Sequence
atgc intronic sequence ATGC exonic sequenceGATTCACCAGCAAAGTTAAGGGAAAGATGGGTTATGAAGACTTTGTGTGGTTTATACTTTCAGAAGAGGACAAATCTTCAGAACCCAGCTTAGAGTACTGgtatgcatctttatacaacccgcatacatgttctgtatctttagtcatggtttcatgaattcagtttttttctatctccgctctcaattgaaaaagaagatatcgctggtagtaccagagcatgaggattgcggagaaaaaccaagatacaatctaattgatgtttatgcatacctgctgcag
Basic information
species | Physcomitrella patens |
transcript | PP1S34_411V6.1 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S34_411V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GRMZM2G148323_T01 (Zea mays), 5'ss of exon 9
GATTCACCAGCAAAGTTAAGGGAAAGATGGGTTATGAAGACTTTGTGTGGTTTATACTTTCAGAAGAGGACAAATCTTCAGAACCCAGCTTAGAGTACTGgtatgcatctttatacaacccgcatacatgttctgtatctttagtcatggtttcatgaattcagtttttttctatctccgctctcaattgaaaaagaagatatcgctggtagtaccagagcatgaggattgcggagaaaaaccaagatacaatctaattgatgtttatgcatacctgctgcag
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AATTCACAAGCATGACAGAAGGAAAGATGGGTTATGAAGACTTTGTTTACTTTATATTATCAGAGGAAGACAAATCATCTGAGCCTAGTCTTGAATATTGgtaagtggtagc-tgtgttctgaatagttgta-tgtattttt--------tttgtagaact--gttccttttt--------tcttaatgtgataagataattccacc-----ttacagtttataa----------------------------------------------------------
upper sequence: PP1S34_411V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GLYMA10G30930.1 (Glycine max), 5'ss of exon 9
GATTCACCAGCAAAGTTAAGGGAAAGATGGGTTATGAAGACTTTGTGTGGTTTATACTTTCAGAAGAGGACAAATCTTCAGAACCCAGCTTAGAGTACTGgtatgcatctttatacaacccgcatacatgttctgtatctttagtcatggtttcatgaattcagtttttttctatctccgctctcaattgaaaaagaagatatcgctggtagtaccagagcatgaggattgcggagaaaaaccaagatacaatctaattgatgtttatgcatacctgctgcag
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AGTTTACCAGCAAGGTTGAGGGAAAGATGGGATATGAAGATTTTGTTTACTTCATACTATCAGAAGAGGATAAATCATCTGAACCAAGTCTTGAGTACTGgtatttatttct---cattcattatccatttcat---tcgttagtttctttttc-tgaaaggagttaacagat-tagttgctc---------aaggatggtgct--ttgtgaaattatg----------------------------------------------------------------
upper sequence: PP1S34_411V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GLYMA20G36530.1 (Glycine max), 5'ss of exon 9
GATTCACCAGCAAAGTTAAGGGAAAGATGGGTTATGAAGACTTTGTGTGGTTTATACTTTCAGAAGAGGACAAATCTTCAGAACCCAGCTTAGAGTACTGgtatgcatctttatacaacccgcatacatgttctgtatctttagtcatggtttcatgaattcagtttttttctatctccgctctcaattgaaaaagaagatatcgctggtagtaccagagcatgaggattgcggagaaaaaccaagatacaatctaattgatgtttatgcatacctgctgcag
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AGTTTACCAGTAAGGTTGAGGGAAAGATGGGATATGAAGATTTTGTTTACTTCATACTGTCAGAAGAGGATAAATCATCTGAACCTAGTCTTGAGTACTGgtatttatttct----------cattcattatccgtttcatttgtta--gtttcttttctgaaaggagttaccagattagttgc---tcagggatggtgctttgtgaaattatgc--------------------------------------------------------------------
upper sequence: PP1S34_411V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GLYMA03G41180.1 (Glycine max), 5'ss of exon 9
GATTCACCAGCAAAGTTAAGGGAAAGATGGGTTATGAAGACTTTGTGTGGTTTATACTTTCAGAAGAGGACAAATCTTCAGAACCCAGCTTAGAGTACTGgtatgcatctttatacaacccgcatacatgttctgtatctttagtcatggtttcatgaattcagtttttttctatctccgctctcaattgaaaaagaagatatcgctggtagtaccagagcatgaggattgcggagaaaaaccaagatacaatctaattgatgtttatgcatacctgctgcag
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GGTTTACCAGTAAGGTTGAGGGAAAGATGGGTTATGAAGATTTTGTTTACTTCATACTGTCAGAAGAGGATAAATCATCCGAGCCAAGTCTTGAGTATTGgtattttgtttcccatccattgtccattttatttgttgcccctgccact-tagtaagatgtcaatggtttagttgctgtgcggtt--tcagacacaaggttaa--------------------------------------------------------------------------------
upper sequence: PP1S34_411V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GLYMA19G43790.1 (Glycine max), 5'ss of exon 9
GATTCACCAGCAAAGTTAAGGGAAAGATGGGTTATGAAGACTTTGTGTGGTTTATACTTTCAGAAGAGGACAAATCTTCAGAACCCAGCTTAGAGTACTGgtatgcatctttatacaacccgcatacatgttctgtatctttagtcatggtttcatgaattcagtttttttctatctccgctctcaattgaaaaagaagatatcgctggtagtaccagagcatgaggattgcggagaaaaaccaagatacaatctaattgatgtttatgcatacctgctgcag
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GGTTTACCAGTAAGGTTGAGGGAAAGATGGGTTATGAAGATTTTGTTTACTTCATACTGTCAGAAGAGGATAAATCATCTGAGCCAAGTCTTGAGTATTGgtatt--ttgtttcccatccattatccattttatttgttgcccctgccacttattaagatgccactggtttagttgctgacttgctgtgcagttcagataca---------------------------------------------------------------------------------
upper sequence: PP1S34_411V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: EFJ32791 (Selaginella moellendorffii), 5'ss of exon 9
GATTCACCAGCAAAGTTAAGGGAAAGATGGGTTATGAAGACTTTGTGTGGTTTATACTTTCAGAAGAGGACAAATCTTCAGAACCCAGCTTAGAGTACTGgtatgcatctttatacaacccgcatacatgttctgtatctttag-tcatggtttcatgaattcagtttttttctatctccgctctcaattgaaaaagaagatatcgctggtagtaccagagcatgaggattgcggagaaaaaccaagatacaatctaattgatgtttatgcatacctgctgcag
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AGTTTACGAGTTCCGTGGAAGGAAAGATGGGTTACGAGGACTTTGTGTGGTTCATTTTATCGGAGGAGGACAAAACGTCTGAACCAAGCTTGGAGTACTGgtaagcgacgtcttgaatcttctgtaagatcgatcgattgacagatcgcgacttccag------------------------------------------------------------------------------------------------------------------------------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|162194704|gb|FC371551.1|FC371551EST: TTTATACTTTCAGAAGAGGACAAATCTTCAGAACCCAGCTTAGAGTACTG GTTCAAGTGTGTGGATCTGGACTGCGATGGTGTGATTACACCGAATGAGAT
genomic: TTTATACTTTCAGAAGAGGACAAATCTTCAGAACCCAGCTTAGAGTACTGgtatgcatct ... cctgctgcagGTTCAAGTGTGTGGATCTGGACTGCGATGGTGTGATTACACCGAATGAGAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GATTCACCAGCAAAGTTAAGGGAAAGATGGGTTATGAAGACTTTGTGTGGTTTATACTTTCAGAAGAGGACAAATCTTCAGAACCCAGCTTAGAGTACTGgtatgcatctttatacaacccgcatacatgttctgtatctttagtcatggtttcatgaattcagtttttttctatctccgctctcaattgaaaaagaagatatcgctggtagtaccagagcatgaggattgcggagaaaaaccaagatacaatctaattgatgtttatgcatacctgctgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA