Sequence
atgc intronic sequence ATGC exonic sequenceGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATAAGACCATTAAACTATGGAAGgtactctcagcctaagcaatgtaaattgtatcctttgttgcaatggtgtgcttcttttcaaacttcttttagtgcttaaagtcttgcatctgtattcttc...
Basic information
species | Physcomitrella patens |
transcript | PP1S425_2V6.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 5'ss of exon 4
GGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATAAGACCATTAAACTATGGAAGgtactctcagcctaagcaatgtaaattgtatcctttgttgcaatggtgtgcttcttttcaaacttcttttagtgc--ttaaagtcttgcatctgtattcttc--
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GGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATAAAACAATAAAATACTGGAAGgtatggagaa---aaatatgttaggacccaggaatggttttcaagattt-ctgcatgccaatatctttctaatctaatgtaacatttaagcctgtcttgaccaa
upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 5'ss of exon 4
GGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATAAGACCATTAAACTATGGAAGgtactc--------tcagcctaagcaa-tgtaaattg-------tatcctttgttgcaatggtgtgctt--cttttcaaacttc--ttttagtgcttaaagtcttg----catctgtattcttc----------------------------------------
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GGAAATAGAGGAGAAAATCAATAAGATCAGATGGTGCCAGACAGCAAATGGTGCCCTGTTTCTTCTATCTACGAATGATAAAACCATTAAGTTTTGGAAGgtaggaagggaaaattgtcttatgaaactttaaacttcctgatttttaatttgttgacagattatgctcaacatcaccaactccagtttggtttctttaactactgatataatatatatcctgcacatgctgattacatagctgtcttttcgagaatgaaacag
upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 5'ss of exon 4
GGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATAAGACCATTAAACTATGGAAGgt-------------actctcagcctaagcaatgtaaattgt-atcctttgttgcaatggtgtgcttcttttcaaacttcttt--tagtgcttaaagtcttgcatctgtattcttc------------------------------------------------
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GGAAATAGAGGAGAAAATCAATAAGATTAGATGGTGTCAAACAGCTAACAATGCATTGTTTCTTCTCTCCACCAATGACAAAACCATCAAGTTTTGGAAGgtaggaaagagaactattttaaagttttttaaagttggtgattatcatttgtaaacagaatgttctaaggttcatgttttcttcatagttggtcacaccttttggtgggcttgttaagtacactttatgtgtctctttgctgttctgctttgagtgttgaacagMapped 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|162255330|gb|FC432056.1|FC432056EST: CCGCTCAGTTTCTACTTTCTACCAATGATAAGACCATTAAACTATGGAAG GTGACTGAAAAGAAAGTGAAGCAGGTCAAGAACCTCAATGTGGATCCCGGA
genomic: CCGCTCAGTTTCTACTTTCTACCAATGATAAGACCATTAAACTATGGAAGgtactctcag ... aatggtgcagGTGACTGAAAAGAAAGTGAAGCAGGTCAAGAACCTCAATGTGGATCCCGGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATAAGACCATTAAACTATGGAAGgtactctcagcctaagcaatgtaaattgtatcctttgttgcaatggtgtgcttcttttcaaacttcttttagtgcttaaagtcttgcatctgtattcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG