |   |   ||  || ||  |  ||   | |  |    | |||  || | |||     || || |||        ||||||||| |      |     | ||  |   |  | |||  |  |||  |||| ||  | ||||||||||| ||||| |||||||||||||| ||||||| |||||| ||  |    |||| | | || ||| ||||||| |||||||  |
---------------gtacatgctataatgtctcctggttttggttgaa---ttgtta-gctgccaca-----tcttgattt--------catcattttatttgttgaatcccggctgattt-tccttttctatggtgtatagGGCGTCCTTGGTATCAAGGTCAAGATCATGCTCGACTGGGATCCCAAGGGCAAGCAGGGCCCCACAACTCCATTGCCTGATCTGGTGACTATTCACACAC

upper sequence: PP1S487_22V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ31038 (Selaginella moellendorffii), 3'ss of exon 5
gcacgtgtggacattttttgtctaatggtggctgtttcttcatgctagagacctattacacttctacaacgtttcatgtttttaatgctacatcattttctacagaaatatgagacttgtcagttgtcttccttactgtgcagGGAGTATTGGGTATCAAGGTGAAGATTATGCTCGACTGGGACCCCAAGGTCAAGCAAGGATCTGTGACTCTACTTCCAGATGTGGTGACCATTCACATGC
                                                                               |   |   ||  ||| ||||     |    ||     || | ||   |      | ||| |||||| || ||||| |||||||||||||| ||||| |||||||| || |||| ||||   ||  |   ||| |  || || ||  ||||||| || ||  | |
------------------------------------------------------------------------------gtgcaagaactcgatcgttttgatttgg---atccagtttctaagcattggattgtgctg-gcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGCAAGACCGGGCCGTCGACACCGCTGCCGGACATGGTGACGATCCAAGTAC

upper sequence: PP1S487_22V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ34304 (Selaginella moellendorffii), 3'ss of exon 5
gcacgtgtggacattttttgtctaatggtggctgtttcttcatgctagagacctattacacttctacaacgtttcatgtttttaatgctacatcattttctacagaaatatgagacttgtcagttgtcttccttactgtgcagGGAGTATTGGGTATCAAGGTGAAGATTATGCTCGACTGGGACCCCAAGGTCAAGCAAGGATCTGTGACTCTACTTCCAGATGTGGTGACCATTCACATGC
                                                                               |   |   ||  ||||||||     | |    |   ||   || | |  |    |     |||||| || ||||| |||||||||||||| ||||| |||||||| || |||| ||||   ||  |   ||| |  || || ||  ||||||| || ||  | |
------------------------------------------------------------------------------gtacaagaactcgatcattttgatttggatccagtttctaagcattggattgtgctggctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGCAAGACCGGGCCGTCGACACCGCTGCCGGACATGGTGACGATCCAAGTAC

upper sequence: PP1S487_22V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ34676 (Selaginella moellendorffii), 3'ss of exon 5
gcacgtgtggacattttttgtctaatggtggctgtttcttcatgctagagacctattacacttctacaacgtttcatgtttttaatgctacatcattttctacagaaatatgagacttgtcagttgtcttccttactgtgcagGGAGTATTGGGTATCAAGGTGAAGATTATGCTCGACTGGGACCCCAAGGTCAAGCAAGGATCTGTGACTCTACTTCCAGATGTGGTGACCATTCACATGC
                                                                               |   |   ||  ||| ||||     | |    |   ||   || | |  |    |     |||||| || ||||| |||||||||||||| ||||| |||||||| || |||| ||||   ||  |   ||| |  || || ||  ||||||| || ||  | |
------------------------------------------------------------------------------gtgcaagaactcgatcgttttgatttggatccagtttctaagcattggattgttctg----gcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGCAAGACCGGGCCGTCGACACCGCTGCCGGACATGGTGACGATCCAAGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatcattttctacagaaatatgagacttgtcagttgtcttccttactgtgcagGGAGTATTGGGTATCAAGGTGAAGATTATGCTCGACTGGGACCCCAAGGTCAAGCAAGGATCTGTGACTCTACTTCCAGATGTGGTGACCATTCACATGC
                                         tccttac  putative branch site (score: 2)
                                   ttgtcttccttact  CT-rich tract
      attttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcacgtgtggacattttttgtctaatggtggctgtttcttcatgctagagacctattacacttctacaacgtttcatgtttttaatgctacatcattttctacagaaatatgagacttgtcagttgtcttccttactgtgcagGGAGTATTGGGTATCAAGGTGAAGATTATGCTCGACTGGGACCCCAAGGTCAAGCAAGGATCTGTGACTCTACTTCCAGATGTGGTGACCATTCACATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG