Sequence
atgc intronic sequence ATGC exonic sequenceCGTGTATTCTGGCGTGGTGTTGTGGAGGAGCTCCTTTGGTTTATTAGTGGGTCTACAAATGCCAAGgtgcgtatattggcgttttattagcggttttagcttgttttggagattgtgactgccacaactgaagttgaactctttttcctcgatttcctttatctgtttattactacacagctaaacgtgctgttatgcatggtag
Basic information
species | Physcomitrella patens |
transcript | PP1S34_360V6.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S34_360V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G421493_T01 (Zea mays), 5'ss of exon 8
CGTGTATTCTGGCGTGGTGTTGTGGAGGAGCTCCTTTGGTTTATTAGTGGGTCTACAAATGCCAAGgtgcgtatattggcgttttattagcggttttagcttgttttggagattgtgactgccacaactgaagttgaactctttttcctcgatttcctttatctgtttattactacacagctaaacgtgctgttatgcatggtag
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AGGGTATTTTGGCGTGGTGTTGTCGAAGAACTCCTTTGGTTCATCAGTGGCTCAACAAATGCAAAGgtgtgca-gtgatagctaggccgaccggaaggtgtcgttgtg----tcgtgtt---catgagcgta--cgtatttgttggtgtctgatggttgccgcagtcatttccta-atagtaacttgtgttggggtttgcag---
upper sequence: PP1S34_360V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G072608_T01 (Zea mays), 5'ss of exon 4
CGTGTATTCTGGCGTGGTGTTGTGGAGGAGCTCCTTTGGTTTATTAGTGGGTCTACAAATGCCAAGgtgcgta-tattggc--gttttattagcggttttagcttgttttggagattgtgactgc-cacaactgaagttgaactctttttcctcgatttcctttatctgtttattactacacagctaaacgtgctgttatgcatggtag
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AGGGTATTTTGGCGTGGTGTTGTCGAAGAACTCCTTTGGTTCATCAGTGGCTCAACAAATGCAAAGgtgtgcagtgatagctaggccgaccggaaggtgtcg-ttgtgtcgt-gttcatgagcgtacgtatttgtgggtg--------tctgatggttgccgcagtc-----atttcctaacagtaacttgtgttggggtttgcag---
upper sequence: PP1S34_360V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G005990_T01 (Zea mays), 5'ss of exon 5
CGTGTATTCTGGCGTGGTGTTGTGGAGGAGCTCCTTTGGTTTATTAGTGGGTCTACAAATGCCAAGgtgcgtatattggcgttttattagcggttttagcttgttttggagattgtgactgccacaactgaagttgaactctttttcctcgatttcctttatctgtttattactacacagctaaacgtgctgttatgcatggtag
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AGGGTATTTTGGCGTGGTGTTGTCGAAGAACTCCTTTGGTTCATCAGTGGCTCAACAAATGCAAAGgtgtgca-------ggactaaaatgggtctagtgctgtcttt-agccaatgatttgatttattgtaggta------tttgccttaatatgtattaacaactcac-atgtcatgat------------------------
upper sequence: PP1S34_360V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G139880_T01 (Zea mays), 5'ss of exon 4
CGTGTATTCTGGCGTGGTGTTGTGGAGGAGCTCCTTTGGTTTATTAGTGGGTCTACAAATGCCAAGgtgcgtatattggcgttttattagcggttttagc-ttgttttggagattgtgactgccacaactgaagttgaactctttttcctcgatttcctttatctgtttattactacacagctaaacgtgctgttatgcatggtag
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AGGGTGTTTTGGCGTGGTGTTGTCGAAGAACTCCTTTGGTTCATCAGTGGCTCAACAAATGCAAAGgtgtgca-------ggattaata-tggctctagtgctatctt-----tagccaatgttttgattt--gttgtaggcttgtagct-gttttccttaatctgtat-tcgcaacccacat-----------------------
upper sequence: PP1S34_360V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA06G01280.1 (Glycine max), 5'ss of exon 5
CGTGTATTCTGGCGTGGTGTTGTGGAGGAGCTCCTTTGGTTTATTAGTGGGTCTACAAATGCCAAGgtgcgtatattggcgttttattagcggttttagcttgttttggagattgtgactgccacaactgaagttgaactctttttcctcgatttcctttatctgtttattactacacagctaaacgtgctgttatgcatggtag
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AAAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAATGCCAAGgtaatgatatc----ttctaccaatctttttcatgcac----gaatcctcacctatt----cttagtttggccacaaacaagctgacatgagccaaatatttgggaacatga---------------------------
upper sequence: PP1S34_360V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA04G01240.1 (Glycine max), 5'ss of exon 5
CGTGTATTCTGGCGTGGTGTTGTGGAGGAGCTCCTTTGGTTTATTAGTGGGTCTACAAATGCCAAGgtgcgtatattggcgttttattagcggttttagcttgttttggagattgtgactgccacaactgaagttgaactctttttcctcgatttcctttatctgtttattactacacagctaaacgtgctgttatgcatggtag
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AGAGTATTTTGGCGAGGGGTTGTTGAAGAGCTTCTTTGGTTTATCAGTGGGTCAACGAATGCCAAGgt------aatgatatctt-ctgcctatcttttttcatacacaaatcctcacctatc----cttagtttggtcacaaacaagctgacatgagccaaatattggggaacatg----------------------------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|162204721|gb|FC381429.1|FC381429EST: GTGTTGTGGAGGAGCTCCTTTGGTTTATTAGTGGGTCTACAAATGCCAAG GTGCTTCATGACAAGGGCGTGAAAATATGGGACGGCAATGGTTCTCGAGAA
genomic: GTGTTGTGGAGGAGCTCCTTTGGTTTATTAGTGGGTCTACAAATGCCAAGgtgcgtatat ... tgcatggtagGTGCTTCATGACAAGGGCGTGAAAATATGGGACGGCAATGGTTCTCGAGAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CGTGTATTCTGGCGTGGTGTTGTGGAGGAGCTCCTTTGGTTTATTAGTGGGTCTACAAATGCCAAGgtgcgtatattggcgttttattagcggttttagcttgttttggagattgtgactgccacaactgaagttgaactctttttcctcgatttcctttatctgtttattactacacagctaaacgtgctgttatgcatggtag
- - - - - - - - - - GTGGAG
- - - - - - - - - - - TGGAGG
- - - - - - - - - - - GGAGGA
- - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - GGAGCT