Sequence
atgc intronic sequence ATGC exonic sequence...tttttgtacctatcttgcactttcggacaaggagtattgttcgctcaatgcatgtttcacgctctcctcattttggtctgtttgtatgtcgattttgcagATGTTGAAGAATTTTATCGGCAGTGTGATCCAG
Basic information
species | Physcomitrella patens |
transcript | PP1S97_167V6.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S97_167V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA09G07970.1 (Glycine max), 3'ss of exon 1
tttttgtacctatcttgcactttcggacaaggagtattgttcgctcaatgcatgtttcacgctctcctcattttggtctgtttgtatgt-------cgattttgcagATGTTGAAGAATTTTATCGGCAGTGTGATCCAG
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-----gttactctctctttctctctaa--attttcttctttctttttcttttttttttaaattctactcactaaagtttatttatttataattttttttttttgcagATGTTGAGGAATTTTACCAGCAGTGTGATCCTG
upper sequence: PP1S97_167V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv04s0008g01670.t01 (Vitis vinifera), 3'ss of exon 1
tttttgtaccta-tcttgcactttcggacaaggagtattgttcgctcaatgcatgtttcacgctctcctcattttggtctgtttgtatgtcgattttgcagATGTTGAAGAATTTTATCGGCAGTGTGATCCAG
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-----gtacttaattttttttttatccttttcaaattttggttttttattttattttttgaggtttgaatgtgg-gctttgtttg---gtcg---ttgcagATGTTGAAGAATTTTATCAGCAGTGCGATCCGG
upper sequence: PP1S97_167V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv09s0002g01600.t01 (Vitis vinifera), 3'ss of exon 1
tttttgtacctatcttgcactttcggacaaggagtattgttcgc-tcaatgcatgtttcacgctctcctcattttg-gtctgtttgtatgtcgattttgcagATGTTGAAGAATTTTATCGGCAGTGTGATCCAG
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-gttttcttttgttttttattttttaatttgagtttgaatttgaatttgaatttgtttttggaatggtttgttttgagtgtttttgttt-ttggtcttgcagATGTGGACGAATTTTATCAGCAGTGTGATCCCGMapped 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|100354113|gb|BY945717.1|BY945717EST: TAAGGACTTTAAGGGGCGGCGATCGGGAATGCTCAAAGCTCTCACGACCG ATGTTGAAGAATTTTATCGGCAGTGTGATCCAG
genomic: TAAGGACTTTAAGGGGCGGCGATCGGGAATGCTCAAAGCTCTCACGACCGgtaggtgatt ... gattttgcagATGTTGAAGAATTTTATCGGCAGTGTGATCCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatgcatgtttcacgctctcctcattttggtctgtttgtatgtcgattttgcagATGTTGAAGAATTTTATCGGCAGTGTGATCCAG
tcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttgtacctatcttgcactttcggacaaggagtattgttcgctcaatgcatgtttcacgctctcctcattttggtctgtttgtatgtcgattttgcagATGTTGAAGAATTTTATCGGCAGTGTGATCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA