Sequence
atgc intronic sequence ATGC exonic sequence...ctggacgacactttatgaagataaaggaaacgagtgaggagcaacaacggccgacaatgagatgaatctgactgtgtgggggtttggttgtggtttgcagGAAAGTCGACTTTAACGGATTCCCTGGTGGCTGCTGCTGGAATCATTGCCCAGGAGACCGCCGGAGATGTGAGGCTGACGGACACTCGGCAGGATGAGGC
Basic information
species | Physcomitrella patens |
transcript | PP1S138_93V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S138_93V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA15G40840.1 (Glycine max), 3'ss of exon 2
------ctggacgacactttatgaagataaaggaaacgagtgaggagcaacaacggc--cgacaatgagatgaatctg-----actgtgtgggggttt---------ggttgtggtttgcagGAAAGTCGACTTTAACGGATTCCCTGGTGGCTGCTGCTGGAATCATTGCCCAGGAGACCGCCGGAGATGTGAGGCTGACGGACACTCGGCAGGATGAGGC
| ||| || ||| | | | || || || | | | | | | || | || | | ||| | || || ||||||||| || || | | ||||| || |||||||||||||| ||||| || || ||||| || |||||||||||| |||| || |||| || |||| ||
gtatgttaatatacttttttgtgttgatgtcaagttttacttcatatcacgtactgcatcattgttttgtttactttgtagtaccagtacagagttttatctaactagctttgggaatgcagGAAAATCCACACTGATAGATTCTCTTGTGGCTGCTGCTGGTATCATAGCACAAGAGACTGCAGGAGATGTGAGGATGACAGATACTCTTCAATATGAAGCMapped 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|100365578|gb|BY966666.1|BY966666EST: CAAGAAGCACAACATCAGGAACATGTCCGTCATCGCCCATGTCGATCACG GAAAGTCGACTTTAACGGATTCCCTGGTGGCTGCTGCTGGAATCATTGCCC
genomic: CAAGAAGCACAACATCAGGAACATGTCCGTCATCGCCCATGTCGATCACGgtatgtcgaa ... tggtttgcagGAAAGTCGACTTTAACGGATTCCCTGGTGGCTGCTGCTGGAATCATTGCCC
EST:
gi|100391905|gb|BY989604.1|BY989604EST: CAAGAAGCACAACATCAGGAACATGTCCGTCATCGCCCATGTCGATCACG GAAAGTCGACTTTAACGGATTCCCTGGTGGCTGCTGCTGGAATCATTGCCC
genomic: CAAGAAGCACAACATCAGGAACATGTCCGTCATCGCCCATGTCGATCACGgtatgtcgaa ... tggtttgcagGAAAGTCGACTTTAACGGATTCCCTGGTGGCTGCTGCTGGAATCATTGCCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacggccgacaatgagatgaatctgactgtgtgggggtttggttgtggtttgcagGAAAGTCGACTTTAACGGATTCCCTGGTGGCTGCTGCTGGAATCATTGCCCAGGAGACCGCCGGAGATGTGAGGCTGACGGACACTCGGCAGGATGAGGC
atctgac putative branch site (score: 3)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctggacgacactttatgaagataaaggaaacgagtgaggagcaacaacggccgacaatgagatgaatctgactgtgtgggggtttggttgtggtttgcagGAAAGTCGACTTTAACGGATTCCCTGGTGGCTGCTGCTGGAATCATTGCCCAGGAGACCGCCGGAGATGTGAGGCTGACGGACACTCGGCAGGATGAGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG