Sequence
atgc intronic sequence ATGC exonic sequencegtgattctttaagtaccatgctgccagttcattagtttgtggatgtttgctcatttttggtcgacgatgcgtgaataattaagagcaaaccataccatgctgctaaaagttcctggtcacctgcagGTCAATGCATCTGATGTAATTATTGTGGAGGGAATATTGATCTTTCATGATGCTCGTGTTCGGGAGTACATGAATATGAAGATCTTTGTTGATACAG
Basic information
species | Physcomitrella patens |
transcript | PP1S83_234V6.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S83_234V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os02g17320.1 (Oryza sativa), 3'ss of exon 5
gtgattctttaagtaccatgctgccagttcattagtttgtggatgtttgctcatttttggtcgacgatgcgtgaataattaagagcaaaccataccatgctgctaaaagttcctggtcacctgcagGTCAATGCATCTGATGTAATTATTGTGGAGGGAATATTGATCTTTCATGATGCTCGTGTTCGGGAGTACATGAATATGAAGATCTTTGTTGATACAG
|| || | || || | ||||| ||| | | | ||||| ||| | || | || | || || |||| ||||| || || || | ||| ||||||||| | || |||||||||||| |||| ||||| || | || |||||| | ||||| ||||| | ||||| ||||||||||||||||| ||||
--gaaaattggatcac--tgattacagtttattcttctctt--tgtttatccatatctgttttactttatgt------ttcagag-aaaccctaatattttg------acttctgt-------cagGTCAATCCTTCAGATGTAATTATTTTGGAAGGAATTCTGGTTTTCCATGATTCACGTGTCCGGGATTTGATGAACATGAAGATCTTTGTTGACACAG
upper sequence: PP1S83_234V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 5
gtgattctttaagtaccatgctgccagttcattagtttgtggatgtttgctcatttttggtcgacgatgcgtgaataattaagagcaaaccataccatgctgctaaaagttcctggtcacctgcagGTCAATGCATCTGATGTAATTATTGTGGAGGGAATATTGATCTTTCATGATGCTCGTGTTCGGGAGTACATGAATATGAAGATCTTTGTTGATACAG-
| || |||| | || ||| | | || || ||| | | || ||| || |||| | || || | | ||||| || | || ||||| || ||| | || || || | | || |||||| | ||||||||||||| |||||||||||||| |||||||| ||||
-----------------aagc-atagaatcatgatattccaaatgcatattttagcttagtt--ttatgaagttgctgtcattctcatttcattttgtgttgcttta---tcatgtt----ttcaggTGAACCCTTCAGATGTTATAATTTTAGAAGGCATCCTTGTTTTCCATGATCCACGTGTTCGGGAGTTGATGAATATGAAGATATTTGTTGACACAGG
upper sequence: PP1S83_234V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 5
gtgattctttaagtaccatgctgccagttcattagtttgtggatgtttgctcatttttggtcgacgatgcgtgaataattaagagcaaaccataccatgctgctaaaagttcctggtcacctgcagGTCAATGCATCTGATGTAATTATTGTGGAGGGAATATTGATCTTTCATGATGCTCGTGTTCGGGAGTACATGAATATGAAGATCTTTGTTGATACAG
|| || | |||| ||| | | |||| | | || | | | ||| || ||| || ||| | || || | | ||||| || | || ||||| || ||| |||| || || | | || ||||| | ||||||||||||| |||||||||||||| |||||||| ||||
------------ataaaatacattttacatgatagtcca--aatgcataat--ttttagttttacaaagttgttgtcattct---catttcattttgtgttgcctta---tcgtgtt----ttcagGTGAACCCTTCAGATGTTATAATTTTGGAAGGCATCCTTGTTTTCCATGACCCACGTGTTCGGGAGTTGATGAATATGAAGATATTTGTTGACACAGMapped 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|100389779|gb|BY971131.1|BY971131EST: CTGAGTATGATTTCAAGAGGCATCAACGCTGCACTGACAAGTTTCGCAAG GTCAATGCATCTGATGTAATTATTGTGGAGGGAATATTGATCTTTCATGAT
genomic: CTGAGTATGATTTCAAGAGGCATCAACGCTGCACTGACAAGTTTCGCAAGgtgattcttt ... tcacctgcagGTCAATGCATCTGATGTAATTATTGTGGAGGGAATATTGATCTTTCATGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaataattaagagcaaaccataccatgctgctaaaagttcctggtcacctgcagGTCAATGCATCTGATGTAATTATTGTGGAGGGAATATTGATCTTTCATGATGCTCGTGTTCGGGAGTACATGAATATGAAGATCTTTGTTGATACAG
tgctaaa putative branch site (score: 2)
aattaaga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattctttaagtaccatgctgccagttcattagtttgtggatgtttgctcatttttggtcgacgatgcgtgaataattaagagcaaaccataccatgctgctaaaagttcctggtcacctgcagGTCAATGCATCTGATGTAATTATTGTGGAGGGAATATTGATCTTTCATGATGCTCGTGTTCGGGAGTACATGAATATGAAGATCTTTGTTGATACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA