Sequence
atgc intronic sequence ATGC exonic sequenceAAGCTACGACCCATCACCTACTTGAGTGGTTCTCAGGGCTCCATCGCCGACTTGCCTACAGGATATATTTGGAGTCCTCATCTTGTTCCTAAACCGAAAGgttcgaactattcacctcctcacctgatacgttcaaatgtttttgacaattgttacgccgatatgttgattgcaaattgtgcacatcagataatccgattattcttgcgtctgattttattagtttgtgacaattgagtgctgaaattatcaggattcttacgaggacgtctcacttttacag
Basic information
species | Physcomitrella patens |
transcript | PP1S110_116V6.1 |
intron # | 10 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S110_116V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: LOC_Os04g04254.1 (Oryza sativa), 5'ss of exon 8
AAGCTACGACCCATCACCTACTTGAGTGGTTCTCAGGGCTCCATCGCCGACTTGCCTACAGGATATATTTGGAGTCCTCATCTTGTTCCTAAACCGAAAGgttcg-aactattcacctcctcacctgatacgttcaaatgtttttgacaattgttacgccgatatgttgattgcaaattgtgcacatcagataatccgattattcttgcgtctgattttattagtttgtgacaattgagtgctgaaattatcaggattcttacgaggacgtctcacttttacag
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AAGTTGCGTCCGGTAACATACCTAAGTGGTGCACAGGGTTCTGGGAATGACATTCCTCATGGTTACATCTGGAGTCCTCACCTTGTTCCAAAACCGAAAGgttcctgatgagtattagctttatctgaaa--tttatatgttat---cccttttcacgtc---atgctta----accttgt---catccttcgattgtatagtttttaaaacttg---------------------------------------------------------------------
upper sequence: PP1S110_116V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GRMZM2G007721_T01 (Zea mays), 5'ss of exon 6
AAGCTACGACCCATCACCTACTTGAGTGGTTCTCAGGGCTCCATCGCCGACTTGCCTACAGGATATATTTGGAGTCCTCATCTTGTTCCTAAACCGAAAGgttcgaactattcacctcctcacctgatacgtt---caaatgtttttgacaattgttacgccgatatgttgattgcaaattgtgcacatcagataatccgattattcttgcgtctgattttattagtttgtgacaattgagtgctgaaattatcaggattcttacgaggacgtctcacttttacag
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AAGCTGCGTCCAGTAACATATCTAAGTGGTTCTCAGGGTTCTGGCAATGACATTCCGCATGGATACATTTGGAGTCCTCATCTTGTTCCGAAACCAAAAGgtttgccatatctattggctagagccggaagttatgcaatttactttgtcatttttt---cccatat-tagttcccaaagcatgtgggtct--taatcttgacctt--------------------------------------------------------------------------------
upper sequence: PP1S110_116V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA18G28130.2 (Glycine max), 5'ss of exon 8
AAGCTACGACCCATCACCTACTTGAGTGGTTCTCAGGGCTCCATCGCCGACTTGCCTACAGGATATATTTGGAGTCCTCATCTTGTTCCTAAACCGAAAGgttcgaactattcacctcctcacctgatacgttcaaatgtttttgacaattgttacgccgatatgttgattgcaaattgtgcacatcagataatccgattattcttgcgtctgattttattagtttgtgacaattgagtgctgaaattatcaggattcttacgaggacgtctcacttttacag
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AAGCTACGACCAGTCACATATTTAAGTGGCTCACAAGGCTCTGAAACTGATGTTCCACATGCATATATATGGAGTCCTCATCTTGTTCCTAAACCAAAAGgt--gggttctctagatcc-cactcttcaaattt---tgtttccg-tagtcattgttatattaagtcccttg--acttttatagtctgtgctctgtgtttatgtgtgtg--------------------------------------------------------------------------
upper sequence: PP1S110_116V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: Vv07s0005g05600.t01 (Vitis vinifera), 5'ss of exon 8
AAGCTACGACCCATCACCTACTTGAGTGGTTCTCAGGGCTCCATCGCCGACTTGCCTACAGGATATATTTGGAGTCCTCATCTTGTTCCTAAACCGAAAGgttcgaactattcacctcctcacctgatacgttcaaatgtttttgacaattgttacgccgatatgttgattgcaaattgtgcacatcagataatccgattattctt-gcgtctgattttattagtttgtgacaattgagtgctgaaattatcaggattcttacgaggacgtctcacttttacag
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AAGCTTCGACCTGTTACATATTTAAGTGGTTCGCAAGGATCTGATTCTGATATTCCACATGGATATATATGGAGTCCTCATCTTGTTCCTAAGCCAAAAGgttattgct-ttgtttttctgattaaaccagaatagatgtctt--aaggttatagct----tgtattatcctctcctagcataaa---aagatttccattatgctaagca--------------------------------------------------------------------------
upper sequence: PP1S110_116V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: Vv04s0023g00050.t01 (Vitis vinifera), 5'ss of exon 8
AAGCTACGACCCATCACCTACTTGAGTGGTTCTCAGGGCTCCATCGCCGACTTGCCTACAGGATATATTTGGAGTCCTCATCTTGTTCCTAAACCGAAAGgttcgaactattcacctcctcacctgatacgttcaaatgtttttgac--aattgttacgccgatatgttgattgcaaattgtgcac--atcagataatccgattattcttgcgtctgattttattagtttgtgacaattgagtgctgaaattatcaggattcttacgaggacgtctcacttttacag
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AAGCTAAGACCTGTGACATATCTAAAAGGATCATATAGCTCTCCTCATGATGTGCCTTATGGATATCTCTGGAGTCCTCACCTTGTTCCTAAACCAAAAGgtc---act-tttacgtatttcatttatatatgatagcgttttttattaaattgctactccaaggtat-aatcgtcagccctgcacttatttctcatatcgatca----------------------------------------------------------------------------------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|162264491|gb|FC440839.1|FC440839EST: CTTGCCTACAGGATATATTTGGAGTCCTCATCTTGTTCCTAAACCGAAAG ATTGGGGGCCTCTTGTCGATGTTGTGGGATTTTGTTTTTTGAATCTTGCTC
genomic: CTTGCCTACAGGATATATTTGGAGTCCTCATCTTGTTCCTAAACCGAAAGgttcgaacta ... acttttacagATTGGGGGCCTCTTGTCGATGTTGTGGGATTTTGTTTTTTGAATCTTGCTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AAGCTACGACCCATCACCTACTTGAGTGGTTCTCAGGGCTCCATCGCCGACTTGCCTACAGGATATATTTGGAGTCCTCATCTTGTTCCTAAACCGAAAGgttcgaactattcacctcctcacctgatacgttcaaatgtttttgacaattgttacgccgatatgttgattgcaaattgtgcacatcagataatccgattattcttgcgtctgattttattagtttgtgacaattgagtgctgaaattatcaggattcttacgaggacgtctcacttttacag
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