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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaactgctgcgggttccatgtcgtctacgatgtattgcgctgtgcagcgttaagtttggtacgtcctgttctgaccgccgtcgccgtggcatgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA

Basic information

species Physcomitrella patens
transcript PP1S58_249V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S58_249V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 3
agaactgctgcgggttccatgtcgtctacgatgtattgcgctgtgcagcgttaagtttggtacgtcctgttctgaccgccgtcgccgtg-gcatgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
| | | | | | | | | | ||| | | | | || | ||| || | || ||| | || ||||||| ||||||||||||||||||||| |||||||| || | || | | | | | ||| |||| |||||||||||||| | ||||||||
---------gtaagcactaag-caccagcaacg-gcaacgccatcc-gtttcaacgacg--acgatgtgcttacgttttggttcgtgtgcgtgtg-tgcagGGCATGATGAACAACTGCTGGTTCAGGGTGAAGACGAAGACGTGCAGGCCGCACAAGGGGGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCGGGCA

upper sequence: PP1S58_249V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os08g36480.1 (Oryza sativa), 3'ss of exon 3
agaactgctgcgggttccatgtcgtctacgatgtattgcgctgtgcagcgttaagtttggtacgtcctgttctgaccgccgtcgccgtggcatgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
| | | | ||| ||||| || | ||| | || || | | | | | ||| | || ||| | ||||||| ||||||||||||||||||||| ||||||||| | | | | | | | | ||| |||| |||||||||||||| | ||| || |
-------gtaggtgcttcattccgtctccggc-caaggcgacg-gcgatgtagacgacgat--ggcaaattcattcgatcggt----tgggtttttgcagGGGATGATGAACAACTGCTGGTTCAAGGTGAAGGTGAACGTGTGCCGGCCGCACAAGGGTGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCCGGGA

upper sequence: PP1S58_249V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G428027_T01 (Zea mays), 3'ss of exon 3
-----------------------agaactgctgcgggttccatgtcgtc---tacgatg--tattgcgctgtgcagcgttaagtttggtacgt-cctgttctgaccgccgtcgccgtggcatgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
| | | || ||| |||| | ||||| | | | || | |||| || | | || || ||| || || || |||||| ||||||||||||||||||||||||||||||||| | | | | | ||| ||| ||||| |||||||||||||| | ||||||||
gtgagttaccgcttcatcgtgcttcctttccggtggcttcgccgtcggtccgtccgatgcttgtcttccacggctgtgttagattaaatgcacgtgtggcttgtccgttcctgc----gcgcgc-gcagGGCATGATGAACAACTGCTGGTTCCGGGTGAAGGTCAACGCGTGCCGGCCGCACAAGGGCGAGATCGGCCTGGTGTTCGAGCACCCGACGCAGCCGGGCA

upper sequence: PP1S58_249V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM5G878558_T01 (Zea mays), 3'ss of exon 3
---------agaactgctgcgggttccatgtcgt----ctacg-atgtattgcgctgtgca---gcgttaagtttggtacgtcctgttctgaccgccgtcgccgtggcatgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
| | | | | || | ||| | | | |||| | | || | | |||| || ||| | | | | | | | | |||||| |||||||||||||||||||||||||||||| || | | | | | ||| ||| | ||| |||||||||||| | | ||||||||
gtgagttgccgctccatcgtgtttcccttcccgtggaaccatgcatgtcctcctctccacgactgtgttagcttaaatacacgcacgtgcgtctgtt-cctctacg------cgcagGGCATGATGAACAACTGCTGGTTCCGGGTGAAGATCAACGCGTGCCGGCCGCACAAGGGCGAGATCGGCATGGTGTTCGAGCACCCGGCGCAGCCGGGCA

upper sequence: PP1S58_249V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G568636_T01 (Zea mays), 3'ss of exon 3
agaactgctgcgggttccatgtcgtctacgatgtattgcgctgtgcagcgttaagtttggtacgtcctgttctgaccgc-cgtcgccgtggc-atgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
| || | ||| | || | | | | | |||||| | || | |||| | || ||| ||||| ||||||||||||||||||||| ||||||||| | | | | | ||| ||| |||| |||||||||||||| | ||| ||||
------------gtacatatatatactagcacataatat-taatactgaat-aagtttc-tgtttctgctcctgatgatatataaatctgatgatggcacagGGGATGATGAACAACTGCTGGTTCAAGGTGAAGGTGAACGTGTGCCGTCCGCACAAGGGCGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCCGGCA

upper sequence: PP1S58_249V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA14G33480.1 (Glycine max), 3'ss of exon 3
agaactgctgcgggttccatgtcgtctac--gatgtattgcgct-gtgcagcgttaagtttggtacgtcctgttctgaccgccgtcgccgtggcatgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
| | | || | | | | | | | || | | || ||| | || | | ||| | | | | || |||| ||||||||||||||||||||| ||||||| || ||||| | | | | | || | | | || || ||||| || | || | |
---atttcaagggaccaaaaagtattttcccgctttttttcacaagtaaagcaattctaatgaatccttttgtgttatgttttgggaatgcaataatgtgtagGGTATGATGAACAACTGCTGGTTCAGGGTGAAAACAAATGTAGCCAAGCCCCACAAGGGTGAGATTGGCATAGTGTTTGAACACCCTACCCAACCAGCAA

upper sequence: PP1S58_249V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv18s0001g03910.t01 (Vitis vinifera), 3'ss of exon 3
--agaactgc---tgcgggttccatgtcgtctacgatgtattgcgctgtgcagcgttaagtttggtacgtcctgttctgaccgccgtcgccgtggcatgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
| | ||| | | | || ||| || || || | | | | | | |||| || || | | | ||| || ||||||||||||||||||||||||||||| | || || | | |||| | | | || | | ||||||||| || |||| || || |
tcatagttgcaaacatgagaggcgtg-cgtttatgacgtgattttcc-tataatttccattttgtcgtttctgattagg---gaaataataatggaattatgcagGGAATGATGAACAACTGCTGGTTCAGAGTAAAAACAAATGTGTGCAAGCGTCACAGGGGAGAGATTGGAATCGTATTCGAGCATCCAACTCTTCCAGGAA

upper sequence: PP1S58_249V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ14822 (Selaginella moellendorffii), 3'ss of exon 4
agaactgctgcgggttccatgtcgtctacgatgtattgcgctgtgcagcgttaagtttggtacgtcctgttctgaccgccgtcgccgtggcatgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
|| || ||| || || | | | || ||| | || || | || | | || ||| |||||| ||||||||||||||||||||||||||||||||| | | |||| || | | ||| | ||||| |||||||||||||| ||||||| ||
--------------------gtgagtggaagtgaatt---ctttggattgatcggt--ggttc-tcatggttcgatctctcgggctatggtg----gcagGGGATGATGAACAACTGCTGGTTCCGGGTGAAGGTCCGTCCCTGCAAGGGGAAGCTCGGGGGCGTGGCGCTGGCGTTCGAGCACCCGACGCGGCCGGCCA

upper sequence: PP1S58_249V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ26567 (Selaginella moellendorffii), 3'ss of exon 5
agaactgctgcgggttccatgtcgtctacgatgtattgcgctgtgcagcgttaagtttggtacgtcctgttctgaccgcc--gtcgccgtggc-atgctg-cagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
||| || ||| | | || | ||| | || ||||||| | || | ||| ||| || ||||| ||||||||||||||||||||||||||||||||| | |||| || | ||| | ||||| |||||||||||||| ||||||||||
--------------------------------gtaagtggcagtggatctttgggattgatcggta--gttctgatggttcgatctctcgggctatggtggcagGGGATGATGAACAACTGCTGGTTCCGGGTGAAGGTCCATCCCTGCAAGGGGAAGCTGGGGGGCGTGGCGCTGGCGTTCGAGCACCCGACGCGGCCGGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagcgttaagtttggtacgtcctgttctgaccgccgtcgccgtggcatgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
                        ttctgac  putative branch site (score: 2)
 ttaagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaactgctgcgggttccatgtcgtctacgatgtattgcgctgtgcagcgttaagtttggtacgtcctgttctgaccgccgtcgccgtggcatgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA

- - -tgctgcg