Sequence
atgc intronic sequence ATGC exonic sequenceTCTGAAGACGAGCGTGAAATGTGTGCACGTACCATCTACTGTACAAATATTGATAAGAAGgtgaagtggagtgaaatagactttcattcttctaggctgccaattagccctgttcatttactgtctaatctgttgtgaaaagttatggcatggttgtgtattcgttgtgccatggttcacgaggtggtgggaagttttcatgctagtaccacattgtaatgtatggccggggctctgagcgagcagtgacttgatgcag
Basic information
species | Physcomitrella patens |
transcript | PP1S196_50V6.1 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S196_50V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM2G014573_T01 (Zea mays), 5'ss of exon 4
TCTGAAGACGAGCGTGAAATGTGTGCACGTACCATCTACTGTACAAATATTGATAAGAAGgtgaagtggagtgaaatagactttcattcttctaggctgccaattagccctgttcatttactgtctaatctgttgtgaaaagttatggcatggttgtgtattcgttgtgccatggttcacgaggtggtgggaagttttcatgctagtaccacattgtaatgtatggccggggctctgagcgagcagtgacttgatgcag
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CCTGACGATGAACGTGAAATGTGTGCAAGGACAATCTACTGCACAAACATTGACAAGAAGgtttggtacctgcactcatgctactaccatt--aggtattcattatgtcatggt--tctattttaatacacgcag----------------------------------------------------------------------------------------------------------------------------
upper sequence: PP1S196_50V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM2G457231_T01 (Zea mays), 5'ss of exon 8
TCTGAAGACGAGCGTGAAATGTGTGCACGTACCATCTACTGTACAAATATTGATAAGAAGgtgaagtggagtgaaatagactttcattcttctaggctgccaattagccctgttcatttactgtctaatctgttgtgaaaagttatggcatggttgtgtattcgttgtgccatggttcacgaggtggtgggaagttttcatgctagtaccacattgtaatgtatggccggggctctgagcgagcagtgacttgatgcag
||||| || || ||||||||||||||| | || |||||||| ||||| ||||| |||||||| || | | |||| || ||| | | | || | | | | | |||| | | | || | || | | | || | || | | || ||| | |||||| | || | || | | | || | | |||| | | | ||| |
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAGGTTTGGT--------ACCTGCACTCATGCTACTA--CCACTAGgtattcattctgtcatgat-tctattttaatacacgtaggtcactcaagcatatctaaac-ttattctttgagtcaatatgtggtgaggt-------tggtcgttctttactccaa-acacaatctcccttctgtacaactaaaagtttgcag---
upper sequence: PP1S196_50V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM2G069102_T01 (Zea mays), 5'ss of exon 6
TCTGAAGACGAGCGTGAAATGTGTGCACGTACCATCTACTGTACAAATATTGATAAGAAGgtgaagtggagtgaaatagactttcattcttctag-gctgccaattagccctgttcatttactgtctaatctgttgtgaaaagttatggcatggttgtgtattcgttgtgccatggttcacgaggtggtgggaagttttcatgctagtaccacattgtaatgtatggccggggctctgagcgagcagtgacttgatgcag
||||| || || ||||||||||||||| | || |||||||| ||||| ||||| |||||||| || | || |||| || ||| || ||| |||| | |||| | | |
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAGgtttggt--------acctacactcatgctactaccactatgtattcattctgtcatggttctgttttaatacacgcag-------------------------------------------------------------------------------------------------------------------------
upper sequence: PP1S196_50V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM2G454261_T01 (Zea mays), 5'ss of exon 2
TCTGAAGACGAGCGTGAAATGTGTGCACGTACCATCTACTGTACAAATATTGATAAGAAGgtgaagtggagtgaaatagactttcattcttctaggctgccaattagccctgttcatttactgtctaatctgttgtgaaaagttatggcatggttgtgtattcgttgtgccatggttcacgaggtggtgggaagttttcatgctagtaccacattgtaatgtatggccggggctctgagcgagcagtgacttgatgcag
||||| || || ||||||||||||||| | || |||||||| ||||| ||||| |||||||| || | | ||||| || ||| | | | ||| | || | | || |||||| | | | | |
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAGgtttggt--------acctgcattcatgctacta--ccactagtta--tttattgtgtcatggt----tctgttttaatacac-gtag---------------------------------------------------------------------------------------------------------------
upper sequence: PP1S196_50V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM2G123866_T01 (Zea mays), 5'ss of exon 11
TCTGAAGACGAGCGTGAAATGTGTGCACGTACCATCTACTGTACAAATATTGATAAGAAGgtgaagtggagtgaaatagactttcattcttctaggctgccaattagccctgttcatttactgtctaatctgttgtgaaaagttatggcatggttgtgtattcgttgtgccatggttcacgaggtggtgggaagttttcatgctagtaccacattgtaatgtatggccggggctctgagcgagcagtgacttgatgcag
||||| || || ||||||||||||||| | || |||||||| ||||| ||||| |||||||| || | | || | | ||||| || | | | || | | | | | | | |
TCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAGgtttggtacctgcactcatgctacta--ccactaggtattcattctgtcatggt--tctgttttaatacacgcag----------------------------------------------------------------------------------------------------------------------------
upper sequence: PP1S196_50V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GRMZM2G166091_T01 (Zea mays), 5'ss of exon 8
TCTGAAGACGAGCGTGAAATGTGTGCACGTACCATCTACTGTACAAATATTGATAAGAAGgtgaagtggagtgaaatagactttcattcttctaggctgccaattagccctgttcatttactgtctaatctgttgtgaaaagttatggcatggttgtgtattcgttgtgccatggttcacgaggtggtgggaagttttcatgctagtaccacattgtaatgtatggccggggctctgagcgagcagtgacttgatgcag
||||| || || ||||||||||||||| | || |||||||| ||||| ||||| |||||||| || | || | | | | ||||| || | | | || | | | | | | | |
TCTGACGATGAACGTGAAATGTGTGCAAGCACTATCTACTGCACAAACATTGACAAGAAGgtttggt--acctgaactcatgctactaccactaggtattcattctgtcatgat--tctgttttaatacacgcag----------------------------------------------------------------------------------------------------------------------------
upper sequence: PP1S196_50V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA08G18810.1 (Glycine max), 5'ss of exon 6
TCTGAAGACGAGCGTGAAATGTGTGCACGTACCATCTACTGTACAAATATTGATAAGAAGgtgaagtggagtgaaatagactttcattcttctaggctgccaattagccctgttcatttactgtctaatctgttgtgaaaagttatggcatggttgtgtattcgttgtgccatggttcacgaggtggtgggaagttttcatgctagtaccacattgtaatgtatggccggggctctgagcgagcagtgacttgatgcag
|| || || ||||||||||||||||| || || ||||| ||||||||||||||||| ||||| | | || | | | | | | | | | || | | | | | || | || | ||| || | | | | | ||| | || |
TCGGATGATGAGCGTGAAATGTGTGCCCGGACTATCTATTGTACAAATATTGATAAAAAGgt---------------atatttacttcttgagaaattacagaacaaatatttttggtaaaactatttttaatttaggaatggtat----tgagtattgacttaatttgctgtctttaa--------------------------------------------------------------------------------
upper sequence: PP1S196_50V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA15G40060.1 (Glycine max), 5'ss of exon 6
TCTGAAGACGAGCGTGAAATGTGTGCACGTACCATCTACTGTACAAATATTGATAAGAAGgtgaagtggagtga----------aatagactttcatt----cttctaggctgccaattagccctgttcatttact--gtctaatctgttgtgaaaagtta-tggcatggttgtgtattcgttgtgccatggttcacg-aggtggtgggaagttttcatgctagtaccacattgtaatgtatggccggggctctgagcgagcagtgacttgatgcag
|| || || ||||||||||||||||| || || |||| ||||||||||||||||| ||||| | | ||| || | | ||| | || | | || | | || ||||||| | | | | || | ||| | | || || | || | | | |||||| | || || | || | ||| | | || | | | | | | |||| | |||
TCAGATGATGAGCGTGAAATGTGTGCCCGGACTGTCTATTGTACAAATATTGATAAAAAGgtatatttacttgagaaattaaagaacatatttttggtaaaactatttaatttagaaatggtattgagtatttacttaatttggtatctttaatatgtttactaggataattata-atacatgcatctatggtttgcatagatgaatattggagttaaatctattgatgctttatcacatttctctcaaa-tatgagtg--cag-------------
upper sequence: PP1S196_50V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: AT1G32790.2 (Arabidopsis thaliana), 5'ss of exon 6
TCTGAAGACGAGCGTGAAATGTGTGCACGTACCATCTACTGTACAAATATTGATAAGAAGgtgaagtggagtgaaatagactttcattcttctaggctgccaattagccctgttcatttactgtctaatctgttgtgaaaagttatggcatggttgtgtattcgttgtgccatggttcacgaggtggtgggaagttttcatgctagtaccacattgtaatgtatggccggggctctgagcgagcagtgacttgatgcag
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ACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAGgtgac-tctcttgaatca---tttctcttaacttaaccgt-acttgatgaagt--atctccctttcacacttgtgtataaattgcttatag------------------------------------------------------------------------------------------------------------
upper sequence: PP1S196_50V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: Vv16s0098g01040.t01 (Vitis vinifera), 5'ss of exon 7
TCTGAAGACGAGCGTGAAATGTGTGCACGTACCATCTACTGTACAAATATTGATAAGAAGgtgaagtggagtgaaatagactttcattcttctaggctgccaattagccctgttcatttactgtctaatctgttgtgaaaagttatggcatggttgtgtattcgttgtgccatggttcacgaggtggtgggaagttttcatgctagtaccacattgtaatgtatggccggggctctgagcgagcagtgacttgatgcag
|||||||| || ||||||||||| || | || || |||||||||||||||||||||||||| || | | | | ||| ||||||| || ||| || | || ||||||| | || | |||| |||| | ||
TCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAGgtatttctgaatctacttg----tca--cttctagtgtggttgagagcacta-------attggaaaatctgta---------tctgatttacttgtttatttgatgcag-----------------------------------------------------------------------------------------
upper sequence: PP1S196_50V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: Vv02s0025g02740.t01 (Vitis vinifera), 5'ss of exon 7
TCTGAAGACGAGCGTGAAATGTGTGCACGTACCATCTACTGTACAAATATTGATAAGAAGgtgaagtggagtgaaatagactttcattcttctaggctgccaattagccctgttcatttactgtctaa----tctgttgtgaaaagttatggcatggttgtgtattcgttgtgccatggttcacgaggtggtgggaagttttcatgctagtaccacattgtaatgtatggccggggctctgagcgagcagtgacttgatgcag
|||||| || || || ||||||||| | || || |||||||||||||||||||||||||| ||| || |||| ||| || | | | ||| || | | | | ||| ||| | |||| | || ||
AATGAAGATGAACGCGAGATGTGTGCAAGAACAATTTACTGTACAAATATTGATAAGAAGgtac----------------tttttatgtttctttatattgaatgtgctccggtgtaggactaggaaacactttttcttttcaaatcaatgttgtatttgtttgtttaatgcag-----------------------------------------------------------------------------------------
upper sequence: PP1S196_50V6.1 (Physcomitrella patens), 5'ss of exon 7
lower sequence: Vv19s0176g00140.t01 (Vitis vinifera), 5'ss of exon 6
TCTGAAGACGAGCGTGAAATGTGTGCACGTACCATCTACTGTACAAATATTGATAAGAAGgtgaagtggagtgaaatagactttcattcttctaggctgccaattagccctgttcatttactgtctaatctgttgtgaaaagttatggcatggttgtgtattcgttgtgccatggtt-cacgaggtggtgggaagttttcatgctagtaccacattgtaatgtatggccggggctctgagcgagcagtgacttgatgcag
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TCAGAGGATGAGCGGGAAATGTGTGCTAGGACTGTCTATTGTACAAATATTGATAAGAAGgtattgtc------------ctcaccttgtcctggttgaatgattaaacttaatagttttctaccacacttaatgc---atctttctgtttcttatgatgcacatcagatcatggtttcatgcctggatgtatattaatggtggcaacttttcgcttaattgagtggttcctagttaaag--atttttttcttagtgcagMapped 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|162272247|gb|FC448756.1|FC448756EST: AGCGTGAAATGTGTGCACGTACCATCTACTGTACAAATATTGATAAGAAG GTGTCGCAGGCCGATGTAAAGCTCTTCTTTGAATCTTTGTGTGGAGAG
genomic: AGCGTGAAATGTGTGCACGTACCATCTACTGTACAAATATTGATAAGAAGgtgaagtgga ... cttgatgcagGTGTCGCAGGCCGATGTAAAGCTCTTCTTTGAATCTTTGTGTGGAGAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TCTGAAGACGAGCGTGAAATGTGTGCACGTACCATCTACTGTACAAATATTGATAAGAAGgtgaagtggagtgaaatagactttcattcttctaggctgccaattagccctgttcatttactgtctaatctgttgtgaaaagttatggcatggttgtgtattcgttgtgccatggttcacgaggtggtgggaagttttcatgctagtaccacattgtaatgtatggccggggctctgagcgagcagtgacttgatgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG