Sequence
atgc intronic sequence ATGC exonic sequencegtaaatcatttcacagcttgtttttacttgttccttgcttttgtggtacatttattggtattttcaatctccagtgacctaactttattgcaattctattcaaagtgaatggagttcagaggatttatctgaggggccgggactggggcttgagtttctgcagACAATTATTTCGGGGATGGGAGAGCTGCATCTTGACATATATGTTGAACGCATTCGTCGTGAATACAAG
Basic information
species | Physcomitrella patens |
transcript | PP1S20_94V6.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S20_94V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 3'ss of exon 12
gtaaatcatttcacagcttgtttttacttgttccttgcttttgtggtacatttattggtattttcaatctccagtgacctaactttattgcaattctattcaaagtgaatggagttcagaggatttatctgaggggccgggactggggcttgagtttctgcagACAATTATTTCGGGGATGGGAGAGCTGCATCTTGACATATATGTTGAACGCATTCGTCGTGAATACAAG
||| | ||| || | | | | | || || | | || || | | ||||||||||||||| |||||||| ||||||||| | || || |||||||||||||| | | || ||||||
-------------------------------------------------------------------------------------gtttgttttgttatctgttgtatttt---tctaaatctatcatttgtgaactttaaagtgtaaattttgatc--gcagACAATTATTTCTGGGATGGGTGAGCTGCATTTGGATATCTATGTTGAACGCATCAGGAGAGAGTACAAG
upper sequence: PP1S20_94V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 12
gtaaatcatttcacagcttgtttttacttgttccttgcttttgtggtacatttattggtattttcaatctccagtgacctaactttattgca--attctattcaaagtgaatggagttcagaggatttatctgaggggccgggactggggcttgagtttctgcagACAATTATTTCGGGGATGGGAGAGCTGCATCTTGACATATATGTTGAACGCATTCGTCGTGAATACAAG
||| | || || | ||||| | ||| | | |||| | ||| | | | | | | ||||||||||||| |||||||| ||||||||||| || ||||| |||||||| ||| | || ||||||
----------------------------------------------------------------------------------gtttgtcacatcatccatttcaatttcaatttgtatttgt--atttttgtgaagttcttaatacataaaatttgcta--gtagACAATTATTTCCGGGATGGGTGAGCTGCATCTGGATATATACGTTGAACGTATTAAGAGAGAGTACAAG
upper sequence: PP1S20_94V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv15s0021g02450.t01 (Vitis vinifera), 3'ss of exon 12
gtaaatcatttcacagcttgtttttacttgttccttgcttttgtggtacatttattggtattttcaatctccagtgacctaactttattgcaattctattcaaagtgaatggagttcagaggatttatctgaggggccgggactggggcttgagtttctgcagACAATTATTTCGGGGATGGGAGAGCTGCATCTTGACATATATGTTGAACGCATTCGTCGTGAATACAAG
|| ||| | |||| | ||| || | || | || ||| || | || | | | | |||| || |||||||||||||||| || ||||||||||||||| | ||||| || |||||||||||||| | || || |||
-------------------------------------------------------------gtttaattt---atgacatgcatttcacacattcct---tagag-gaagaagttttatcatgcctaaccatgacatcaaaat----gcttt--cttgtgcagACAATTATTTCTGGAATGGGAGAGCTGCATTTGGACATTTACGTTGAACGCATTCGGAGGGAGTATAAG
upper sequence: PP1S20_94V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: EFJ18610 (Selaginella moellendorffii), 3'ss of exon 12
gtaaatcatttcacagcttgtttttacttgttccttgcttttgtggtacatttattggtattttcaatctccagtgacctaactttattgcaattctattcaaagtgaatggagttcagaggatttatctgaggggccgggactggggcttgagtttctgcagACAATTATTTCGGGGATGGGAGAGCTGCATCTTGACATATATGTTGAACGCATTCGTCGTGAATACAAG
| ||||| | | | || | | | ||| | | ||||| | |||||||||||||| ||||||||||||||||| || || |||||||| | ||||| |||
----------------------------------------------------------------------------------------------------------gtatggatgttgtatgcttcaat--aatattttttctgaccgtttgtctcgtttcagACCCTCATTTCGGGGATGGGGGAGCTGCATCTTGACATTTACGTGGAACGCATGAAGAGAGAATATAAG
upper sequence: PP1S20_94V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: EFJ36205 (Selaginella moellendorffii), 3'ss of exon 12
gtaaatcatttcacagcttgtttttacttgttccttgcttttgtggtacatttattggtattttcaatctccagtgacctaactttattgcaattctattcaaagtgaatggagttcagaggatttatctgaggggccgggactggg-gcttgagtttctgcagACAATTATTTCGGGGATGGGAGAGCTGCATCTTGACATATATGTTGAACGCATTCGTCGTGAATACAAG
| ||||| | | | || | | ||| | ||| | | ||||| | |||||||||||||| ||||||||||||||||| || || |||||||| | ||||| |||
----------------------------------------------------------------------------------------------------------gtatggatgttgtatgcttca---gtaatattttttctgaccgtttgtctcgtttcagACCCTCATTTCGGGGATGGGGGAGCTGCATCTTGACATTTACGTGGAACGCATGAAGAGAGAATATAAGMapped 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|162163647|gb|FC340272.1|FC340272EST: AAAAAGAGGATCCAACATTCCGGGTCAGTTTGGATCCAGATAGTGGCCAG ACAATTATTTCGGGGATGGGAGAGCTGCATCTTGACATATATGTTGAACGC
genomic: AAAAAGAGGATCCAACATTCCGGGTCAGTTTGGATCCAGATAGTGGCCAGgtaaatcatt ... gtttctgcagACAATTATTTCGGGGATGGGAGAGCTGCATCTTGACATATATGTTGAACGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atggagttcagaggatttatctgaggggccgggactggggcttgagtttctgcagACAATTATTTCGGGGATGGGAGAGCTGCATCTTGACATATATGTTGAACGCATTCGTCGTGAATACAAG
tttctgc CT-rich tract
atttatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatcatttcacagcttgtttttacttgttccttgcttttgtggtacatttattggtattttcaatctccagtgacctaactttattgcaattctattcaaagtgaatggagttcagaggatttatctgaggggccgggactggggcttgagtttctgcagACAATTATTTCGGGGATGGGAGAGCTGCATCTTGACATATATGTTGAACGCATTCGTCGTGAATACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC