Sequence
atgc intronic sequence ATGC exonic sequence...gatcttacgattcaaatgttgttagctgataacttttttgcatcataaacagctcatttgggtcgtagttcatgggtttcattgtctggcttaaatgcagGTGGTAACATTGTGGTACAGAGCACCAGAAATTCTCTTAGGTTCTCGCCACTACTCTACACCTGTAGATGTGTGGTCTGTAGGATGCATTTTCGCTGAGA
Basic information
species | Physcomitrella patens |
transcript | PP1S25_198V6.7 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S25_198V6.6 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os02g03060.1 (Oryza sativa), 3'ss of exon 3
--gatcttacgattcaa--atgttgttagctgata-acttttttgcatcataaacagctcatttgggtcgtagttcatgggtttcattgtctggcttaaatgcagGTGGTAACATTGTGGTACAGAGCACCAGAAATTCTCTTAGGTTCTCGCCACTACTCTACACCTGTAGATGTGTGGTCTGTAGGATGCATTTTCGCTGAGA
| || | |||| | || | ||||| || ||| | | | | | || | || | || | ||| || ||||||| ||||||||||| |||||||| |||||||| | ||| | | || || || || ||||| || ||||||| || || |||||||| ||||| |
gcaggcataagtatcaacgaggtcttcttgtgatatacaccttttgcccctccatgtttacatcatttcatctttaacataacccact--ttggtttgt---tagGTGGTGACATTGTGGTATAGAGCACCTGAAATTCTTCTTGGTGCAAGGCATTATTCCACCCCTGTTGACATGTGGTCAGTTGGTTGCATTTTTGCTGAAA
upper sequence: PP1S25_198V6.6 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA08G08330.1 (Glycine max), 3'ss of exon 4
gatcttacgattcaaatgttgttagctgataacttttttgcatcataaacagctcatttgggtcgtagttcatgggtttcattgtctggc--ttaaatgcagGTGGTAACATTGTGGTACAGAGCACCAGAAATTCTCTTAGGTTCTCGCCACTACTCTACACCTGTAGATGTGTGGTCTGTAGGATGCATTTTCGCTGAGA
| | || || | |||| | | || | | | | | | ||| | || || ||| | | |||| || || ||||||||||| ||||||||||||| ||||||||| | | || || | || || ||||| || || ||| | ||||| || |||||||| || || ||||
-cttaaaaaatataattcttgtgaaaaggtacaatggtagagggacagtaaaaacatcaaattatctttttctgagttatag-atttggcgattgtttgtagGTGGTAACACTGTGGTACAGAGCTCCAGAAATTTTGCTTGGATCCCATCATTATTCTACCCCAGTTGATATTTGGTCAGTGGGATGCATATTTGCAGAGA
upper sequence: PP1S25_198V6.6 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT3G48750.1 (Arabidopsis thaliana), 3'ss of exon 5
gatcttacgattcaa-atgttgttagctgataacttttttgcatcataa--acagctcatttgggtcgtagttcatgggtttcattgtctggcttaaatgcagGTGGTAACATTGTGGTACAGAGCACCAGAAATTCTCTTAGGTTCTCGCCACTACTCTACACCTGTAGATGTGTGGTCTGTAGGATGCATTTTCGCTGAGA
| ||||| || ||| | | || | | | |||| | ||| || || | || |||| || ||| | | | |||| || || | |||||| |||||||||| || ||| |||| |||| || |||||||||||||| ||| | |||||||| || ||||| || |||||||
agtaagctagttcaagatactgtaaaat-atttcaatgctacatccagatttcagatctcttcc-tggttattcacacaattt-ttgcatattgttcctttagGTTGTTACTCTCTGGTACCGAGCACCAGAGATACTCCTAGGATCTCATCATTACTCTACACCTGTTGATATTTGGTCTGTGGGGTGCATATTTGCTGAGA
upper sequence: PP1S25_198V6.6 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 5
----------gatcttacgattcaaatgttgttagctgataacttttttgcatcataaacagctcatttgggtcgtagttcatgggtttcattgtctggcttaaatgcagGTGGTAACATTGTGGTACAGAGCACCAGAAATTCTCTTAGGTTCTCGCCACTACTCTACACCTGTAGATGTGTGGTCTGTAGGATGCATTTTCGCTGAGA
|||| | ||| ||||| | ||| || |||| | ||| | || ||| |||||| | || | | |||||||| || |||||||||||||||| ||||| || | || || |||||||| ||||| ||||| |||||||||||||| || || || || |||||||
tacctccacagatcacatatgaggaat-ttgtttggtga--accttttgataccatctctcatta--ttatgtctgggttcataaacattggtggttctccc-----cagGTGGTGACCCTGTGGTACAGAGCACCCGAAATACTGCTTGGATCACGCCACTATTCTACTCCTGTTGATGTGTGGTCTGTGGGCTGTATATTTGCTGAGAMapped 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: TTGGCCTTGCACGAGCTTTTGGTATTCCTGTCAGGACATTCACTCATGAG GTGGTAACATTGTGGTACAGAGCACCAGAAATTCTCTTAGGTTCTCGCCAC
genomic: TTGGCCTTGCACGAGCTTTTGGTATTCCTGTCAGGACATTCACTCATGAGgtaattatta ... ttaaatgcagGTGGTAACATTGTGGTACAGAGCACCAGAAATTCTCTTAGGTTCTCGCCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaacagctcatttgggtcgtagttcatgggtttcattgtctggcttaaatgcagGTGGTAACATTGTGGTACAGAGCACCAGAAATTCTCTTAGGTTCTCGCCACTACTCTACACCTGTAGATGTGTGGTCTGTAGGATGCATTTTCGCTGAGA
ttaaat TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatcttacgattcaaatgttgttagctgataacttttttgcatcataaacagctcatttgggtcgtagttcatgggtttcattgtctggcttaaatgcagGTGGTAACATTGTGGTACAGAGCACCAGAAATTCTCTTAGGTTCTCGCCACTACTCTACACCTGTAGATGTGTGGTCTGTAGGATGCATTTTCGCTGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG