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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaatccgttgtgaacctcgtatcatttgcattggaatgatgatcgctgctgtgaatagtttttaccatctcgcggtcgtactgttcgtttggaagttaatcaatccactaatggccggaacgtgctgcttcttgctattgcagGTAGTAGGCACTCCAAATTACATGTGTCCAGAGCTACTTGCAGACATCCCATATGGATTCAAATCAGACATTTGGTCATTAG

Basic information

species Physcomitrella patens
transcript PP1S22_216V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S22_216V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os01g64490.1 (Oryza sativa), 3'ss of exon 9
gtaagtaatccgttgtgaacctcgtatcatttgcattggaatgatgatcgctgctgtgaatagtttttaccatctcgcggtcgtactgttcgtttggaagttaatcaatccactaatggccggaacgtgctgcttcttgctattgcagGTAGTAGGCACTCCAAATTACATGTGTCCAGAGCTACTTGCAGACATCCCATATGGATTCAAATCAGACATTTGGTCATTAG
                               |   | | | ||||         |   | | |  |  | |||   |    |  | |     | ||     |  ||||     ||      ||  | || ||||||||        |||| || || || |||||||||||||| |||||||| ||||||||||| || || |||||||| |||||||| |||||  | |
-------------------------------tatgtcgaattgatccctatatgttcaagtggaat--atcattatgttagctaaatacctttatg-----ttctcaaattcttatattttgg--catgatgcttctt--------agGTTGTGGGAACACCAAATTACATGTGCCCAGAGCTGCTTGCAGACATTCCTTACGGATTCAAGTCAGACATATGGTCTCTTG

upper sequence: PP1S22_216V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os05g36960.1 (Oryza sativa), 3'ss of exon 8
gtaagtaatccgttgtgaacctcgtatcatttgcattggaatgatgatcgctgctgtgaatagtttttaccatctcgcggtcgtactgttcgtttggaagtta--atcaatccactaatggccggaacgtgctgcttcttgctat-tgcagGTAGTAGGCACTCCAAATTACATGTGTCCAGAGCTACTTGCAGACATCCCATATGGATTCAAATCAGACATTTGGTCATTAG
                                        ||  | ||| ||  |    | |   |||| |     |   | |||   |  ||   |||||||  || | |   |||   ||   |||   | || |  |||| | |  |||| || || || || |||||||||||||||||||| ||  |||| ||||| ||||||||||| |||||||| |||||  | |
---------------------------------------tatagttatctcttttacacaca---tttatc----tgaatttgtaaaataggt---gaagttattattatttttctat--gctcaaactgacagcataatgctttctttagGTTGTTGGAACACCGAATTACATGTGTCCAGAGCTTCTCACAGATATCCCTTATGGATTCAAGTCAGACATCTGGTCTCTTG

upper sequence: PP1S22_216V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G074262_T01 (Zea mays), 3'ss of exon 9
-----------------------------------------gtaagtaatccgttgtgaacctcgtatcatttgcattggaatgatgatcgctgctgtga--atagtttttaccatctcgcggtcgtactgttcgtttgg--aagttaatcaatccactaatggccggaacgtgctgcttc---ttgctattgc--agGTAGTAGGCACTCCAAATTACATGTGTCCAGAGCTACTTGCAGACATCCCATATGGATTCAAATCAGACATTTGGTCATTAG
                                          |  ||  | | ||       | || |||| | |  |  |||  | ||     | |  |  | |  ||| || |  ||  |   ||  |  |  |||    | |||| |               | |||  |  || |      || | || |  |||| || || || |||||||| ||||| |||||| | ||| ||||||| || ||||||||||| ||||| || |||||  | |
gtagccttttttctcttatttcttttgtttcttgcttgaaaatttgtccttcatttctgtttttgtttcatattc--taaaatcctaatgaaaacaggaaccacatgtttgactaattcatgtctgtttttctgctttcattatgttagttgccttgtctgctctcagaatcttatgttctagaatgatgttccttagGTTGTGGGAACACCAAATTATATGTGCCCAGAGTTGCTTACAGACATTCCCTATGGATTCAAGTCAGATATATGGTCTCTTG

upper sequence: PP1S22_216V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G137118_T02 (Zea mays), 3'ss of exon 9
gtaagtaatccgttgtgaacctcgtatcatttgcattggaatgatgatcgctgctgtgaatagtttttaccatctcgcggtcgtactgttcgtttggaagttaatcaatccactaatggccggaacgtgctgcttcttgctattgc-agGTAGTAGGCACTCCAAATTACATGTGTCCAGAGCTACTTGCAGACATCCCATATGGATTCAAATCAGACATTTGGTCATTAG
                                              ||      |||  |||   |   |||||||  ||      | |     || || |       | || |  || |   |||  |  ||  | || | ||   |||| || || || |||||||||||||| |||||||| || || || || || ||||| ||||| |||||||| |||||  | |
----------------------------------------------atgaaccatgtagatatgctagtccatctcatgg--aatgtatggaagtgtaattgtgcttttgcattcgtg-caataactggtggcaccatgttttttttagGTGGTCGGGACACCAAATTACATGTGCCCAGAGCTGCTAGCTGATATTCCCTATGGTTTCAAGTCAGACATCTGGTCTCTCG

upper sequence: PP1S22_216V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA11G18340.1 (Glycine max), 3'ss of exon 8
gtaagtaatccgttgtgaacctcgtatcatttgcattggaatgatgatcgctgctgtgaatagtttttaccatctcgcggtcgtactgttcgtttggaagt---taatcaatccactaatggccggaacgtgctgct--tcttgctattgcagGTAGTAGGCACTCCAAATTACATGTGTCCAGAGCTACTTGCAGACATCCCATATGGATTCAAATCAGACATTTGGTCATTAG
                                                    |||   |||  |||   ||||||      |||    ||| |    ||     || |||    |     |      |  |||||    | || |||| |||||| ||||| ||||| |||||||||||||| || || ||||| || || || |||||||||||||| || ||||||||| | |
----------------------------------------------------gcttccaattttttaatccatctgattagcgtgacattcatagacaaacacatagtcaccatatatgggattaataattgctgtaaatgtttctat-gcagGTGGTAGGAACTCCTAATTACATGTGTCCTGAACTGCTTGCTGATATTCCGTATGGATTCAAATCTGATATTTGGTCACTCG

upper sequence: PP1S22_216V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA12G09910.1 (Glycine max), 3'ss of exon 8
gtaagtaatccgttgtgaacctcgtatcatttgcattggaatgatgatcgctgctgtgaatagtttttaccatctcgcggtcgtactgttcgtttggaagt---taatcaatccactaatggccggaacgtgctgct--tcttgctattgcagGTAGTAGGCACTCCAAATTACATGTGTCCAGAGCTACTTGCAGACATCCCATATGGATTCAAATCAGACATTTGGTCATTAG
                                                    |||   |||  |||   |||| |      ||||   ||| |    || |   || |||   ||     |      |  |||||    | || |||| | |||| ||||| ||||| ||||||||||| || || || ||||| || || ||||||||||||||||| || ||||||||| |||
----------------------------------------------------gcttccaattttttaatccatatgattagcgtaacattcatagacaaatacatagtcaccacatatgggattaataattgctgtaaatgtttctat-gtagGTGGTAGGAACTCCTAATTACATGTGCCCTGAACTGCTTGCTGATATTCCATATGGATTCAAATCTGATATTTGGTCACTAG

upper sequence: PP1S22_216V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA12G31330.1 (Glycine max), 3'ss of exon 8
gtaagtaatccgttgtgaacctcgtatcatttgcattggaatgatgatcgctgctgtgaatagtttttaccatctcgcggtcgtactgttcgtttggaagttaatcaat--ccactaatggccggaacgtgctgcttcttgctat-tgcagGTAGTAGGCACTCCAAATTACATGTGTCCAGAGCTACTTGCAGACATCCCATATGGATTCAAATCAGACATTTGGTCATTAG
                                                   |    |      ||  |||||| |      | |  ||||  |||   |  |   || |  |   |  |||  |  |  |||||    |   | | ||||||| ||||| ||||| || || |||||||| || || |||||||| || || |||||||||||||| || ||||||||| |||
---------------------------------------------------tataatatgacattggtaccatattattagcattgtgtttatttcataaatgtgcagttactggttgtggaagttaattgctgtaaatatttgtgtgcagGTGGTAGGAACTCCCAACTATATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGATTCAAATCTGATATTTGGTCACTAG

upper sequence: PP1S22_216V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA13G38980.1 (Glycine max), 3'ss of exon 8
gtaagtaatccgttgtgaacctcgtatcatttg-cattggaatgatgatcgctgctgt-gaatagtttttaccatctcgcggtcgtactgttcgtttggaagttaatcaatccactaatggccggaacgtgctgcttcttgctattgcagGTAGTAGGCACTCCAAATTACATGTGTCCAGAGCTACTTGCAGACATCCCATATGGATTCAAATCAGACATTTGGTCATTAG
                        ||| || || |||||| |  || |||  | |  | | ||   ||| |  |    || ||  ||||| | ||  ||||||||||  ||  |  |||                ||  ||    ||||||| ||||| ||||| || || |||||||| || || ||||| || || || |||||||||||||| || ||||||||| |||
------------------------tataatatgacattggtaccat-atcattaccattgcatttatttcataaatgtgcagt--tactggttgt--ggaagttaattgattta--aata---------------tttgtg----tgcagGTGGTAGGAACTCCCAACTATATGTGTCCTGAACTGCTTGCTGATATTCCTTATGGATTCAAATCTGATATTTGGTCACTAG

upper sequence: PP1S22_216V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 8
gtaagtaatccgttgtgaacctcgtatcatttgcattggaatgatgatcgctgctgtgaatagtttttaccatctcgcggtcgtactgttcgtttggaagttaatcaatccactaatggccggaacgtgctgcttcttgctattgcagGTAGTAGGCACTCCAAATTACATGTGTCCAGAGCTACTTGCAGACATCCCATATGGATTCAAATCAGACATTTGGTCATTAG
                                   ||| |||  ||   |    |||       | ||   || || ||| | |   ||   ||||     |     |  | || |   ||    | |  | || |||       |||||||| || ||||| |||||||||||||| || || |||||||| || || ||||| |||||||| || || |||||  |||
----------------------------------gttgaaatcttgcctgtgcttgtc-----ctgttgatat-tcacggacttg--gtaaatttgagcaatgg--gacacgctca---cctattcat-ttcctacttatgtgcacagGTAGTTGGAACTCCCAATTACATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGCTTCAAATCTGATATCTGGTCTCTAG

upper sequence: PP1S22_216V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ32716 (Selaginella moellendorffii), 3'ss of exon 8
gtaagtaatccgttgtgaacctcgtatcatttgcattggaatgatgatcgctgctgtgaatagtttttaccatctcgcggtcgtactgttcgtttggaagttaatcaatccactaatggccg-gaacgtg-ctgcttcttgctattgcagGTAGTAGGCACTCCAAATTACATGTGTCCAGAGCTACTTGCAGACATCCCATATGGATTCAAATCAGACATTTGGTCATTAG
                                                                                               | |||||   | || |  |  |||| | |||  || | |         ||||||||| || || || |||||||| ||||| || || || ||||| |||||||||||||| ||||||||||| || ||||| ||||
-----------------------------------------------------------------------------------------------gtaagtt---ctattctgttttggcagcgaatttgacaggaagaaaacattgcagGTGGTTGGGACCCCAAATTATATGTGCCCGGAACTTCTTGCCGACATCCCATATGGCTTCAAATCAGATATATGGTCGTTAG

upper sequence: PP1S22_216V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ20709 (Selaginella moellendorffii), 3'ss of exon 8
gtaagtaatccgttgtgaacctcgtatcatttgcattggaatgatgatcgctgctgtgaatagtttttaccatctcgcggtcgtactgttcgtttggaagttaatcaatccactaatggccggaacgtgctgcttcttgctattgcagGTAGTAGGCACTCCAAATTACATGTGTCCAGAGCTACTTGCAGACATCCCATATGGATTCAAATCAGACATTTGGTCATTAG
                                                                                               | |||||    | |    |    |||     |  | |         ||||||||| || || || |||||||| ||||| || || || ||||| |||||||||||||| ||||||||||| || ||||| ||||
-----------------------------------------------------------------------------------------------gtaagttctatactgttttctcagccaatttg-acaggaagaaaacattgcagGTGGTTGGGACCCCAAATTATATGTGCCCGGAACTTCTTGCCGACATCCCATATGGCTTCAAATCAGATATATGGTCGTTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggaagttaatcaatccactaatggccggaacgtgctgcttcttgctattgcagGTAGTAGGCACTCCAAATTACATGTGTCCAGAGCTACTTGCAGACATCCCATATGGATTCAAATCAGACATTTGGTCATTAG
                 cactaat  putative branch site (score: 2)
                                       cttcttgct  putative PPT
       ttaatcaat  TA-rich tract