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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgaaagtcccacagcatgtctaaccgtgttcagaaatataattggtgtgattgatttctcttgttcatttgctgctgtgtgacgtatgccaccttcagGTTTCGTATTCTATCCTGGTTTTCTTCTCCGGCATGTTCATCACCGTGGAGGGCTTTAACAGAACTGGAGCTCCAGCACGGTTCTGGTTAGCAGTGGAGC

Basic information

species Physcomitrella patens
transcript PP1S155_48V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S155_48V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv02s0025g03310.t01 (Vitis vinifera), 3'ss of exon 2
------tctgaaag------tcccacagcatgtct-aaccgtgttcagaaatataattggtgtga--ttgatttctcttgttcatttgctgctgtgtgacgtatgccacct---tcagGTTTCGTATTCTATCCTGGTTTTCTTCTCCGGCATGTTCATCACCGTGGAGGGCTTTAACAGAACTGGAGC-TCCAGCACGGTTCTGGTTAGCAGTGGAGC
||| |||| ||| || |||| || || | | ||||| | || |||| | || | | | | | | | || |||||||| ||||||||| | | ||||| | |||||||||||||| ||||| |||||||||||||| || | ||||| ||||| | ||||
gtagaatctaaaagttttgatcctactgcattcctgaaatatcaactagtatatacctaatgctcctttgagctgctaaattgtcatagtccctaattccatctcttttctgaaccagGTTTCATATTCTATCTTAATCTTCTTTTGTGGCATGTTCATCACAGTGGATGGCTTTAACAGAACAGGGATACCTAGCACT-CTCTGGAACCTAACCGAGC

upper sequence: PP1S155_48V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ14419 (Selaginella moellendorffii), 3'ss of exon 2
-tctgaaagtcc-cacagcatgtctaaccgtgttcagaaatataattggtgtgattgatttctcttgttcatttgctgctgtgtgacgtatgccaccttcagGTTTCGTATTCTATCCTGGTTTTCTTCTCCGGCATGTTCATCACCGTGGAGGGCTTTAACAGAACTGGAGCTCCAGCACGGTTCTGGTTAGCAGTGGAGC
||| | | | | | | | | || |||| | || || | | || || | | | |||| | | | ||||| || ||||| | || || ||||| ||||| ||||||||||||||||| || |||||||| ||||| ||||||| | ||||||| || || ||||
ctctcatctttttctcttccttttttctcgcgttc-gcggtactatggagactgtggaga-ctaaagccttgatctcgtcctgtgctctttctttgttccagGTCTCTTATTCGCTGCTCGTCTTCTTTTCCGGGATGTTCATCACCGTGGATGGATTTAACAGCACTGGCGCTCCAGGCCAGTTCTGGAACGCTGTTGAGC

upper sequence: PP1S155_48V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ26015 (Selaginella moellendorffii), 3'ss of exon 2
-tctgaaagtcc-cacagcatgtctaaccgtgttcagaaatataattggtgtgattgatttctcttgttcatttgctgctgtgtgacgtatgccaccttcagGTTTCGTATTCTATCCTGGTTTTCTTCTCCGGCATGTTCATCACCGTGGAGGGCTTTAACAGAACTGGAGCTCCAGCACGGTTCTGGTTAGCAGTGGAGC
||| | | | | | | | | || |||| | || || | || || || | | | | | || | | | ||||| || ||||| | || || ||||| ||||| ||||| ||||||||||| || |||||||| ||||| ||||||| | ||||||| || || ||||
ctctcatctttttctcttccttttttctcgcgttc-gcggtactatggagactatggaga-ctaaagccttgatttcgttctttgctctttctttgttccagGTCTCTTATTCGCTGCTCGTCTTCTTTTCCGGGATGTTTATCACCGTGGATGGATTTAACAGCACTGGCGCTCCAGGCCAGTTCTGGAACGCTGTCGAGC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|18336026|gb|BJ168048.1|BJ168048
EST:     TGATTCTGACGGTGGTCGATTTCTC--ATGCCACTGAAACTCTGGACAAG                         GTTTCGTATTCTATCCTGGTTTTCTTCTCCGGCATGTTCATCACCGTGGAG
genomic: TGATTCTGACGGTGGTCGATTTCTCAGATGCCACTGAAACTCTGGACAAGgtattgtgct ... ccaccttcagGTTTCGTATTCTATCCTGGTTTTCTTCTCCGGCATGTTCATCACCGTGGAG
EST: gi|162172959|gb|FC347869.1|FC347869
EST:     TGATTCTGACGGTGGTCGATTTCTCAGATGCCACTGAAACTCTGGACAAG                         GTTTCGTATTCTATCCTGGTTTTCTTCTCCGGCATGTTCATCACCGTGGAG
genomic: TGATTCTGACGGTGGTCGATTTCTCAGATGCCACTGAAACTCTGGACAAGgtattgtgct ... ccaccttcagGTTTCGTATTCTATCCTGGTTTTCTTCTCCGGCATGTTCATCACCGTGGAG
EST: gi|37824150|gb|BJ582216.1|BJ582216
EST:     TGATTCTGACGGTGGTCGATTTCTCAGATGCCACTGAAACTCTGGACAAG                         GTTTCGTATTCTATCCTGGTTTTCTTCTCCGGCATGTTCATCACCGTGGAG
genomic: TGATTCTGACGGTGGTCGATTTCTCAGATGCCACTGAAACTCTGGACAAGgtattgtgct ... ccaccttcagGTTTCGTATTCTATCCTGGTTTTCTTCTCCGGCATGTTCATCACCGTGGAG
EST: gi|18335349|gb|BJ167367.1|BJ167367
EST:     TGATTCTGACGGTGGTCGATTTCTC--ATGCCACTGAAACTCTGGACAAG                         GTTTCGTATTCTATCCTGGTTTTCTTCTCCGGCATGTTCATCACCGTGGAG
genomic: TGATTCTGACGGTGGTCGATTTCTCAGATGCCACTGAAACTCTGGACAAGgtattgtgct ... ccaccttcagGTTTCGTATTCTATCCTGGTTTTCTTCTCCGGCATGTTCATCACCGTGGAG
EST: gi|162172960|gb|FC347870.1|FC347870
EST:     TGATTCTGACGGTGGTCGATTTCTCAGATGCCACTGAAACTCTGGACAAG                         GTTTCGTATTCTATCCTGGTTTTCTTCTCCGGCATGTTCATCACCGTGGAG
genomic: TGATTCTGACGGTGGTCGATTTCTCAGATGCCACTGAAACTCTGGACAAGgtattgtgct ... ccaccttcagGTTTCGTATTCTATCCTGGTTTTCTTCTCCGGCATGTTCATCACCGTGGAG
EST: gi|37836503|gb|BJ594511.1|BJ594511
EST:     TGATTCTGACGGTGGTCGATTTCTCAGATGCCACTGAAACTCTGGACAAG                         GTTTCGTATTCTATCCTGGTTTTCTTCTCCGGCATGTTCATCACCGTGGAG
genomic: TGATTCTGACGGTGGTCGATTTCTCAGATGCCACTGAAACTCTGGACAAGgtattgtgct ... ccaccttcagGTTTCGTATTCTATCCTGGTTTTCTTCTCCGGCATGTTCATCACCGTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgtgattgatttctcttgttcatttgctgctgtgtgacgtatgccaccttcagGTTTCGTATTCTATCCTGGTTTTCTTCTCCGGCATGTTCATCACCGTGGAGGGCTTTAACAGAACTGGAGCTCCAGCACGGTTCTGGTTAGCAGTGGAGC
     gattgat  putative branch site (score: 4)
 ccaccttc  putative PPT
 attgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgaaagtcccacagcatgtctaaccgtgttcagaaatataattggtgtgattgatttctcttgttcatttgctgctgtgtgacgtatgccaccttcagGTTTCGTATTCTATCCTGGTTTTCTTCTCCGGCATGTTCATCACCGTGGAGGGCTTTAACAGAACTGGAGCTCCAGCACGGTTCTGGTTAGCAGTGGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG