Sequence
atgc intronic sequence ATGC exonic sequenceCATTGGATAGTGATGATTTGCTTTACTTAAAAGAGCAAATGGAAGCTGAGGAGGATGCGGAGCGGTTGCGGCGACGAACTGAGAAACGGGCGTTCGCAgcttttaaaatatccttatgacatttatttattatatttttctatcagtgctacaatatcaaaattggattatctaaaaatgtcagaagtgatggtagag...
Basic information
species | Physcomitrella patens |
transcript | PP1S402_46V6.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S402_46V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os02g42540.1 (Oryza sativa), 5'ss of exon 4
CATTGGATAGTGATGATTTGCTTTACTTAAAAGAGCAAATGGAAGCTGAGGAGGATGCGGAGCGGTTGCGGCGACGAACTGAGAAACGGGCGTTCGCAgcttttaaaatatcct--tatgacatttatttattatatttttc-ta--tcagtgctacaatatcaaaattgg----attatctaaaaatgtcagaagtgatggtagag
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-------CAGTGATGATTTACTGTACCTAAAAGAACAAATGGAAGCTGAGGAAGACGCAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGCTTTTAAGatatcctcttcttttagtcatagcttatgttttgcatagtacagtttcatgaaaaaaaaaaagggactattagctcaatatagctcaaaccagtcttatg
upper sequence: PP1S402_46V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G146786_T01 (Zea mays), 5'ss of exon 4
CATTGGATAGTGATGATTTGCTTTACTTAAAAGAGCAAATGGAAGCTGAGGAGGATGCGGAGCGGTTGCGGCGACGAACTGAGAAACGGGCGTTCGCAgcttttaaaatatccttatgacatttatttattatatttttctatcagtgctacaatatcaaaattggattatctaaaaatgtcaga--agtgatggtagag----------------------------------------------------------------------------------------------------
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-------CAGCGATGATTTGCTTTACCTGAAAGAGCAAATGGAAGCTGAAGAAGATGCAGAGCGCCTTCTTCGTCATACTGAGAAGCGGGCATTTGCTGCTTTTAAGatatcctt-tattaatcatcaacaactttgcttttcctgttatacagttaatgatacggtctgattaatatggttcagttagcttttctggaaacttttcgcacctttacaattcagtttccttccgttcaaatagtgcaatagaaacatgtggtctaagctatctctttgctatctttaactctgacattac
upper sequence: PP1S402_46V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA16G33570.2 (Glycine max), 5'ss of exon 4
CATTGGATAGTGATGATTTGCTTTACTTAAAAGAGCAAATGGAAGCTGAGGAGGATGCGGAGCGGTTGCGGCGACGAACTGAGAAACGGGCGTTCGCAgcttttaaaatatccttatgacatttatttattatatttttctatcagtgctacaatatcaaaattggatt-atctaaaaatg--tcagaagtgatggtagag--------
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-------CAGTGATGATCTACTTTATCTCAAGGAGCAAATGGAAGCCGAGGAGGATGCAGAGCGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGCATTTAAGatatccttttgtggtca--ttgcgacacataacaatccatgttttcttcttcatcttgggttgatttgatactgatttttatgtcctactactacaagtatc
upper sequence: PP1S402_46V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA09G28980.2 (Glycine max), 5'ss of exon 4
CATTGGATAGTGATGATTTGCTTTACTTAAAAGAGCAAATGGAAGCTGAGGAGGATGCGGAGCGGTTGCGGCGACGAACTGAGAAACGGGCGTTCGCAgcttttaaaatatccttatgacatttatttattatatttttctatcagtgctacaatatcaaaattggattatctaaaaatgtca-gaagtgatggtagag----------
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-------CAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGCATTTAAGatatccttttgtggtca--ttgcgacacataacaatccatgtttcttcatcttgggttgattttgactgatttttatgtcctactactacaattaccttgct
upper sequence: PP1S402_46V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: AT1G73350.2 (Arabidopsis thaliana), 5'ss of exon 4
CATTGGATAGTGATGATTTGCTTTACTTAAAAGAGCAAATGGAAGCTGAGGAGGATGCGGAGCGGTTGCGGCGACGAACTGAGAAACGGGCGTTCGCAgcttttaaaatatccttat---gacatttatttattatatttttctatcagtgctacaatatc-aaaattggattatctaaaaatgtc--agaagtgatggtagag----------
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-------TAGCGACGATTTACTTTATCTGAAAGAACAGATGGAAGCAGAGGAAGATGCAGAACGTCTTCTGAGACGAACTGAGAAACGGGCTTTTGCTGCCTTTAAAatatcctttcttaaatgctcagatatcatgattttg----agcactaagttatttgatatatacttgcctagatgtttttttgtaatctttcttgaccatatatcacMapped 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|162164790|gb|FC340499.1|FC340499EST: AGGAGGATGCGGAGCGGTTGCGGCGACGAACTGAGAAACGGGCGTTCGCA G
genomic: AGGAGGATGCGGAGCGGTTGCGGCGACGAACTGAGAAACGGGCGTTCGCAgcttttaaaa ... gacaatatag-
EST:
gi|162164790|gb|FC340499.1|FC340499EST: AGGAGGATGCGGAGCGGTTGCGGCGACGAACTGAGAAACGGGCGTTCGCA G
genomic: AGGAGGATGCGGAGCGGTTGCGGCGACGAACTGAGAAACGGGCGTTCGCAgcttttaaaa ... gacaatatag-
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CATTGGATAGTGATGATTTGCTTTACTTAAAAGAGCAAATGGAAGCTGAGGAGGATGCGGAGCGGTTGCGGCGACGAACTGAGAAACGGGCGTTCGCAgcttttaaaatatccttatgacatttatttattatatttttctatcagtgctacaatatcaaaattggattatctaaaaatgtcagaagtgatggtagag
- - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - AGGATG