Sequence
atgc intronic sequence ATGC exonic sequenceTGCTACAAACATGGACAAAGTCTTCAATCTGGATTGGCTGAACAGCGCTTCGAAGAATGAATGCACTGCAGCTGTTGGTTTCAAGTGGATGCTCAACCAGgtagatttcatcgaatcctacaaatacttgtgattcgagtgcagtatatgtatatatatatatatatatatatatatatggttttctttgcttttcttctatctttaactgtacctgtgtcatgtttttgttatgctgcag
Basic information
species | Physcomitrella patens |
transcript | PP1S4_216V6.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S4_216V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os03g27760.1 (Oryza sativa), 5'ss of exon 3
TGCTACAAACA-TGGACAAAGTCTTCAATCTGGATTGGCTGAACAGCGCTTCGAAGAATGAATGCACTGCAGCTGTTGGTTTCAAGTGGATGCTCAACCAGgtagatttcatcgaatcctacaaatacttgtgattcgagtgcagtatatgtatatatatatatatatatatatatatatggttttctttgcttttcttctatctttaactgtacctgtgtcatgtttttgttatgctgcag
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-AACAAAGACACTGGATAAGGTGTACAATTTGGATTGGAATAGTAGTGCTTCTAAGAATGAATGCACTGCTGCTGTTGGCTTAAAATGGATGCTTAATCAGgtgagaagaa--gagtgaaatctagattaacattttgtttttttttaattcaccctccttgcccttcctcgaagtttgttattttttttacttgataagcaa---------------------------------------
upper sequence: PP1S4_216V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G003530_T01 (Zea mays), 5'ss of exon 3
TGCTACAAACA-TGGACAAAGTCTTCAATCTGGATTGGCTGAACAGCGCTTCGAAGAATGAATGCACTGCAGCTGTTGGTTTCAAGTGGATGCTCAACCAGgtagatttcatcgaatcctacaaatacttgtgattcgagtgcagtatatgtat-atatatatatatatatatatatatatggttttctttgcttttcttctatctttaactgtacctgtgtcatgtttttgttatgctgcag
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-AATAGATACCCTGGATAAAGTGTACAATTTGGACTGGAACAGTAGCGCTTCCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtg-------------cggactaaaacatgcagtatagataatttatttggatgatcctttttcatttatttttccatttagttc-cagtatgtttcaattattagtatgtgta----------------------------
upper sequence: PP1S4_216V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G136538_T03 (Zea mays), 5'ss of exon 3
TGCTACAAACATGGACAAAGTCTTCAATCTGGATTGGCTGAACAGCGCTTCGAAGAATGAATGCACTGCAGCTGTTGGTTTCAAGTGGATGCTCAACCAGgtagatttcatcgaatcctacaaatacttgtgattcgagtgcagtatatgtatatatatatatatatatatatatatatggt-tttctttgcttttcttctatctttaactgtacctgtgtcatgtttttgttatgctgcag
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AGTAAATGCCATGGATAGAGTGTACAGCTTGGATTGGAACAGTAGTGCTTCCAAGAATGAGTGCACTGCTGCTATTGGCTTCAAGTGGATGCTTAATCAGgtga---tgactaaaacatgcag-tatagataatttaattgga-tatcattttgttcatttattttttcattcagtcccagtacattcacaactaggtgctagat-------------------------------------
upper sequence: PP1S4_216V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA04G03960.1 (Glycine max), 5'ss of exon 3
TGCTACAAACA-TGGACAAAGTCTTCAATCTGGATTGGCTGAACAGCGCTTCGAAGAATGAATGCACTGCAGCTGTTGGTTTCAAGTGGATGCTCAACCAGgtagatttcatcgaatcctacaaatacttgtgattcgagtgcagtatatgtatatatatatatatatatatatatatatggttttctttgcttttcttctatctttaactgtacctgtgtcatgtttttgttatgctgcag
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-TTTAGAGACAATGGATAGAGTGTATAATCTTGATTGGTTTTCTAGTGCTTCCAAGAATGAGTGCACTGCAGCTGTTGGCTTCAAGTGGATGCTTAATCAGgtaga---caccaatt--tactaaaggacaaaacttaaatg---tatttctttaggtactttagtgt-----tatttttaattaaaattgtaattttaccatggtaacctatg----------------------------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|18366226|gb|BJ198304.1|BJ198304EST: CGAAGAATGAATGCACTGCAGCTGTTGGTTTCAAGTGGATGCTCAACCAG GGGCCGATGGAATACAATG
genomic: CGAAGAATGAATGCACTGCAGCTGTTGGTTTCAAGTGGATGCTCAACCAGgtagatttca ... tatgctgcagGGGCCGATGGAATACAATG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGCTACAAACATGGACAAAGTCTTCAATCTGGATTGGCTGAACAGCGCTTCGAAGAATGAATGCACTGCAGCTGTTGGTTTCAAGTGGATGCTCAACCAGgtagatttcatcgaatcctacaaatacttgtgattcgagtgcagtatatgtatatatatatatatatatatatatatatggttttctttgcttttcttctatctttaactgtacctgtgtcatgtttttgttatgctgcag
- - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA