Sequence
atgc intronic sequence ATGC exonic sequencegtgcgtatgattggctctgtttatattctctttgtttgtgtgtccttttgtaagttgaactattttgtgacattttgtactaaactagtgtatctgattttgccatagGTCGAACTTGCTGAGAAAACTGCTGTATTGTTCACAAAGGATGGTGATCAGCACAATAACTTGTTCGACATGCAATGCATGTG
Basic information
species | Physcomitrella patens |
transcript | PP1S67_222V6.2 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S67_222V6.2 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GRMZM2G047093_T01 (Zea mays), 3'ss of exon 15
gtgcgtatgattggctctgtttatattctctttgtttgtgtgtccttttgtaagttgaactattttgtgacattttgtactaaactagtgtatctgattttgccatagGTCGAACTTGCTGAGAAAACTGCTGTATTGTTCACAAAGGATGGTGATCAGCACAATAACTTGTTCGACATGCAATGCATGTG
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------atgggtagactagcacttatccaaaaagaaagcactggagtttcttggcaatatacttgcacgctcttttgcatttatctggtttctgtgctgca--tgaagGTTGGCCTTGCCGAGAAGACTGCTGTCTTGTTTACAAAAGATGGTGATCAACACAATAATCTTCATGACATGCAGTGCATGTG
upper sequence: PP1S67_222V6.2 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA07G03850.1 (Glycine max), 3'ss of exon 15
---------------gtgcgtatgattggct-ctgtttatattctctttgt--ttgtgtgtccttttgtaagttgaactattttgtgacattttgtactaaactagtgtatctgattttgccatagGTCGAACTTGCTGAGAAAACTGCTGTATTGTTCACAAAGGATGGTGATCAGCACAATAACTTGTTCGACATGCAATGCATGTG
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gtttttgtctagctttggattatatttggttgttaatcacacaggcattgtaattggtggtgtttttttcattttcattttcttattctgctttattt---atttatttatttccttgatacaaagGTGGCATTGGCTGAAAAAACTGCTGTATTGTTCACAAAAGATGGGGATCAACACAATAACCTTCATGACATGCAGTGCATGTG
upper sequence: PP1S67_222V6.2 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA08G22180.1 (Glycine max), 3'ss of exon 15
gtgcgtatgattggctctgtttatattctctttgtttgtgtgtcctt------ttgtaagt----tgaactatt-ttgtgacattttg----tactaaactagtgtatctgattttgccatagGTCGAACTTGCTGAGAAAACTGCTGTATTGTTCACAAAGGATGGTGATCAGCACAATAACTTGTTCGACATGCAATGCATGTG
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--gtttttgtctagctttgaat-tattatatttggttgttaaccacacgggcattgtaattggtgtggtttatcattttcattttctgattctgctatatttatttattcccttgataccaagGTGGCTTTGGCTGAAAAAACTGCTGTATTGTTCACAAAAGATGGGGATCAACACAATAACCTTCATGACATGCAGTGCATGTG
upper sequence: PP1S67_222V6.2 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA13G43760.1 (Glycine max), 3'ss of exon 15
gtgcgtatgattggctctgtttatattctctttg--tttgtgtgtccttttgtaagttgaactattttgtgacattttgtactaaactagtgtatctgattttgccat--agGTCGAACTTGCTGAGAAAACTGCTGTATTGTTCACAAAGGATGGTGATCAGCACAATAACTTGTTCGACATGCAATGCATGTG
|| || ||| ||| || | | |||||| | | | || | | | || || || ||| | || | | ||| || |||||| | || || ||||||||||| ||||||||||| ||||||||||||||||| ||| | || ||||| ||||||||
gttttggctatctatataatttgaatttcattcgcactcgtgtgttgtaatatgtgtagttttctcttttgcgtgttctgactttcttttggtccattctcttgatatccagGTCGCTTTGGCAGAAAAAACTGCTGTGTTGTTCACAAAAGATGGTGATCAGCACAACAACCTACATGATATGCAGTGCATGTG
upper sequence: PP1S67_222V6.2 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA15G01580.2 (Glycine max), 3'ss of exon 15
gtgcgtatgattggctctgtttatattctctttgt--ttgtgtgtccttttgtaagttgaactattttgtgacattttgtactaaactagtgtatctgattttgccat--agGTCGAACTTGCTGAGAAAACTGCTGTATTGTTCACAAAGGATGGTGATCAGCACAATAACTTGTTCGACATGCAATGCATGTG
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gttttttctatcta-tatatttgaatttcattcacactcgagtgctgtaatatgtgtagttttctcttttgcctgttctgattttcttttggtctgttcccttgatatccagGTGGCTTTGGCAGAAAAAACTGCTGTGTTGTTCACAAAAGATGGTGATCAACACAACAACCTGCATGATATGCAGTGCATGTGMapped 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|162189874|gb|FC365577.1|FC365577EST: ACCGGTTTTTGAACAGTGAATGTGTGAAACGCATGCTGCAAGCTGACCAG GTCGAACTTGCTGAGAAAACTGCTGTATTGTTCACAAAGGATGGTGATCAG
genomic: ACCGGTTTTTGAACAGTGAATGTGTGAAACGCATGCTGCAAGCTGACCAGgtgcgtatga ... tttgccatagGTCGAACTTGCTGAGAAAACTGCTGTATTGTTCACAAAGGATGGTGATCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgaactattttgtgacattttgtactaaactagtgtatctgattttgccatagGTCGAACTTGCTGAGAAAACTGCTGTATTGTTCACAAAGGATGGTGATCAGCACAATAACTTGTTCGACATGCAATGCATGTG
ttttgcc CT-rich tract
actatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcgtatgattggctctgtttatattctctttgtttgtgtgtccttttgtaagttgaactattttgtgacattttgtactaaactagtgtatctgattttgccatagGTCGAACTTGCTGAGAAAACTGCTGTATTGTTCACAAAGGATGGTGATCAGCACAATAACTTGTTCGACATGCAATGCATGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG