Sequence
atgc intronic sequence ATGC exonic sequenceTTGTATGGGAGTTTACAAGGGGGTCACTACTAGTCAGCTTGATGAATTAGCCGCTGAGACTGCTGCGGCCATGACTGCGAACCATCCTGACTATGCCATTgtaagttcgtaacgtctggatgggctggtgtctgtctgttggctcggaaattttacttctttgtgcaattatgcccaatacaattcgcctcaagcctctttttggttgcttaacgaattccacgaattcttatggcag
Basic information
species | Physcomitrella patens |
transcript | PP1S64_38V6.1 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S64_38V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: AT2G21790.1 (Arabidopsis thaliana), 5'ss of exon 1
TTGTATGGGAGTTTACAAGGGGGTCACTACTAGTCAGCTTGATGAATTAGCCGCTGAGACTGCTGCGGCCATGACTGCGAACCATCCTGACTATGCCATTgtaagttcgtaacgtctggatgggctggtgtctgtctgttggctcggaaattttacttctttgtgcaattatgcccaatacaattcgcctcaagcctctttt-------------tggttgcttaacgaattccacgaattcttatggcag
||| || || || || || |||||||| ||||| |||||||| || || ||||| |||||||| || |||||| ||||||||||| ||||| ||| ||| | ||| | | | |||| | ||| | ||| | ||| || | || | | ||| | | | || ||| || | || || || | ||| |||| |||
CTGTGCCGGTGTCTATAAAGGAGTCACTACGAGTCAACTTGATGAGTTGGCTGCTGAAACTGCTGCTGCTATGACTTGTAACCATCCTGATTATGCATCTgtgagt-----atctctcttcgttttcctttctgggtattgcttgattttgattagtcgtttctggagaagtgatctctgtcattggattggtgtttcatttgattgaattgatctgtataatttacatgttatctgtgttcatatgtcag
upper sequence: PP1S64_38V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 5'ss of exon 1
TTGTATGGGAGTTTACAAGGGGGTCACTACTAGTCAGCTTGATGAATTAGCCGCTGAGACTGCTGCGGCCATGACTGCGAACCATCCTGACTATGCCATTgtaagttcgtaacgtctggatgggctggtgt-ctgtctgttggctcggaaattttacttctttgtgcaattatgcccaatacaattcgcctcaagcctctttttggttgcttaacgaattccacgaattcttatggcag
|| || || |||||||| |||||||| || |||||||||||||| |||||||| || || || || |||||||| || || || || |||||| || ||| | | | | | | | | || | ||| || | | | || ||| |||||| | || || | || | | || || ||
GTGCGCTGGGGTCTACAAGGGCGTCACTACCAGCCAGCTTGATGAATTGGCCGCTGAAACCGCCGCTGCTATGACTGCCAATCACCCCGATTATGCCTCGgttggtttttctccttttatttctttctttttctccattttgtcttaaatacataggttaattg----attatgggtggt-catttt---tgaaacttggttctgttt-------------------------------
upper sequence: PP1S64_38V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ20157 (Selaginella moellendorffii), 5'ss of exon 1
TTGTATGGGAGTTTACAAGGGGGTCACTACTAGTCAGCTTGATGAATTAGCCGCTGAGACTGCTGCGGCCATGACTGCGAACCATCCTGACTATGCCATTgtaagttcgtaacgtctggatgggctggtgtctgtctgttggctcggaaattttacttctttgtgcaattatgcccaatacaattcgcctcaagcctctttttggttgcttaacgaattccacgaattcttatggcag
|| || ||||||||||| || ||||| |||||||| || ||||| || || |||||||| || |||||||| | | |||||||||||||| |||||||| | | | | | | || || | | |||| || |||| || | || | |||| |||
ATGCGCTGGGGTTTACAAGGGTGTTACTACCAGTCAGCTGGACGAATTGGCTGCCGAGACTGCGGCTTCCATGACTACAAGTCATCCTGACTATGCAATTgtaagctagaagcttttt------ctcgtttgt-tctgcaagcct-----ttttctttgtcagtttacttatagttttcacag-------------------------------------------------------
upper sequence: PP1S64_38V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ14283 (Selaginella moellendorffii), 5'ss of exon 1
TTGTATGGGAGTTTACAAGGGGGTCACTACTAGTCAGCTTGATGAATTAGCCGCTGAGACTGCTGCGGCCATGACTGCGAACCATCCTGACTATGCCATTgtaagttcgtaacgtctggatgggctggtgtctgtctgttggctcggaaattttacttctttgtgcaattatgcccaatacaattcgcctcaagcctctttttggttgcttaacgaattccacgaattcttatggcag
|| || ||||||||||| || ||||| |||||||| || ||||| || || |||||||| || |||||||| | | |||||||||||||| |||||||| | | ||| || || |||| | |||| || | || | |||| |||
ATGCGCTGGGGTTTACAAGGGTGTTACTACCAGTCAGCTGGACGAATTGGCTGCCGAGACTGCGGCTTCCATGACTACAAGTCATCCTGACTATGCAATTgtaagct------------agaagcttgttctcgtttgttctgcaagcctttttctttgtcagtttacttatagttttcacag-------------------------------------------------------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|100375483|gb|BY948883.1|BY948883EST: CCGCTGAGACTGCTGCGGCCATGACTGCGAACCATCCTGACTATGCCATT CTAGCGGCGAGAATTGCAGTCTCGAATCTACATAAGAATACGAAGAAATCA
genomic: CCGCTGAGACTGCTGCGGCCATGACTGCGAACCATCCTGACTATGCCATTgtaagttcgt ... cttatggcagCTAGCGGCGAGAATTGCAGTCTCGAATCTACATAAGAATACGAAGAAATCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTGTATGGGAGTTTACAAGGGGGTCACTACTAGTCAGCTTGATGAATTAGCCGCTGAGACTGCTGCGGCCATGACTGCGAACCATCCTGACTATGCCATTgtaagttcgtaacgtctggatgggctggtgtctgtctgttggctcggaaattttacttctttgtgcaattatgcccaatacaattcgcctcaagcctctttttggttgcttaacgaattccacgaattcttatggcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC