Sequence
atgc intronic sequence ATGC exonic sequenceGATATGGTGTACGAGGCAAGAGTCAAGCGTGATAAATATAGATATGAAAGCAAATATTTGCTGTGTGAAGTACAACCCAGGATCAAGCAACTATGTTGCAgtaagtacttcgatcctccaaaatgatttaccatcatcttgatgtgataatgacctgttgaaactctgttccaatatctgtctaaactgtatactatcaactcatttttggattgtaccttgctgcag
Basic information
species | Physcomitrella patens |
transcript | PP1S86_153V6.2 |
intron # | 10 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S86_153V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GRMZM2G126795_T02 (Zea mays), 5'ss of exon 12
GATATGGTGTACGAGGCAAGAGTCAAGCGTGATAAATATAGATATGAAAGCAAATATTTGCTGTGTGAAGTACAACCCAGGATCAAGCAACTATGTTGCAgtaagtacttcgatcctccaaaatg-atttaccatcatcttgatgtgataatgacctgttgaaactctgttccaatatctgtctaa-actgtatactatcaactcatttttggattgtaccttgctgcag
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AGTGTGGTGCACAAAACAAGAAGCAAGCGTGATCAATATTGATATGAAAGCAAATATTTGTTCGGTTAAATATAATCCTGGGTCAAGCTTCTATGTTGCAgtatgttgcttcatttcttagcttatattgaatagttaatttgtttgctttt--ccaaccaaaatgttatttgtttacttatcagatactacataatttcag----------------------------
upper sequence: PP1S86_153V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GRMZM2G104920_T03 (Zea mays), 5'ss of exon 10
GATATGGTGTACGAGGCAAGAGTCAAGCGTGATAAATATAGATATGAAAGCAAATATTTGCTGTGTGAAGTACAACCCAGGATCAAGCAACTATGTTGCAgtaagtacttcgatcctccaaaatgatttaccatcatcttgatgtgataatgacctgttgaaactctgttccaatatctgtctaa-actgtatactatcaactcatttttggattgtaccttgctgcag
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AGTGTGGTGCACAAATCAAGAAGCAAGTGTGATCAATATTGATATGAAAGCAAATATTTGCTCGGTTAAATATAATCCTGGATCAAGCTTCTACGTTGCAgtatgttgcttcatgtctagcttatattgaatacttaatttgtttgctttt--ccaaccgaaatgttatttgtttacctatcaaatactacaatatttcag----------------------------
upper sequence: PP1S86_153V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GRMZM2G104920_T02 (Zea mays), 5'ss of exon 9
GATATGGTGTACGAGGCAAGAGTCAAGCGTGATAAATATAGATATGAAAGCAAATATTTGCTGTGTGAAGTACAACCCAGGATCAAGCAACTATGTTGCAgtaagtacttcgatcctccaaaatgatttaccatcatcttgatgtgataatgacctgttgaaactctgttccaatatctgtctaa-actgtatactatcaactcatttttggattgtaccttgctgcag
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AGTGTGGTGCACAAATCAAGAAGCAAGTGTGATCAATATTGATATGAAAGCAAATATTTGCTCGGTTAAATATAATCCTGGATCAAGCTTCTACGTTGCAgtatgttgcttcatgtctagcttatattgaatacttaatttgtttgctttt--ccaaccgaaatgttatttgtttacctatcaaatactacaatatttcagg---------------------------
upper sequence: PP1S86_153V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA14G05430.1 (Glycine max), 5'ss of exon 10
GATATGGTGTACGAGGCAAGAGTCAAGCGTGATAAATATAGATATGAAAGCAAATATTTGCTGTGTGAAGTACAACCCAGGATCAAGCAACTATGTTGCAgtaagtacttcgatcctccaaaatgatttaccatcatcttgatgtgataatgacctgttgaaactctgttccaat-atctgtctaaactgtatactatcaactcatttttggattgtaccttgctgcag
|| |||||||| | || || | || || |||||||||| ||||||||||| || |||||||| || || || || ||||| |||| ||| ||||||||||||| | || | || || | | ||| |||| | || | | ||| | || || || | || ||| || | ||||
AATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATATTGCAgtaagtacctt--tcattcag---------tcaaaacttagatttgatcctatccatgtattatcttgtgtcgatcattcagcttagcttccaacttgtgacat-tgcttgg-----------------
upper sequence: PP1S86_153V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: AT2G32950.1 (Arabidopsis thaliana), 5'ss of exon 10
GATATGGTGTACGAGGCAAGAGTCAAGCGTGATAAATATAGATATGAAAGCAAATATTTGCTGTGTGAAGTACAACCCAGGATCAAGCAACTATGTTGCAgtaagtacttcgatcctccaaaat--gatttaccatcatcttgatgtga-taatgacctgt-tgaaactct-----gttcc--aatatctgtctaaactgtata---ctatcaactcatttttggattgtaccttgctgcag
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AGTTTGGTGCACGAGGCAGGAAGCAAGTGTGATTAATATTGATATGAAAGCAAACATATGTTGTGTCAAGTACAATCCTGGCTCAAGCAACTACATTGCGgtatatacttccacgcctcaactttgcatctcacatttattcgctaccactcatgatcagcatgacactatcacacgtctctagatataatctttaattagatagagagacttagacgtttaagcctgttgacttatcacagMapped 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|100399476|gb|BY972738.1|BY972738EST: CAAATATTTGCTGTGTGAAGTACAACCCAGGATCAAGCAACTATGTTGCA GTTGGTTCTGCGGATCATCATATTCATTATTTTGATGTGCGTAATTCTCAT
genomic: CAAATATTTGCTGTGTGAAGTACAACCCAGGATCAAGCAACTATGTTGCAgtaagtactt ... cttgctgcagGTTGGTTCTGCGGATCATCATATTCATTATTTTGATGTGCGTAATTCTCAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GATATGGTGTACGAGGCAAGAGTCAAGCGTGATAAATATAGATATGAAAGCAAATATTTGCTGTGTGAAGTACAACCCAGGATCAAGCAACTATGTTGCAgtaagtacttcgatcctccaaaatgatttaccatcatcttgatgtgataatgacctgttgaaactctgttccaatatctgtctaaactgtatactatcaactcatttttggattgtaccttgctgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA