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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttctcattttgtttgtgggatccttacctgcaacatgtgcagagttcggcgcctacttgcgtgttgacgcttgccagcgtttgttcggttctatgaagtaacaccatgaatcgttttttcagATGAACGACGGATGCCAGTGGCGGAAGTACGGTCAGAAGATGGCTAAAGGGAATCCCTGTCCTCGTGCATACTACCGTTGCACTGTTGCGCCTGGGTGCC

Basic information

species Physcomitrella patens
transcript PP1S158_166V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S158_166V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os01g14440.1 (Oryza sativa), 3'ss of exon 3
gtacgttctcattttgtttgtgggatccttacctgcaacatgtgcagagttcggcgcctacttgcgtgttgacgcttgccagcgtttgttcggttctatgaagtaacaccatgaatcgtttt-------ttcagATGAACGACGGATGCCAGTGGCGGAAGTACGGTCAGAAGATGGCTAAAGGGAATCCCTGTCCTCGTGCATACTACCGTTGCACTGTTGCGCCTGGGTGCC
                                         ||  |||   |  | |   |   |   | ||   |  |  || |||  ||      | |   | | |     |||||||||       | |||||   ||| || ||||| ||| |||||||||||||||||||||| || || || || ||||| || || |||||||| |||||  | ||  | || ||||
-----------------------------------------gta-agaccccaccactagcaaccacatcga---tcacaggcattttctcatcgagacgtgctga-attccaaatcgttttggttccgtgcagATCGCCGATGGGTGCCAATGGAGGAAGTACGGTCAGAAGATGGCGAAGGGAAACCCTTGTCCACGCGCGTACTACCGCTGCACCATGGCCACCGGCTGCC

upper sequence: PP1S158_166V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM5G871347_T02 (Zea mays), 3'ss of exon 3
gtacgttctcatttt-gtttgtgggatccttacctgcaacatgtgcagagttcggcgcctacttgcgtgttgacgcttgccagcgtttgttcggttctatgaagtaacaccatgaatcgtttttt-cagATGAACGACGGATGCCAGTGGCGGAAGTACGGTCAGAAGATGGCTAAAGGGAATCCCTGTCCTCGTGCATACTACCGTTGCACTGTTGCGCCTGGGTGCC
||| |      |||| |||| |    ||  |  ||        | |    ||       |  ||   | ||    | |  |    ||| ||   |||| |    | | |      ||  |  |   |||||   |||||| ||||||||||| |||||||| ||||||||||| || || || || || || || || |||||||| |||||  | ||    || ||||
gtaaggaggagtttttgtttttcctttctctttctttctttctttctttctttcttctatctttctttattttttcctttctttctttctttctttctttcttctcatatggaagatgatcgtgggcagATCGCCGACGGCTGCCAGTGGCGCAAGTACGGGCAGAAGATGGCCAAGGGCAACCCATGCCCGCGAGCCTACTACCGGTGCACCATGGCCAACGGCTGCC

upper sequence: PP1S158_166V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G327349_T01 (Zea mays), 3'ss of exon 4
gtacgttctcattttgtttgtgggatccttacctgcaacatgtgcagagttcggcgcctacttgcgtgttgacgcttgccagcgtttgttcggttctatgaagtaacaccatgaatcgttttttcagATGAACGACGGATGCCAGTGGCGGAAGTACGGTCAGAAGATGGCTAAAGGGAATCCCTGTCCTCGTGCATACTACCGTTGCACTGTTGCGCCTGGGTGCC
                         |||  || |  |     | ||    |   | | || |   ||    |  |   || ||  |||      | |||     |  |  ||    | |   |  |||| | |||||| || || |||||||||||||| ||||||||||| ||||| || || || ||  | |||||||| || |||||  | ||    |  ||||
----------------------ctctccgcacatatagttattccaataat--acacatagtgatgtacatagtccgtcctgcaattgc---aatgtatatgacattattattttgcctaactgtagATTAGCGACGGGTGTCAATGGCGGAAGTACGGGCAGAAGATGGCCAAAGGTAACCCATGCCCGAGAGCATACTATCGGTGCACAATGGCTGTGGCATGCC

upper sequence: PP1S158_166V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA18G16170.1 (Glycine max), 3'ss of exon 2
-------------------------------------------gtacgttctcattttgtt----tgtgggatccttacctgcaacatgtgcagagttcggcgcctacttgcgtgttgacgcttg---ccagcgtttgttcggttctatgaagtaacaccatgaatcgttttttcagATGAACGACGGATGCCAGTGGCGGAAGTACGGTCAGAAGATGGCTAAAGGGAATCCCTGTCCTCGTGCATACTACCGTTGCACTGTTGCGCCTGGGTGCC
                                            ||| |    ||||||||    | |   |   | |  | ||| ||        |||      | |       || |    ||     || | ||  | |  | | |  |   |    ||  ||  | | |  ||||||| || || ||||| ||| | || || || ||||| ||||| ||||||||||| || ||||| |||||||| || ||||||||| | ||    || |
gttagtataaacttactacactgaacataatacttgaaatgaactacatctaaattttgttctattatataaatataaatttcaatattgatgtttttcctttttttcaaattctttcatagctgaacttagagcttaattgagtttttatatatatgt-atatat-atatatatagATGAATGATGGGTGCCAATGGAGAAAATATGGACAGAAAATGGCAAAAGGGAATCCGTGCCCTCGAGCATACTATCGATGCACTGTTTCTCCATCTTGTC

upper sequence: PP1S158_166V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT4G01720.1 (Arabidopsis thaliana), 3'ss of exon 4
gtacgttctcattttgtttgtgggatccttacctgcaacatgtgcagagttcggcgcctacttgcgt-gttgacgcttgccagcgtttgttcggttctatgaagtaa--caccatgaatcgttttttcagATGAACGACGGATGCCAGTGGCGGAAGTACGGTCAGAAGATGGCTAAAGGGAATCCCTGTCCTCGTGCATACTACCGTTGCACTGTTGCGCCTGGGTGCC
                                  | ||| |      ||||       |  |||  | ||| |  ||| |     | | |   ||| |   || | |  ||  || |||   |  |  || | || |||||||| || ||| | || ||||||||||| ||||| ||||||||||| |||||||| || || || ||||||||  | ||   ||| || |
----------------------------------gtaactttctataagttactaatttttttgattcgtttaaccttacatatatatatg-agttatgaaaattgaatcaatattaatatataatatagGTAAATGACGGATGTCAATGGAGAAAATACGGTCAGAAAATGGCGAAAGGGAATCCATGTCCTCGCGCTTATTATCGTTGCACCATGGCCGTTGGATGTC

upper sequence: PP1S158_166V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT1G62300.1 (Arabidopsis thaliana), 3'ss of exon 4
gtacgttctcattttgtttgtgggatccttacctgc-aacatgtgcagagttcggcgcctacttgcgtgttgacgcttgccagcgtttgttcggttctatgaagtaacaccatgaatcgttttttcagATGAACGACGGATGCCAGTGGCGGAAGTACGGTCAGAAGATGGCTAAAGGGAATCCCTGTCCTCGTGCATACTACCGTTGCACTGTTGCGCCTGGGTGCC
               ||  || |  |  |||  | | || |  |  |    |        | |    | |    ||||   || | ||  |    | | |      ||   |||     ||| |  |||| | ||| ||||| || ||| | || || || ||||||||||| ||||||||||| ||||| || ||||| ||||| |||||  | ||  | || || |
---------------gtaagttgatttattagatactaatacttataagactatataaaaaataaactat--gtgctt--tagagattaattatctttgt------actttatg-----tttctatagATAAGCGATGGATGTCAATGGAGAAAATATGGCCAGAAGATGGCCAAAGGGAATCCTTGTCCGCGGGCATATTACCGCTGCACGATGGCCACGGGCTGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcttgccagcgtttgttcggttctatgaagtaacaccatgaatcgttttttcagATGAACGACGGATGCCAGTGGCGGAAGTACGGTCAGAAGATGGCTAAAGGGAATCCCTGTCCTCGTGCATACTACCGTTGCACTGTTGCGCCTGGGTGCC
                            aagtaac  putative branch site (score: 2)
                                           tcgttttttc  putative PPT
                                              ttttttca  TA-rich tract