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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttctcgatgcattctggccttttccatgtttttaagcctttgtccatttcgaccttcttccagcgttgtcctggcaaagagtccacttcttccagttcgttgataatgtcaactgcttacgtttcccgttgcgcagTTCATCATTGATTGTCAAGCCCTACCGTGTCTGCTCGCACTACTCACCAACAACCACAAGAAGAGTATCAAAAAGGAAGCATGCTGGACCATTTCCAACA

Basic information

species Physcomitrella patens
transcript PP1S63_171V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S63_171V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G009845_T02 (Zea mays), 3'ss of exon 7
gtaatttctcgatgcattctggccttttccatgtttttaagcctttgtccatttcgaccttcttccagcgttgtcctggcaaagagtccacttcttccagttcgttgataatgtcaactgcttacgttt-cccgttgcgcagTTCATCATTGATTGTCAAGCCCTACCGTGTCTGCTCGCACTACTCACCAACAACCACAAGAAGAGTATCAAAAAGGAAGCATGCTGGACCATTTCCAACA
                                     | |   || |    |||| ||  | ||  | | |  |        | | || |||      |  |  ||     | |  |    |    ||| ||| |   |||||   |||||||   |||||| || || || ||  |    ||||| |||| |||||||||||| || ||||| || |||||||||||||| || || ||||
-------------------------------------tcaaaattagc---tttccacactgttgtaccatattgacatttcatattcaactgaacttaaatgttt--ctgtatttatcattattatttgcccttcctgcagTGTGTCATTGACAATCAAGCACTTCCATGCCTTTTGAACCTACTGACCACCAACCACAAGAAAAGCATCAAGAAAGAAGCATGCTGGACAATCTCAAACA

upper sequence: PP1S63_171V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT4G02150.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaatttctcgatgcattctggccttttccatgtttttaagcctttgtccatttcgaccttcttccagcgttgtcctggcaaagagtccactt--cttccagttcgttgat---aatgtcaactgcttacgtttcccgttgcgcagTTCATCATTGATTGTCAAGCCCTACCGTGTCTGCTCGCACTACTCACCAACAACCACAAGAAGAGTATCAAAAAGGAAGCATGCTGGACCATTTCCAACA
                                                                     ||     |   | |    ||| |    ||| ||||    ||    ||||||     ||||  || |   |  | ||| |  |  | ||    ||||| || || |||||  |    || || |  |||||  |||||||||||||||| |||||||| |||||||| || |||||||
---------------------------------------------------------------------gtgcatataatacattcaccattcgatttcgagttttcagaagcaaatgtctctaacttattttcc---taacacagATGGTTCTCGACCAGCAAGCGCTTCCTTGTCTTTTGAACCTTCTAAAAAACAATTACAAGAAGAGTATCAAGAAGGAAGCTTGCTGGACTATCTCCAACA

upper sequence: PP1S63_171V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT1G02690.2 (Arabidopsis thaliana), 3'ss of exon 7
gtaatttctcgatgcattctggccttttccatgtttttaagcctttgtccatttcgaccttcttccagcgttgtcctggcaaagagtccact-tcttccagttcgttgataatgtcaactgcttacgtttcccgttgcgcagTTCATCATTGATTGTCAAGCCCTACCGTGTCTGCTCGCACTACTCACCAACAACCACAAGAAGAGTATCAAAAAGGAAGCATGCTGGACCATTTCCAACA
                                                     | | |  |  |||     ||||           ||  || |  |   | |  ||  | | || ||     |  |||| |       |||    | |||    ||||||| || ||  ||||| |    ||  | |  ||||   |||||||||||||||| |||||||| |||||||| || || ||||
----------------------------------------------------gtagtctattatccgtaactgtctgccttttatatctcctatagttttgatgtttacttaagtaaatcatctctgttttctccataacagGCGGTTATTAGCAGTCAAGCGCTTCCTGGTCTGTTAAACCTTTTGAAGAACACATACAAGAAGAGTATCAAGAAGGAAGCTTGCTGGACTATCTCTAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccacttcttccagttcgttgataatgtcaactgcttacgtttcccgttgcgcagTTCATCATTGATTGTCAAGCCCTACCGTGTCTGCTCGCACTACTCACCAACAACCACAAGAAGAGTATCAAAAAGGAAGCATGCTGGACCATTTCCAACA
                                tgcttac  putative branch site (score: 2)
                                        tttcccgtt  CT-rich tract
                  ttgataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttctcgatgcattctggccttttccatgtttttaagcctttgtccatttcgaccttcttccagcgttgtcctggcaaagagtccacttcttccagttcgttgataatgtcaactgcttacgtttcccgttgcgcagTTCATCATTGATTGTCAAGCCCTACCGTGTCTGCTCGCACTACTCACCAACAACCACAAGAAGAGTATCAAAAAGGAAGCATGCTGGACCATTTCCAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA