Sequence
atgc intronic sequence ATGC exonic sequence...agcaaggaagatcaatttcaacatctgtgaggttgtaggatgtattatattcttctggtatgaggtgctaatgcatgtcgtcattctttatgacaggcagCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAG
Basic information
species | Physcomitrella patens |
transcript | PP1S168_104V6.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA19G25870.1 (Glycine max), 3'ss of exon 3
---agcaaggaagatcaatttcaacatctgtgag--gttgtaggatgtattatattcttctggtatgaggtgctaatgcatgtcgtcattctttatgacaggcagCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAG
| | || ||| | | | || | ||||| | || | | ||| | ||| | | | | | || | | ||||||||||||||||| ||||| |||||||| ||||| |||||||| || || ||||| ||| ||||| || ||||| ||||||
attcgaatttaaatataatgactaaaattgaaaaaagttgttg-atagacaaaattaaatttagttgattatttgcttactttgaaagtcctgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGGGAATCAAGGTTTCCAGCTCAG
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA16G06100.1 (Glycine max), 3'ss of exon 3
-agcaaggaagatcaatttcaacatctgtga--ggttgtaggatgtattatattcttctggtatgaggtgctaatgcatgtcgtcattcttta-tgacaggcagCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAG
| | | | | || | | | || | || || | | || | | | | || | | | | | | ||||||||||||||||| ||||| |||||||| ||||| |||||||| || || ||||| ||| ||||| || ||||| ||||||
ttcttgcatcctttagtattattatttttaaccacttttcaaatataatggctaaaattgaaaaaatttagttgattatttgcttaccttgaaattgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGCGAATCAAGGTTTCCAGCTCAG
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA19G25870.2 (Glycine max), 3'ss of exon 3
---agcaaggaagatcaatttcaacatctgtgag--gttgtaggatgtattatattcttctggtatgaggtgctaatgcatgtcgtcattctttatgacaggcagCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAG----------------
| | || ||| | | | || | ||||| | || | | ||| | ||| | | | | | || | | ||||||||||||||||| ||||| |||||||| ||||| |||||||| || || ||||| ||| ||||| || ||||| ||||||
attcgaatttaaatataatgactaaaattgaaaaaagttgttg-atagacaaaattaaatttagttgattatttgcttactttgaaagtcctgtgttgcagGCAGCAAGTTTTGGTGGCTCTAACATAGATCCAACTGCCTGGGAGGATAAAAAATGCAAAGGGGAATCAAGGTTTCCAGCTCAGGTAGTAGAATATAGGA
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv14s0068g02040.t01 (Vitis vinifera), 3'ss of exon 3
-agcaaggaagatcaatttcaacatctgtgaggttgtaggatgtattatattctt-ctggtatgaggtgctaatg--catgtcgtcattctttatgacaggcagCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAG
| ||| | | || || || || | ||| | ||||| || | | ||| | |||| | | | | | | | ||||||||| |||||||| ||||| ||||| || |||||||| ||||||||||| ||||| ||| |||||||| ||||||||||||
aaaatcttaaggttttatacatttatggttagttttgcgcatgaaagatattattattattttgaattcttaatagttctataatttgtttcttttacagGCAGCTAGTTTTGGGGGCTCTAACATTGATCCAACCGCATGGGAAGACAAAAAATGCAAAGGCGAATCGAGGTTTCCTGCTCAG
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv18s0089g01080.t01 (Vitis vinifera), 3'ss of exon 2
-----------agcaaggaagatcaatttcaacatctgtgaggttgtaggatgtattatattcttctggtatgaggtgctaatgcatgtcgtcattctttatgacaggcagCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAG
||| || || | || | | | | | || || | ||| | || | || || | |||| | | | | |||| || ||||| |||||||| ||||||||||| || |||||||||||||| || |||||||||| |||||||| || |||
ttttttttactctcaaaaaaataatatataaaagtgtttttgataaaagtttgcaa-ataggcc-ctagaatctaaccatatttaatgtgataaaacc-----aaagGCCATGAGCTTTGGGGGCTCAAATATAGACCCAACAGCATGGGAAGACAAGAAGTGCAGAGGAGAATCCAGATTTCCAGCCCAG
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ35508 (Selaginella moellendorffii), 3'ss of exon 2
agcaaggaagatcaatttcaacatctgtgaggttgtag-gatgtattatattcttctggtatgaggtgctaatgcatgtcgtcattctttatgacaggcagCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAG
| | | | | || | | || | || | ||| |||| | || | ||| || | |||||| |||||||||||||||| ||||| || |||| || ||||| |||||||| || || ||||| |||||||| || ||||||
--------------------gtacgtattacacttaagtgcttctttgccgttgtcctctttgaaactctaaagaatct-atcaatcc--aatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ22023 (Selaginella moellendorffii), 3'ss of exon 2
agcaaggaagatcaatttcaacatctgtgaggttgtaggatgtattatattctt-ctggtatgaggtgctaatgcatgtcgtcattctttatgacaggcagCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAG
|| | | ||||| | | | | || | || | || | || || ||| | ||| |||||| || |||||||| |||||||||||||| || || || |||||||||||||| ||||| |||||||| | || ||||| |||
-----------------gtaaagctacctctctcgcaggatttgtgacactcatgttgatggcgagtccaaacttttg-cgtgactct-----acagGCTGCGAGTTTTGGGGGCTCAAACATAGATCCTACTGCGTGGGAAGACAAGAAGTGTCGTGGAGAATCTCGGTTCCCTGCACAG
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ18285 (Selaginella moellendorffii), 3'ss of exon 2
agcaaggaagatcaatttcaacatctgtgaggttgtaggatgtattatattcttctggtatgaggtgctaatgcatgtcgtcattctttatgacaggcagCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAG
| | | | | || ||| | ||| | | || | | || | || | | | || || ||| | ||| |||||| || |||||||| |||||||||||||| || || || |||||||||||||| ||||| |||||||| | || ||||| |||
------gtaaagctacctc----tctctcaggatttgtgac-tctcatgt-----tgatggcgaatccaaacttttg-cgtgactct-----acagGCTGCGAGTTTTGGGGGCTCAAACATAGATCCTACTGCGTGGGAAGACAAGAAGTGTCGTGGAGAATCTCGGTTCCCTGCACAG
upper sequence: PP1S168_104V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ24245 (Selaginella moellendorffii), 3'ss of exon 2
agcaaggaagatcaatttcaacatctgtgaggttgtaggatgtattatattctt--ctggtatgaggtgctaatgcatgtcgtcattctttatgacaggcagCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAG
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--------------------gtacgtattacact-taagttcttctttgccgttgtcctctttggaactctaaagaatct-atcaatcc--aatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAGMapped 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|22132955|gb|BQ827456.1|BQ827456EST: CCCTTTTTCTGTACAATTATACTACACACCAGCTTCATGGGATATTCGAG CAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAAT
genomic: CCCTTTTTCTGTACAATTATACTACACACCAGCTTCATGGGATATTCGAGgtgattgtcc ... tgacaggcagCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatattcttctggtatgaggtgctaatgcatgtcgtcattctttatgacaggcagCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAG
tgctaat putative branch site (score: 2)
ttctttat putative PPT
attctttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agcaaggaagatcaatttcaacatctgtgaggttgtaggatgtattatattcttctggtatgaggtgctaatgcatgtcgtcattctttatgacaggcagCAAGTTTTGGAGGCTCAAACATAGACCCAACCGCCTGGGAAGACAAGAAATGTCGAGGAGAATCGAGATTTCCTGCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA