Sequence
atgc intronic sequence ATGC exonic sequenceTGAAAAAAATACGGCTGGAGCAAGAAGATGAAGGTGTTCCAAGCACCGCCATTCGAGAAATTTCACTCCTGAAAGAAATGCACCATGGCAACATCGTTCGgtacaatctcagcacgactggattttagaatttgcgatatgctcctattttgtcatcgtagactctcatcgtactatcaaggctctgcctactcttaagc...
Basic information
species | Physcomitrella patens |
transcript | PP1S25_198V6.7 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S25_198V6.5 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA08G08330.1 (Glycine max), 5'ss of exon 2
TGAAAAAAATACGGCTGGAGCAAGAAGATGAAGGTGTTCCAAGCACCGCCATTCGAGAAATTTCACTCCTGAAAGAAATGCACCATGGCAACATCGTTCGgtaca--atctcagcacgactggattttagaatttgcgatatgctcctattttgtcatcgtagactctcatcgtactatcaaggctctgcctactcttaagc
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TGAAGAAGATTCGCTTGGAGCAGGAGGATGAGGGGGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatattatatctctgctaagtgtttctgaagaatgtgttggtcttcaattgtgtgatt-catgtgctgagca-acaacattctctgggcgtagagatagag
upper sequence: PP1S25_198V6.5 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA05G25320.1 (Glycine max), 5'ss of exon 1
TGAAAAAAATACGGCTGGAGCAAGAAGATGAAGGTGTTCCAAGCACCGCCATTCGAGAAATTTCACTCCTGAAAGAAATGCACCATGGCAACATCGTTCGgtacaatctcagcacgactggattttagaatttgcgatatgctcctattttgtcatcgtagactctcatcgtactatcaaggctctgcctactcttaagc
|||| || || || || ||||| || ||||| || ||||| |||||||||||||| || ||||| ||| ||||||||||||| || | ||||| ||| |||| | | || | | | || | ||| | | || ||| | | || | || || |
TGAAGAAGATTCGCCTCGAGCAGGAGGATGAGGGGGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatataatatatctgaagaatgtgttggtcttcaattgtgcaattcatgtgctgagaaagaatattatatggacgtagtggtagaaattagaaaaatag
upper sequence: PP1S25_198V6.5 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA15G14390.1 (Glycine max), 5'ss of exon 2
TGAAAAAAATACGGCTGGAGCAAGAAGATGAAGGTGTTCCAAGCACCGCCATTCGAGAAATTTCACTCCTGAAAGAAATGCACCATGGCAACATCGTTCGgtaca--atctcagcacgactggattttagaatttgcgatatgct----cctattttgtcatcgtagactctcatcgtactatcaaggctctgcctactcttaagc
| || || || || || ||||| || || ||||| ||||| |||||||||||||| || ||||| ||||| ||||| ||||| ||| | ||||| ||| |||| | |||| | | || || ||| || || | | || || || | || | | || | | || || || ||| | |
TCAAGAAGATTCGCCTCGAGCAGGAGGACGAAGGCGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCCTCAAAGAGATGCAGCATAGGAACATTGTTAGgtatatcatctaattccttctcctttcattggaatgcaatgtgttgttgtcgatgatgaaattggagggt-taataatgttgtcgccgcact--ctatttgtc---
upper sequence: PP1S25_198V6.5 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT3G48750.1 (Arabidopsis thaliana), 5'ss of exon 3
TGAAAAAAATACGGCTGGAGCAAGAAGATGAAGGTGTTCCAAGCACCGCCATTCGAGAAATTTCACTCCTGAAAGAAATGCACCATGGCAACATCGTTCGgtacaatctcagcacgactg--gattttagaatttgcgatatgctcctattttgtcatcgtagactct-catcgtactatcaaggctctgcctactcttaagc
|||| || || |||| ||||| || |||||||||||||| ||||| || || ||||||| || ||| ||||||||||||| || ||||||| || ||| || | | || | || || || | || ||| || | || | | | | ||| ||
TGAAGAAGATCAGGCTAGAGCAGGAGGATGAAGGTGTTCCTAGCACAGCAATCAGAGAAATCTCCCTCTTGAAAGAAATGCAGCACAGCAACATTGTCAAgtatgatgttaataccattgttgaaaactgattcagcatgatgactctggtaaacaattttgattgatgttttttgctacacag-------------------
upper sequence: PP1S25_198V6.5 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv15s0045g00310.t01 (Vitis vinifera), 5'ss of exon 3
TGAAAAAAATACGGCTGGAGCAAGAAGATGAAGGTGTTCCAAGCACCGCCATTCGAGAAATTTCACTCCTGAAAGAAATGCACCATGGCAACATCGTTCGgtacaatctcagcacgactgg-attttagaatttgcgatatgctcctattttgtcatcgtagac--tctcatcgtactatcaaggctctgcctactcttaagc
|||| || || || ||||||| ||||||||||| || |||||||| || || |||| ||||| ||| ||||||| ||||| ||||| ||||| || |||| || ||| || | | | | || | | | | | | || | | | | | | | | | | ||| | | |||| |
TGAAGAAGATCCGCTTGGAGCAGGAAGATGAAGGAGTACCAAGCACTGCTATCAGAGAGATTTCCCTCTTGAAAGAGATGCAACATGGTAACATTGTCAGgta-ggtcacagtgggagtattgtgtgtgtatgtatggcttttttttttgtttccttttttgtccttttggtgatgccttcatctcctggtgtacttagat--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|162252581|gb|FC428612.1|FC428612EST: ATTCGAGAAATTTCACTCCTGAAAGAAATGCACCATGGCAACATCGTTCG GCTACAAGATGTGGTGCATAGTGAGAAACGATTGTACTTGGTTTTTGAATA
genomic: ATTCGAGAAATTTCACTCCTGAAAGAAATGCACCATGGCAACATCGTTCGgtacaatctc ... gtggtagcagGCTACAAGATGTGGTGCATAGTGAGAAACGATTGTACTTGGTTTTTGAATA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGAAAAAAATACGGCTGGAGCAAGAAGATGAAGGTGTTCCAAGCACCGCCATTCGAGAAATTTCACTCCTGAAAGAAATGCACCATGGCAACATCGTTCGgtacaatctcagcacgactggattttagaatttgcgatatgctcctattttgtcatcgtagactctcatcgtactatcaaggctctgcctactcttaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA