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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagtgacacatgacacttgccgcaggtcttgatgattctcaaatggagtgtctcgtcgttcctagttgaaggtagttgtgttatctattgatgaacttttgcaccttaatattgtgctgagcgttgatgagtcggctggttatattggcatttgttcacttcctgtgttcccgcatctctcagGATTTAATGTGGAAAAAGTTCAATACAAGAATGTCGAGTTCACAGTATGGGATGTTGGAGGTCAGGAGAAATTGCGGCCCCTTTGGCGGCATTACTTCAA

Basic information

species Physcomitrella patens
transcript PP1S91_59V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S91_59V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os10g42940.1 (Oryza sativa), 3'ss of exon 2
gtaaagtgacacatgacacttgccgcaggtcttgatgattctcaaatggagtgtctcgtcgttcctagttgaaggtagttgtgttatctattgatgaacttttgcaccttaat-attgtgctgagcgttgatgagtcggctggttatattggcatttgttcacttcctgtgttcccgcatctctcagGATTTAATGTGGAAAAAGTTCAATACAAGAATGTCGAGTTCACAGTATGGGATGTTGGAGGTCAGGAGAAATTGCGGCCCCTTTGGCGGCATTACTTCAA
                                                                          |||| |    | || ||   |       | | ||| |   | | |  |      |  |||| |        ||     |      | || || |      |  ||||   |||| || || ||||| |||||||||||||||||||| | |||||| || ||||||||||| || ||||| |||||| ||||| | ||| |||| ||||||||
--------------------------------------------------------------------------gtaggttcactctc-atccctccctccctccgcctcatcgaatcttttattttgttttgagccaa------atccaaacccaacctaacatcatcatcatcatcatcatgcagGCTTCAACGTGGAGAAAGTTCAATACAAGAATGTGGTGTTCACTGTGTGGGATGTTGGTGGCCAGGAAAAATTGAGGCCCTTATGGAGGCACTACTTCAA

upper sequence: PP1S91_59V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G011518_T03 (Zea mays), 3'ss of exon 2
gtaaagtgacacatgacacttgccgcaggtcttgatgattctcaaatggagtgtctcgtcgttcctagttgaaggtagttgtgttatctattgatgaacttttgcaccttaatattgtgctgagcgttgatgagtcggctggttatattggcatttgttcacttcctgtgttcccgcatctctcagGATTTAATGTGGAAAAAGTTCAATACAAGAATGTCGAGTTCACAGTATGGGATGTTGGAGGTCAGGAGAAATTGCGGCCCCTTTGGCGGCATTACTTCAA
                         | | |  |      | ||   | | |  | || |   |  | |||  |   | |  |  |  |  |||   |||| | ||||||         ||   ||  |  ||| ||| | | | ||||     |||  | ||  | ||   |    ||  |   ||| || ||||| || || ||||||||||||||||| | |||||| || ||||||||||| || ||||||||  |  ||||||| ||| |||| ||||||||
-----------------------gtccgattgtaccacctatctgcttgtgcatttcataacttttggtttcaaccattgctaattacagttgtccaactct-gcacct---------gccatgcaat--tgattcgtccgttcatat----gtttagtgacagcatgcactttatcacattgtagGTTTCAATGTTGAGAAGGTTCAATACAAGAATGTAGTGTTCACCGTGTGGGATGTTGGTGGCCAGGAGAAGCTCAGGCCCCTGTGGAGGCACTACTTCAA

upper sequence: PP1S91_59V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA12G02110.1 (Glycine max), 3'ss of exon 2
gtaaagtgacacatgacacttgccgcaggtcttgatgattctcaaatggagtgtctcgtcgttcctagttgaaggtagttgtgttatctattgatgaacttttgcaccttaatattgtgctgagcgttgatgagtcggctggttatattggcatttgttcacttcctgtgttcccgcatctctcagGATTTAATGTGGAAAAAGTTCAATACAAGAATGTCGAGTTCACAGTATGGGATGTTGGAGGTCAGGAGAAATTGCGGCCCCTTTGGCGGCATTACTTCAA
                                                                                     |   ||  |  |  | |  ||| | | | |      |   |     ||     |   | || |||    ||     ||| | |  ||   |    |  |||| ||||||||||| || ||||| || |||||||| |  ||||| || |||||||||||||| || ||||||||  || | |||||| |||| || || ||
------------------------------------------------------------------------------------caaacatgtaccag-tatcacacttaagtttaacaggggaagaactagaaataacctat-atgttgtttatttaaggcttacggatttgtagtgctttgcagGTTTTAATGTGGAGAAGGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGGATGTTGGAGGGCAAGAGAAATTAAGGGCACTTTGGAGGCACTATTTTAA

upper sequence: PP1S91_59V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA01G43910.2 (Glycine max), 3'ss of exon 3
gtaaagtgacacatgacacttgccgcaggtcttgatgattctcaaatggagtgtctcgtcgttcctagttgaaggtagttgtgttatctattgatgaacttttgcaccttaatattgtgctgagcgttgatgagtcggctggttatattggcatttgttcacttcctgtgttcccgcatctctcagGATTTAATGTGGAAAAAGTTCAATACAAGAATGTCGAGTTCACAGTATGGGATGTTGGAGGTCAGGAGAAATTGCGGCCCCTTTGGCGGCATTACTTCAA
                                                                   |||||| ||   | || |||    ||  |       ||   ||| | |||  |  |||    |||||||  |    | | |    |  | || |  |  | | || ||     |  |||| || |||||||| |||||||| || ||||||||    |||||||| |||||||||||||| || |||||| |  |||| |||||| |||| |||||  |
-------------------------------------------------------------------gttgaatgtctatatggtat----tggcg-----ccgcttgttagttttggcc--agca--aatgagtctacataatgtttctctaggtttttaaatt-tatattgcc-----ttgcagGTTTCAATGTGGAGAAAGTTCAGTATAAGAATGTTATTTTCACAGTCTGGGATGTTGGAGGACAAGAGAAACTAAGGCCACTTTGGAGGCACTACTTTGA

upper sequence: PP1S91_59V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA11G09790.3 (Glycine max), 3'ss of exon 1
gtaaagtgacacatgacacttgccgcaggtcttgatgattctcaaatggagtgtctcgtcgttcctagttgaaggtagttgtgttatctattgatgaacttttgcaccttaatattg-tgctgagcgttgatgagtcggctggttatat-tggcatttgttca---cttcctgtgttcccgcatctctcagGATTTAATGTGGAAAAAGTTCAATACAAGAATGTCGAGTTCACAGTATGGGATGTTGGAGGTCAGGAGAAATTGCGGCCCCTTTGGCGGCATTACTTCAA
                                                                                           ||    | | |  ||| | | | | | ||  ||    | |  ||| |        ||| |    |||| | |   |||   |  ||   |    |  |||| ||||||||||| || ||||| || |||||||| |  ||||| || |||||||||||||| || ||||||||  || | |||||| |||| || || ||
-------------------------------------------------------------------------------------------tgtaccagtatcacacttaagtttagctgaggaagaattagaagtagaaataacctatatattgtttgattaaggcttatagatttgtagtgctttgcagGTTTTAATGTGGAGAAGGTTCAGTATAAGAATGTTGTTTTCACGGTTTGGGATGTTGGAGGGCAAGAGAAATTAAGGGCACTTTGGAGGCACTATTTTAA

upper sequence: PP1S91_59V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G17060.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaaagtgacacatgacacttgccgcaggtcttgatgattctcaaatggagtgtctcgtcgttcctagttgaaggtagttgtgttatctattgatgaacttttgcaccttaatattgtgctgagcgttgatgagtcggctggttatattggcatttgttcacttcctgtgttcccgcatctctcagGATTTAATGTGGAAAAAGTTCAATACAAGAATGTCGAGTTCACAGTATGGGATGTTGGAGGTCAGGAGAAATTGCGGCCCCTTTGGCGGCATTACTTCAA
                                                                                   |  | |     |  ||||||     | | |||||| |||  | ||      | || || ||  |||    | || | ||    |    |   |  |  ||||||||| ||||| || |||||||| |||||||||||   ||||||||| ||||||||||| || || |||||| || | || |||||| |||||||||||||
----------------------------------------------------------------------------------ttcttgtgacattatacttttatctatgattattgttctgt-cattttccttttggttgtttggatta-tgtctgctgacaatttaaacttatg--ttactcagGATTCAATGTTGAGAAAGTTCAGTACAAGAATGTGATGTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAACTGAGACCTCTTTGGAGGCATTACTTCAA

upper sequence: PP1S91_59V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G03120.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaaagtgacacatgacacttgccgcaggtcttgatgattctcaaatggagtgtctcgtcgttcctagttgaaggtagttgtgttatctattgatgaacttttgcaccttaatattgtgctgagcgttgatgagtcggctggttatattggcatttgttcacttcctgtgttcccgcatctctcagGATTTAATGTGGAAAAAGTTCAATACAAGAATGTCGAGTTCACAGTATGGGATGTTGGAGGTCAGGAGAAATTGCGGCCCCTTTGGCGGCATTACTTCAA
                                                                             || |       |  | | | | ||||     ||     | | ||   | || ||    |  | |||| || ||    || |  | ||| |                |||| || ||||| || |||||||| ||||||||||||   |||||||| ||||||||||| || || |||||  || ||||| | ||| |||||||||||||
-----------------------------------------------------------------------------gtaggtcagattgctcaagcatttttattttttttgcgttttct---catttatcttacaacgggtt-tactgaggattttaaatttcttaca-------------cagGTTTCAATGTTGAGAAAGTTCAGTACAAGAATGTCATCTTCACAGTTTGGGATGTTGGTGGCCAAGAGAAGCTGAGGCCCTTGTGGAGGCATTACTTCAA

upper sequence: PP1S91_59V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EDP05355 (Chlamydomonas reinhardtii), 3'ss of exon 1
gtaaagtgacacatgacacttgccgcaggtcttgatgattctcaaatggagtgtctcgtcgttcctagttgaaggtagttgtgttatctattgatgaacttttgcaccttaatattgtgctgagcgttgatgagtcggctggttatattggcatttgttcacttcctgtgttcccgcatctctcagGATTTAATGTGGAAAAAGTTCAATACAAGAATGTCGAGTTCACAGTATGGGATGTTGGAGGTCAGGAGAAATTGCGGCCCCTTTGGCGGCATTACTTCAA
                                                                               | |   | |   || |  |  | | | ||||| ||  |  | || |      || ||  |     | |     ||     |||  |||| |  |    | |   |||| || || || || || || ||||||||||| || | |||||| || ||||| || || || ||||||||  ||||||| || |||||||||||||||||
--------------------------------------------------------------------------cccagtatcccagcccatgctcca--tgtaccccttattacagc-ccgaaca-----gaatcccccacacacaca---atccacacaca-cctgcgccctgcaaaccgacagGCTTCAACGTTGAGAAGGTGCAATACAAGAACGTTGTGTTCACGGTGTGGGACGTGGGCGGCCAGGAGAAGCTGCGGCCACTGTGGCGGCATTACTTCAA

upper sequence: PP1S91_59V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ24533 (Selaginella moellendorffii), 3'ss of exon 2
gtaaagtgacacatgacacttgccgcaggtcttgatgattctcaaatggagtgtctcgtcgttcctagttgaaggtagttgtgttatctattgatgaacttttgcaccttaatattgtgctgagcgttgatgagtcggctggttatattggcatt--tgttcacttcctgtgttcccgc--atctct--cagGATTTAATGTGGAAAAAGTTCAATACAAGAATGTCGAGTTCACAGTATGGGATGTTGGAGGTCAGGAGAAATTGCGGCCCCTTTGGCGGCATTACTTCAA
                                                                                                                  |  | ||      || |   | ||||  | || ||| | ||  || ||  || ||    |   |   |||  |   ||||||||| ||||| || || || ||||||||||| | |||||| || ||||||||||| || ||||||||  |  | || || |||  ||| ||||| | 
-----------------------------------------------------------------------------------------------------------------gtaatccttttttctggtttcttggctt-tcatcttgaccttcttgctcgatttctcgactgatgtgaatccttgctagGATTTAACGTGGAGAAGGTCCAGTACAAGAATGTGGTGTTCACGGTGTGGGATGTTGGTGGCCAGGAGAAGCTAAGACCGCTCTGGAAGCACTACTTTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtcggctggttatattggcatttgttcacttcctgtgttcccgcatctctcagGATTTAATGTGGAAAAAGTTCAATACAAGAATGTCGAGTTCACAGTATGGGATGTTGGAGGTCAGGAGAAATTGCGGCCCCTTTGGCGGCATTACTTCAA
                                       ttcccgcatctctc  CT-rich tract
           ttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagtgacacatgacacttgccgcaggtcttgatgattctcaaatggagtgtctcgtcgttcctagttgaaggtagttgtgttatctattgatgaacttttgcaccttaatattgtgctgagcgttgatgagtcggctggttatattggcatttgttcacttcctgtgttcccgcatctctcagGATTTAATGTGGAAAAAGTTCAATACAAGAATGTCGAGTTCACAGTATGGGATGTTGGAGGTCAGGAGAAATTGCGGCCCCTTTGGCGGCATTACTTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA