Sequence
atgc intronic sequence ATGC exonic sequenceGGGATGTGTTATGACAGCTCAGAAAGGAGAAGGTCGAGCATGGATGCAGCCGATGATTTTCAATGGAGAAACATTTAACGAGTTTCATGCTCCTCGTGAGgtgtgtgtctcctcggttgttgatcctacagaagcgaccttttgtgagccagttgagaaggccaattctagtcattcttttactgctggtctagcagata...
Basic information
species | Physcomitrella patens |
transcript | PP1S158_188V6.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S158_188V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA13G31850.1 (Glycine max), 5'ss of exon 2
-------GGGATGTGTTATGACAGCTCAGAAAGGAGAAGGTC-GAGCATGGATGCAGCCGATGATTTTCAATGGAGAAACATTTAACGAGTTTCATGCTCCTCGTGAGgtgtgtgtctcctcggttgttgatcctacagaagcgaccttttgtgagccagttgagaaggccaattctagtcattcttttactgctggtctagcagata--
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CCATTGACAATCCTGCACTGGCCACTTTTTGTGAACCAGTTGAGAAGGCCAATTCAAGCCATTCTTTTACA-GCAGGACTGGCTCACAGTGTTGGT----CTCA-Ggtgcatttattttttcattcaatcttagtat-gaattaccctcttgctctcctatttactctcttgatttttacc--tgtgtggttgtcaaccta-tagacata
upper sequence: PP1S158_188V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA15G07450.1 (Glycine max), 5'ss of exon 2
-------GGGATGTGTTATGACAGCTCAGAAAGGAGAAGGTC-GAGCATGGATGCAGCCGATGATTTTCAATGGAGAAACATTTAACGAGTTTCATGCTCCTCGTGAGgtgtgtgtctcctcggttgttgatcctacagaagcgaccttttgtgagccagttgagaaggccaattctagtcattcttttactgctggtcta-gcagata
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CCATTGACAATCCTGCACTTGCCACTTTCTGTGAACCAGTTGAGAAGGCCAATTCAAGCCATTCTTTTACA-GCAGGACTGGCTCACAGTGTTGGT----CTCA-Ggtgcatttattttttcattcaatctcagtatc-aattaccctcttcctctcctatttactctcttgatttttacc--tgtgaggttgtcaacctataaacata
upper sequence: PP1S158_188V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv00s0301g00050.t01 (Vitis vinifera), 5'ss of exon 2
------GGGATGTGTTATGACAGCTCAGAAAGGAGAAGGTCGAGCATG--GATGCAGCCGATGATTTTCAATGGAGAAACATTTAACGAGTTTCATGCTCCTCGTGAGgtgtgtgtctcctcggttgttgatcctacagaagcgaccttttgtgagccagttgagaaggccaattctagtcattcttttactgctggtctagcagata
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CCATTGATAATCCAGCATTGGCAACCTTCTGTGAGCCAGTTGAGAAGGCAAATTCAAGCCATT-CCTTCACAACAGGACTGGCTCAC-AGCGTAGGGCTTAGgtctgtattttttccattccactattttttttcagggtttctactctttcatatacatttcattcaggc--tcccagacaaattggtaaccaggatcaaatt----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|18334029|gb|BJ166045.1|BJ166045EST: CGATGATTTTCAATGGAGAAACATTTANCGAGTTTCATGCTCCTCGTGAG GAATCAGCCGCTGCGAGTCTACAGTATGGCCAAATACGCAGCCATTGCTCG
genomic: CGATGATTTTCAATGGAGAAACATTTAACGAGTTTCATGCTCCTCGTGAGgtgtgtgtct ... atttaaccagGAATCAGCCGCTGCGAGTCTACAGTATGGCCAAATACGCAGCCATTGCTCG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGGATGTGTTATGACAGCTCAGAAAGGAGAAGGTCGAGCATGGATGCAGCCGATGATTTTCAATGGAGAAACATTTAACGAGTTTCATGCTCCTCGTGAGgtgtgtgtctcctcggttgttgatcctacagaagcgaccttttgtgagccagttgagaaggccaattctagtcattcttttactgctggtctagcagata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC