Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgagtgagtgagtgtgaattgcattggtctttgatgagacggaatttggatttgttttagggtttggattttgacgatcgtggcggatttcgaggatggccttgcagGTGTATCCAGAGGGAACGCATTTTATGATTCCCTGGTTCGACAGGCCTGTGATATATGATGTCCGTGCACGACCTAACATTGTCGAGAGCACGTCGGGGA
Basic information
species | Physcomitrella patens |
transcript | PP1S41_59V6.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S41_59V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA12G33520.1 (Glycine max), 3'ss of exon 2
gtgagtgagtgagtgagtgtgaattgcattggtctttgatgagacggaatttggatttgttttagggtttggattttgacgatcgtggcggattt----cgaggatggccttgcagGTGTATCCAGAGGGAACGCATTTTATGATTCCCTGGTTCGACAGGCCTGTGATATATGATGTCCGTGCACGACCTAACATTGTCGAGAGCACGTCGGGGA
| | ||||| ||| || || | | | | | || | || | ||| | || || | | || | | || | | | ||||||| ||||| || ||||| || ||||||||||| ||||| || |||||||| || |||||||||||||||||||| | | || ||||| || || || |
--------------ccttctaaattg-attcgttattactaataagtgtgtgtgaccattgtttgagttctg-ttatggtggttgtagtaaaattgatatgttggttaatgtgcagGTCTATCCTGAAGGAACACACTTTATGATTCCGTGGTTTGAGAGGCCTGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGTA
upper sequence: PP1S41_59V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA11G11670.2 (Glycine max), 3'ss of exon 2
gtgagtgagtgagtgagtgtgaattgcattggtctttgatgagacggaatttggatttgttttagggtttggattttgacgatcgtggcggatttcgaggatggccttgcagGTGTATCCAGAGGGAACGCATTTTATGATTCCCTGGTTCGACAGGCCTGTGATATATGATGTCCGTGCACGACCTAACATTGTCGAGAGCACGTCGGGGA
| | | | | || | | | | | || | || | || | || ||| | | || | | | | ||| ||||| ||||| || || || ||| |||||||||| |||||||| ||||||||||| || ||||| |||||||| ||| | | || ||||| || || ||||
---ttttcccaaactaatc--acttcccaagcccacagctagagacctatattgactagtaatcttattgcaattatatcaat-atagtatgccttttgaatg------cagGTCTATCCTGAAGGGACACATATTATGATTCCTTGGTTCGAGAGGCCTGTGATCTACGATGTACGTGCACGCCCTCATTTAGTAGAGAGTACATCAGGGA
upper sequence: PP1S41_59V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA09G30410.1 (Glycine max), 3'ss of exon 3
gtgagtgagtgagtgagtgtgaattgcattggtctttgatgagacggaatttggatttgttttagggtttggattttgacgatcgtggcggattt----cgaggatggccttgcagGTGTATCCAGAGGGAACGCATTTTATGATTCCCTGGTTCGACAGGCCTGTGATATATGATGTCCGTGCACGACCTAACATTGTCGAGAGCACGTCGGGGA
| | | | ||| || | | | | | | ||| | |||| | | || || || | | | | | || | | | | ||||||| ||||| || ||||| || || || ||||| ||||| || ||||| || || |||||||||||||||||||| | | || ||||| || || ||||
-------------taccttctcagttgatttgttatcacttaca-agtgtctggccattgtttaagttctg--ttctggtgttgggagtaaaattgatatgttggttaacgtgcagGTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGA
upper sequence: PP1S41_59V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA12G01850.1 (Glycine max), 3'ss of exon 1
gtgagtgagtgagtgagtgtgaattgcattggtctttgatgagacggaatttggatttgttttagggtttggattttgacgatcgtggcggatttcgaggatggccttgcagGTGTATCCAGAGGGAACGCATTTTATGATTCCCTGGTTCGACAGGCCTGTGATATATGATGTCCGTGCACGACCTAACATTGTCGAGAGCACGTCGGGGA
| | || | | || | | | | || | || | || | || ||| | | || | | | | ||| |||| ||||| || || || ||| |||||||||| | |||||| ||||||||||| || || || |||||||||||| | | || ||||| || || ||||
---ttttcccaaacgaatc--acttcccaaacccacagctagagacctatattgactagtaatcttattgcaattatatcaat-atagtatgccttttgaatga------agGTTTATCCTGAAGGGACACATATTATGATTCCTTTGTTCGAGAGGCCTGTGATCTACGACGTACGTGCACGACCTCATTTAGTAGAGAGTACATCAGGGA
upper sequence: PP1S41_59V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ20024 (Selaginella moellendorffii), 3'ss of exon 1
gtgagtgagtgagtgagtgtgaattgcattggtctttgatgagacggaatttggatttgttttagggtttgga--ttttgacgatcgtggcggatttcgaggatggccttgcagGTGTATCCAGAGGGAACGCATTTTATGATTCCCTGGTTCGACAGGCCTGTGATATATGATGTCCGTGCACGACCTAACATTGTCGAGAGCACGTCGGGGA
|| | ||| | | | || |||||| ||| | ||| ||| ||| | | ||||| || | ||| | | ||||| ||||| ||||| || ||||||||||| ||| | || ||||| |||||||| ||||| || ||||||||||| |||| ||| | |||||||| || || || |
gtaggcgagcttgcc-gcaagcatcgcattgctctct----------------cttttatttcggggatcgccctttttgtagagttcgattgatctt-----ttgccttccagGTCTATCCCGAAGGAACGCATTTGATGGTGCCGTGGTTTGACAGGCCAGTGATCTACGATGTCCGTGCTAGACCCAACTTGGTCGAGAGTACTTCTGGCA
upper sequence: PP1S41_59V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ07463 (Selaginella moellendorffii), 3'ss of exon 1
gtgagtgagtgagtgagtgtgaattgcattggtctttgatgagacggaatttggatttgttttagggtttgga--ttttgacgatcgtggcggatttcgaggatggccttgcagGTGTATCCAGAGGGAACGCATTTTATGATTCCCTGGTTCGACAGGCCTGTGATATATGATGTCCGTGCACGACCTAACATTGTCGAGAGCACGTCGGGGA
|| | ||| | | | || |||||| ||| | ||| ||| ||| | | ||||| || | ||| | | ||||| ||||| ||||| || ||||||||||| ||| | || ||||| |||||||| ||||| || ||||||||||| |||| ||| | |||||||| || || || |
gtaggcgagcttgcc-gcaagcatcgcattgctctct----------------cttttatttcggggatcgccctttttgtagagttcgattgatctt-----ttgccttccagGTCTATCCCGAAGGAACGCATTTGATGGTGCCGTGGTTTGACAGGCCAGTGATCTACGATGTCCGTGCTAGACCCAACTTGGTCGAGAGTACTTCCGGCAMapped 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|18359062|gb|BJ191122.1|BJ191122EST: GAGGGCACCGAGCCATTGTGTTTAATCGCATTGTAGGTGTCAAGGATAAG GTGTATCCAGAGGGAACGCATTTTATGATTCCCTGGTTCGACAGGCCTGTG
genomic: GAGGGCACCGAGCCATTGTGTTTAATCGCATTGTAGGTGTCAAGGATAAGgtgagtgagt ... ggccttgcagGTGTATCCAGAGGGAACGCATTTTATGATTCCCTGGTTCGACAGGCCTGTG
EST:
gi|162223901|gb|FC398907.1|FC398907EST: GAGGGCACCGAGCCATTGTGTTTAATCGCATTGTAGGTGTCAAGGATAAG GTGTATCCAGAGGGAACGCATTTTATGATTCCCTGGTTCGACAGGCCTGTG
genomic: GAGGGCACCGAGCCATTGTGTTTAATCGCATTGTAGGTGTCAAGGATAAGgtgagtgagt ... ggccttgcagGTGTATCCAGAGGGAACGCATTTTATGATTCCCTGGTTCGACAGGCCTGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttttagggtttggattttgacgatcgtggcggatttcgaggatggccttgcagGTGTATCCAGAGGGAACGCATTTTATGATTCCCTGGTTCGACAGGCCTGTGATATATGATGTCCGTGCACGACCTAACATTGTCGAGAGCACGTCGGGGA
ttttgac putative branch site (score: 3)
attttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgagtgagtgagtgtgaattgcattggtctttgatgagacggaatttggatttgttttagggtttggattttgacgatcgtggcggatttcgaggatggccttgcagGTGTATCCAGAGGGAACGCATTTTATGATTCCCTGGTTCGACAGGCCTGTGATATATGATGTCCGTGCACGACCTAACATTGTCGAGAGCACGTCGGGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA