Sequence
atgc intronic sequence ATGC exonic sequence...cccatgttttggttgcacgattacgggggaatataacagagactgtctcgttgattcttactcaagtcagccgttaaaagcagatggggggattttgcagGTTAAGCTTTGGTGCACTAATCAGGAGGCTAGTGTTTTTAGTATAGACATGAAGGCCAACATCTGCTGCGTTAAGTACAATCCTGGTTCAAGCAACCATA
Basic information
species | Physcomitrella patens |
transcript | PP1S25_325V6.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S25_325V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 9
cccatgttttggttgcacgattacgggggaatataacagagactgtctcgt-tgattcttactcaagtcagccgttaaaagcagatggggggattttgcagGTTAAGCTTTGGTGCACTAATCAGGAGGCTAGTGTTTTTAGTATAGACATGAAGGCCAACATCTGCTGCGTTAAGTACAATCCTGGTTCAAGCAACCATA
||||| || | | | | | | | | | || ||||| | | | | ||| | | || |||||| || ||||||||||||||||||| ||||||||| | | |||||||||||| || ||||| || || || || || |||||||| || |||| |||
tttgcattttgcttagtcaaatttaaattttcttggcgtggtatctgttgtatgattgaaagttac-tgagctaaatgtaatgtgtcttttctttgagcagGTCAAAATTTGGTGCACTAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGTTGTGTCAAATATAATCCTGGATCTGGCAATTATA
upper sequence: PP1S25_325V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA14G05430.1 (Glycine max), 3'ss of exon 9
-cccatgttttggttgcacgattacgggggaatataacagagactgtctcgt-tgattcttactcaagtcagccgttaaaagcagatggggggatttt--gcagGTTAAGCTTTGGTGCACTAATCAGGAGGCTAGTGTTTTTAGTATAGACATGAAGGCCAACATCTGCTGCGTTAAGTACAATCCTGGTTCAAGCAACCATA
|||||||| | ||| | | || | | | | || ||||| | | | | || || | | | ||| |||||| || ||||||| || |||||||| ||||||||| | | |||||||||||| || ||||| ||||| || || || |||||||| || |||| |||
tttggcattttggttagtcaatt-caaattttcttggcatggtatctgttgtatgattgaaagtta---ttgatgtaaatgtaatgtctcttgtctttgagcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATA
upper sequence: PP1S25_325V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: EFJ35654 (Selaginella moellendorffii), 3'ss of exon 9
cccatgttttggttgcacgattacgggggaatataacagagactgtctcgttgattcttactcaagtcagccgttaaaagcagatggggggattttgcagGTTAAGCTTTGGTGCACTAATCAGGAGGCTAGTGTTTTTAGTATAGACATGAAGGCCAACATCTGCTGCGTTAAGTACAATCCTGGTTCAAGCAACCATA
||| | ||| |||| || | || | | || || | | |||||| | || | |||| ||| |||||| || || | | || |||||||| ||||||||||||||||| |||| |||||| | || ||||| |
----------------------------------gttagaacgtatctttttgaaaattctttgtttc---catctaactt---tgagaaaaacttgcagCTCAAAGTGTGGTCTACTCGACAGGAGAGCAGCGTCATGGGAATCGACATGAAAGCCAACATCTGCTGCGTCAAGTTCAATCCCAGCTCCAGCAATTTTGMapped 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|162188191|gb|FC363957.1|FC363957EST: TTTCCCGGACGGATCCTTCAATGCTGGTCTCTGGAAGTGATGATGGCAAG GTTAAGCTTTGGTGCACTAATCAGGAGGCTAGTGTTTTTAGTATAGACATG
genomic: TTTCCCGGACGGATCCTTCAATGCTGGTCTCTGGAAGTGATGATGGCAAGgtctgtctca ... gattttgcagGTTAAGCTTTGGTGCACTAATCAGGAGGCTAGTGTTTTTAGTATAGACATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcgttgattcttactcaagtcagccgttaaaagcagatggggggattttgcagGTTAAGCTTTGGTGCACTAATCAGGAGGCTAGTGTTTTTAGTATAGACATGAAGGCCAACATCTGCTGCGTTAAGTACAATCCTGGTTCAAGCAACCATA
ttcttac putative branch site (score: 2)
ttaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cccatgttttggttgcacgattacgggggaatataacagagactgtctcgttgattcttactcaagtcagccgttaaaagcagatggggggattttgcagGTTAAGCTTTGGTGCACTAATCAGGAGGCTAGTGTTTTTAGTATAGACATGAAGGCCAACATCTGCTGCGTTAAGTACAATCCTGGTTCAAGCAACCATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA