Sequence
atgc intronic sequence ATGC exonic sequenceCGCAAAAACCATGGATAAAGTCTACAACTTAGATTGGCTGAATAGTGCTGCTAAGAATGAATGTACTGCAGCTGTTGGTTTCAAGTGGATGCTCAACCAGgtaaatttcataagatcctatcatgctcttagttccatcaggtcatacacgacttttttcgttttgctgttagtttcagagcattattcctccatttcgt...
Basic information
species | Physcomitrella patens |
transcript | PP1S310_50V6.2 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S310_50V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: LOC_Os01g57550.2 (Oryza sativa), 5'ss of exon 3
CGCAAAAACCATGGATAAAGTCTACAACTTAGATTGGCTGAATAGTGCTGCTAAGAATGAATGTACTGCAGCTGTTGGTTTCAAGTGGATGCTCAACCAGgtaaatttcataagatcctatcatgctcttagttccatcaggtcatacacgacttttttcgttttgctgttagtttcagagcat-tattcctccatttcgt-
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CACAAAAACATTGGATAAATTGTACAATCTGGACTGGCTCAGCAGTGCTGCTAAAAATGAATGTACTGCAGCAGTGGGGTTGAAATGGATGCTGAATCAGgtaatattttcgccataatagt-tatttttactactcctatctcatg-gtaagttgcacagtttcatttttgttacttaattatatattttcttgtggaaca
upper sequence: PP1S310_50V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: LOC_Os03g27760.1 (Oryza sativa), 5'ss of exon 3
CGCAAAAACCATGGATAAAGTCTACAACTTAGATTGGCTGAATAGTGCTGCTAAGAATGAATGTACTGCAGCTGTTGGTTTCAAGTGGATGCTCAACCAGgtaaatttcataagatcctatcatgctcttagttccatcaggtcatacacgacttttttcgttttgctgttagtttcagagcattattcctccatttcgt--
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AACAAAGACACTGGATAAGGTGTACAATTTGGATTGGAATAGTAGTGCTTCTAAGAATGAATGCACTGCTGCTGTTGGCTTAAAATGGATGCTTAATCAGgtgagaa--gaagagtgaaatctagattaacattttgtttttttttaattcaccctccttgcccttcctcgaagtttgttattttttttacttgataagcaa
upper sequence: PP1S310_50V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM5G877077_T01 (Zea mays), 5'ss of exon 3
CGCAAAAACCATGGATAAAGTCTACAACTTAGATTGGCTGAATAGTGCTGCTAAGAATGAATGTACTGCAGCTGTTGGTTTCAAGTGGATGCTCAACCAGgtaaatttcataagatcctatcatgctcttagttccatcaggtcatacacgacttttttcgttttgctgttagtttcagagc---attattcctccatttcgt--
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TAAGAAAACACTGGACAAATTGTACAATTTGGATTGGTACAGCAGTGCTGCTAAGAATGAATGTACAGCTGCTGTGGGGCTGAAATGGATGCTCAATCAGgtaatccttata----ttcatcacacttgttggtggagcaaaa-acttgctcacgtgataatttcacagaacatttttcatcttgattatttatactcttaatgg
upper sequence: PP1S310_50V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM2G136538_T03 (Zea mays), 5'ss of exon 3
CGCAAAAACCATGGATAAAGTCTACAACTTAGATTGGCTGAATAGTGCTGCTAAGAATGAATGTACTGCAGCTGTTGGTTTCAAGTGGATGCTCAACCAGgtaaatttcataagatcctatcatgctcttagttccatcaggtcatacacgacttttttcgttttgctgttagtttcagagcatt-attcctccatttcgt--
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AGTAAATGCCATGGATAGAGTGTACAGCTTGGATTGGAACAGTAGTGCTTCCAAGAATGAGTGCACTGCTGCTATTGGCTTCAAGTGGATGCTTAATCAGgtga---tgactaaaacatgcagtatagataatttaattggatatcattttgttcatttattttttcattcagtcccagtacattcacaactaggtgctagat
upper sequence: PP1S310_50V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM2G003530_T01 (Zea mays), 5'ss of exon 3
CGCAAAAACCATGGATAAAGTCTACAACTTAGATTGGCTGAATAGTGCTGCTAAGAATGAATGTACTGCAGCTGTTGGTTTCAAGTGGATGCTCAACCAGgtaaatttcataagatcctatcatgctcttagttccatcaggtcatacacgacttttttcgttttgctgttagtttcagagcattattcct-ccatttcgt---
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AATAGATACCCTGGATAAAGTGTACAATTTGGACTGGAACAGTAGCGCTTCCAAGAATGAGTGCACTGCAGCTATTGGCTTCAAGTGGATGCTAAATCAGgtgcggactaaaacatgcagtatagat---aatttatttggatgatccttt-ttcatttatttttccatttagttccagtatgtttcaattattagtatgtgta
upper sequence: PP1S310_50V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA04G03960.1 (Glycine max), 5'ss of exon 3
CGCAAAAACCATGGATAAAGTCTACAACTTAGATTGGCTGAATAGTGCTGCTAAGAATGAATGTACTGCAGCTGTTGGTTTCAAGTGGATGCTCAACCAGgtaaatttcataagatcctatcatgctcttagttccatcaggtcatacacgacttttttcgttttgctgttagtttcagagcattattcctccatttcgt------
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TTTAGAGACAATGGATAGAGTGTATAATCTTGATTGGTTTTCTAGTGCTTCCAAGAATGAGTGCACTGCAGCTGTTGGCTTCAAGTGGATGCTTAATCAGgtagacacca----atttactaaaggacaaaacttaaatgtatt-tctttaggtactttagtgttatttttaatta-aaattgtaattttaccatggtaacctatg
upper sequence: PP1S310_50V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: AT2G15730.1 (Arabidopsis thaliana), 5'ss of exon 3
CGCAAAAACCATGGATAAAGTCTACAACTTAGATTGGCTGAATAGTGCTGCTAAGAATGAATGTACTGCAGCTGTTGGTTTCAAGTGGATGCTCAACCAGgtaaatttcataagatcctatcatgctcttagttccatcaggtcatacacgacttttttcgttttgctgttagtttcagagcattattcctccatttcgt
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TTTTGAGACGTTGGACAAAGTATATAATTTAGATTGGTTGAGTAGTGCTTCTAAGAACGAGTGTACATCTGCTGTTGGTTTGAAATGGATGCTTAATCAGgtaaagttctgaatgttatagaaatttgctagtctctttttaccgaatggttactaaatagcttagatgctgaatttatcaatttgtgatatattttctt
upper sequence: PP1S310_50V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: AT4G34420.1 (Arabidopsis thaliana), 5'ss of exon 3
CGCAAAAACCATGGATAAAGTCTACAACTTAGATTGGCTGAATAGTGCTGCTAAGAATGAATGTACTGCAGCTGTTGGTTTCAAGTGGATGCTCAACCAGgtaaatttcataagatcctatcatgct----cttagttccatcaggtcatacacgacttttttcgttttgctgttagtttcagagcattattcctccatttcgt
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TTTCGAGACTCTTGACAAAGTCTATAATCTAGACTGGTTGAGTAGTGCCTCTAAGAACGAGTGCACTTCCGCTGTTGGCTTCAAGTGGATGCTTAATCAGgtaaagtgattgttattcacggacactgtgacatatctttagtctttcttactcatatgttttcgactcgtctctgtttccatttgagtgcttgaacaaa----
upper sequence: PP1S310_50V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: Vv07s0031g00880.t01 (Vitis vinifera), 5'ss of exon 4
CGCAAAAACCATGGATAAAGTCTACAACTTAGATTGGCTGAATAGTGCTGCTAAGAATGAATGTACTGCAGCTGTTGGTTTCAAGTGGATGCTCAACCAGgtaaat---ttcataagatccta-tcatgctcttagttccatcaggtcat-acacgacttttttcgttttgctgttagtttcagagcattattcctccatttcgt
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TGTGAAGACACTAGATAAAATTTACAATTTGGACTGGTTCAGTAGTGCTTCCAAGAATGAGTGTTCAGCTGCAGTTGGCTTCAAGTGGATGCTCAATCAGgtaaatactttcttcaaatttaagttccaagctcacttatttgaactttttacatggctgcttccatt--gatgagtacttaaatatgtatatctgaaaaat---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|162183021|gb|FC360587.1|FC360587EST: CTAAGAATGAATGTACTGCAGCTGTTGGTTTCAAGTGGATGCTCAACCAG GGACCGATGGAATACAACAGGGAGGTCAGGGAATACTTTGAGAGAATGGGT
genomic: CTAAGAATGAATGTACTGCAGCTGTTGGTTTCAAGTGGATGCTCAACCAGgtaaatttca ... tctattatagGGACCGATGGAATACAACAGGGAGGTCAGGGAATACTTTGAGAGAATGGGT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CGCAAAAACCATGGATAAAGTCTACAACTTAGATTGGCTGAATAGTGCTGCTAAGAATGAATGTACTGCAGCTGTTGGTTTCAAGTGGATGCTCAACCAGgtaaatttcataagatcctatcatgctcttagttccatcaggtcatacacgacttttttcgttttgctgttagtttcagagcattattcctccatttcgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA