Sequence
atgc intronic sequence ATGC exonic sequence...caaggaagtgtaagaagctgtacagggtgtggaaagaaaaacagttattgacctgtctatgtgaggccaactcatcagattgcaaacttggaattggcagGACAAGAATCACGATTCTTTCGACTTCATCTTCGTAGACGCGGACAAAGACAACTATCTGAACTACCACAAGAAGCTCATGAAGTTGGTGAGGGTGGGAG
Basic information
species | Physcomitrella patens |
transcript | PP1S16_28V6.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S16_28V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA07G33780.2 (Glycine max), 3'ss of exon 4
--caaggaagtgtaagaagctgtacagggtgtggaaagaaaaacagttattgacctgtctatgtgaggccaactcatcagattgcaaacttggaattggcagGACAAGAATCACGATTCTTTCGACTTCATCTTCGTAGACGCGGACAAAGACAACTATCTGAACTACCACAAGAAGCTCATGAAGTTGGTGAGGGTGGGAG---
| | || ||| || | ||| | | ||| ||||||| || | | | | | | | ||||| ||| || ||||| ||||| || | | ||||||||||| || || |||||||| |||||||| || ||||||||||||| | | || || | || | || || |
tctatgagagactaaaaa--tatactagtatttaaaaaaaaaacaattggaggagtaaaaaagggtaattgggtagt--gattgtgtgtggtgaaatg-caggagAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGACAACTACCTCAACTACCACAAGAGGTTGATAGAGCTTGTAAAAGTTGGGGGCG
upper sequence: PP1S16_28V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA07G33780.1 (Glycine max), 3'ss of exon 4
-----caaggaagtgtaagaagctgtacagggtgtggaaagaaaaacagttattgacctgtctatgtgaggccaactcatcagattgcaaacttggaattggcagGACAAGAATCACGATTCTTTCGACTTCATCTTCGTAGACGCGGACAAAGACAACTATCTGAACTACCACAAGAAGCTCATGAAGTTGGTGAGGGTGGGAG
| | || ||| || | ||| | | ||| ||||||| || | | | | | | | ||||| ||| || ||||| ||||| || | | ||||||||||| || || |||||||| |||||||| || ||||||||||||| | | || || | || | || || |
aattctatgagagactaaaaa--tatactagtatttaaaaaaaaaacaattggaggagtaaaaaagggtaattgggtagt--gattgtgtgtggtgaaatg-cagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGACAACTACCTCAACTACCACAAGAGGTTGATAGAGCTTGTAAAAGTTGGGG
upper sequence: PP1S16_28V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA02G11530.1 (Glycine max), 3'ss of exon 4
-caaggaagtgtaagaagctgtacagggtgtggaaagaaaaacagttattgacctgtctatgtgaggccaactcatca--gattgcaaacttggaattggcagGACAAGAATCACGATTCTTTCGACTTCATCTTCGTAGACGCGGACAAAGACAACTATCTGAACTACCACAAGAAGCTCATGAAGTTGGTGAGGGTGGGAG
|| || || ||| | | ||| | || || || | || || | |||| || | | |||||| ||| || ||||| ||||| || | | ||||||||||| || ||||| ||||| |||||||| || ||||||||||||| | | || || | || | || || |
taaaaaaaatgcaagtttttccatcactcaataaaaaataatcaatt-tagaggagtaaaaa-gagggtaattgggtagcgattgcgtgtggtgaaatg-cagGAGAAGAACCATGGGAGCTATGACTTCATCTTTGTGGACGCAGACAAGGACAACTACCTCAACTACCACAAGAGGTTGATAGAGCTTGTCAAAGTTGGGG
upper sequence: PP1S16_28V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv03s0063g00140.t01 (Vitis vinifera), 3'ss of exon 4
caaggaagtgtaagaagctgtacagggtgtggaaagaaaaac-agttattgacctgtctatgtgaggccaactcatcagattgcaaacttggaattggcagGACAAGAATCACGATTCTTTCGACTTCATCTTCGTAGACGCGGACAAAGACAACTATCTGAACTACCACAAGAAGCTCATGAAGTTGGTGAGGGTGGGAG
| ||| | | || || | | | | | | || || | | || || | | || | || || |||| ||| |||||| || ||||||||||| ||||| ||||| ||||| ||||| ||||||||||||||||||| | || | ||||||| |||||| |
---gtaagcttcacaaaa-acccatcatccaaacattgtatttaaatccaaacatgattgaaacaagctaattgactttgtttctgtgatgaaa--aacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGACAATTATCTGAACTACCACAAGAGATTGATCGATTTGGTGAAGGTGGGGG
upper sequence: PP1S16_28V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv07s0031g00350.t01 (Vitis vinifera), 3'ss of exon 4
caaggaagtgtaagaagctgtacagggtgtggaaagaaaaacagttattgacctgtctatgtgaggccaactcatcagattgcaaacttggaattggcagGACAAGAATCACGATTCTTTCGACTTCATCTTCGTAGACGCGGACAAAGACAACTATCTGAACTACCACAAGAAGCTCATGAAGTTGGTGAGGGTGGGAG
| |||| || || || || | | | | | ||| | || | | | ||| | | || | ||||| ||| |||| | | ||||| || || ||||| ||||| ||||| |||||||| |||||||||||||| | ||| || | |||| | ||| ||||
---gtaagtacaataatgcccctagcccactccaatattctccatgcctcatctgaaca---gaattgtaatttcaaaattatcacc----aaattgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGACAACTACCTGAACTACCACAAAAGGCTGATTGATCTGGTCAAGGTTGGAGMapped 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|208390036|gb|DC938091.1|DC938091EST: ACTTCCGGGACGGACCTGCAATGGACAGCATTGAAGTTCTCCTACAAGAT GACAAGAATCACGATTCTTTCGACTTCATCTTCGTAGACGCGGACAAAGAC
genomic: ACTTCCGGGACGGACCTGCAATGGACAGCATTGAAGTTCTCCTACAAGATgtaaaatcag ... gaattggcagGACAAGAATCACGATTCTTTCGACTTCATCTTCGTAGACGCGGACAAAGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattgacctgtctatgtgaggccaactcatcagattgcaaacttggaattggcagGACAAGAATCACGATTCTTTCGACTTCATCTTCGTAGACGCGGACAAAGACAACTATCTGAACTACCACAAGAAGCTCATGAAGTTGGTGAGGGTGGGAG
tattgac putative branch site (score: 2)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caaggaagtgtaagaagctgtacagggtgtggaaagaaaaacagttattgacctgtctatgtgaggccaactcatcagattgcaaacttggaattggcagGACAAGAATCACGATTCTTTCGACTTCATCTTCGTAGACGCGGACAAAGACAACTATCTGAACTACCACAAGAAGCTCATGAAGTTGGTGAGGGTGGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - -ctgtaca