Sequence
atgc intronic sequence ATGC exonic sequenceGAATGGCGTATGGTCTCTTTTCTGCCCCAATGAGGCTCCAGGACTGGCAGATTGCTGGGGTGAAGAGTTTGAGAAGCTCTACACCCGTTACGAAGTTGAGgtgaacttccgtctccattgcttagtattgaggtgcttcattccaaggccctacatcttactgtgagattgttactctatatagatagtgtcttaacgagacgggtccagtgagaaccttgattaacgttcagtttggatgtcctggtacgcacgtcctacag
Basic information
species | Physcomitrella patens |
transcript | PP1S195_46V6.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S195_46V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 5'ss of exon 7
GAATGGCGTATGGTCTCTTTTCTGCCCCAATGAGGCTCCAGGACTGGCAGATTGCTGGGGTGAAGAGTTTGAGAAGCTCTACACCCGTTACGAAGTTGAGgtgaacttccgtctccattgcttagtattgaggtgcttcattccaaggccctacatcttactgtgagattgttactctatatagatagtgtcttaacgagacgggtccagtgagaaccttgattaacgttcagtttggatgtcctggtacgcacgtcctacag
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TAACCAAGAATGGTCATTGTTTTGTCCCAATGAAGCTCCAGGGTTAGCTGATTGCTGGGGTGATGAGTTTGAGAAACTGTACACAAAATATGAGAGAGAGgtaagttggaaacgaaatttaattgtactacagt---ttattg-aagttggaaaagattacaataacatag---ctttgtactttcag---------------------------------------------------------------------------
upper sequence: PP1S195_46V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G340527_T01 (Zea mays), 5'ss of exon 7
GAATGGCGTATGGTCTCTTTTCTGCCCCAATGAGGCTCCAGGACTGGCAGATTGCTGGGGTGAAGAGTTTGAGAAGCTCTACACCCGTTACGAAGTTGAGgtgaacttccgtctccattgcttagtattgag-gtgcttcattccaa-ggccctacatcttactgtgagattgttactctatatagatagtgtcttaacgagacgggtccagtgagaaccttgattaacgttcagtttggatgtcctggtacgcacgtcctacag
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TAATGGAGAATGGTCATTGTTTTGCCCTAATGAAGCTCCAGGGTTGGCTGATTGCTGGGGTGAGGAGTTTGATAATTTGTACAAGAAATATGAGAGCCAAgtaagctgaaaagtgaacactgtatttgtatgtacgctttattgaaatgggaatgtgctttact-----aaccttgctttctggattcag---------------------------------------------------------------------------
upper sequence: PP1S195_46V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA05G32070.1 (Glycine max), 5'ss of exon 7
GAATGGCGTATGGTCTCTTTTCTGCCCCAATGAGGCTCCAGGACTGGCAGATTGCTGGGGTGAAGAGTTTGAGAAGCTCTACACCCGTTACGAAGTTGAGgtgaacttccgtctccattgcttagtattgaggtgcttcattccaaggccctacatcttactgtgagattgttactctatatagatagtgtcttaacgagacgggtccagtgagaaccttgattaacgttcagtttggatgtcctggtacgcacgtcctacag
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CAATGGGCAATGGTCTTTGTTTTGCCCCAATGAAGCGCCAGGTTTGGCTGATTGCTGGGGTGAAGAATTTGAGAAATTGTACACTCAATATGAAAGAGAAgtaagttttggtctttgt------atgttgacctgttttaat-----gttttgcatgtt--ttgaatattccttttgcttattattgccttgcttttctaaccaaattgatgtgtacatag------------------------------------------
upper sequence: PP1S195_46V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: EFJ20157 (Selaginella moellendorffii), 5'ss of exon 7
GAATGGCGTATGGTCTCTTTTCTGCCCCAATGAGGCTCCAGGACTGGCAGATTGCTGGGGTGAAGAGTTTGAGAAGCTCTACACCCGTTACGAAGTTGAGgtgaacttccgt-ctccattgcttagtattgaggtgcttcattccaaggccctacatcttactgtgagattgttactctatatagatagtgtcttaacgagacgggtccagtgagaaccttgattaacgttcagtttggatgtcctggtacgcacgtcctacag
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CAATAGCGATTGGTCTCTGTTCTGTCCGAACGAGGCTCCTGGATTGGCTGACTGCTGGGGTGAGGAGTTTGAAAGCTTGTACACGAGATATGAAAGGGAGgtcagtctccttgctctacttctt-----ttatgagcttaatttttgcggtgtttatcag--------------------------------------------------------------------------------------------------------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|162268643|gb|FC443697.1|FC443697EST: ATTGCTGGGGTGAAGAGTTTGAGAAGCTCTACACCCGTTACGAAGTTGAG GGTAAGGCCAAAAAGGTCGTACAAGCTCAAAAGCTTTGGTTTGCCGTTCTG
genomic: ATTGCTGGGGTGAAGAGTTTGAGAAGCTCTACACCCGTTACGAAGTTGAGgtgaacttcc ... cgtcctacagGGTAAGGCCAAAAAGGTCGTACAAGCTCAAAAGCTTTGGTTTGCCGTTCTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GAATGGCGTATGGTCTCTTTTCTGCCCCAATGAGGCTCCAGGACTGGCAGATTGCTGGGGTGAAGAGTTTGAGAAGCTCTACACCCGTTACGAAGTTGAGgtgaacttccgtctccattgcttagtattgaggtgcttcattccaaggccctacatcttactgtgagattgttactctatatagatagtgtcttaacgagacgggtccagtgagaaccttgattaacgttcagtttggatgtcctggtacgcacgtcctacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC