Sequence
atgc intronic sequence ATGC exonic sequence...agatttcaacttttgtatgggccttacttttgcatgattctggaccaaaataggccaacattggagaaactgtttgaaggcaaaaatgtccacttcacagGCATGCTGTCAGGCGAAGAGCTCTCACAAGCCTATGCCAGCGGTGATATATTTATCACACCATCAGAGTCTGAAACTTTAGGATTTGTGGTTTTAGAAGC
Basic information
species | Physcomitrella patens |
transcript | PP1S83_95V6.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S83_95V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: LOC_Os01g04920.1 (Oryza sativa), 3'ss of exon 10
------------------------------------------agatttcaacttttgtatgggccttac-ttttgcatgat-tctggac---caaaataggccaacattggagaaactgtttgaaggcaaaaatgtccacttcacagGCATGCTGTCAGGCGAAGAGCTCTCACAAGCCTATGCCAGCGGTGATATATTTATCACACCATCAGAGTCTGAAACTTTAGGATTTGTGGTTTTAGAAGC
| || ||| | | || |||| | |||| | || | ||| ||||||| ||||||| || | || | ||||| || ||| || |||||||||||| ||||| || ||||||||||||||| | ||
cggtttacagaaaatgttcattggacaccttcggtgaatcaattactttgggctttttgccactagtgtgccttacatgctctctgcaattacatgacagGAGTGAGCTGGAGAAGATGTTTGAGGGGATGCCTGCCGTGTTCACTGGAATGATGCAAGGCGAAGAGCTATCACAGGCATATGCCAGCGGTGATGTTTTC-----------------------------------------------
upper sequence: PP1S83_95V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: EFJ29760 (Selaginella moellendorffii), 3'ss of exon 10
---agatttcaacttttgta-tgggccttacttttgcatgattctggaccaaaataggccaacattggagaaactgtttgaaggcaaaaatgtccacttcacagGCATGCTGTCAGGCGAAGAGCTCTCACAAGCCTATGCCAGCGGTGATATATTTATCACACCATCAGAGTCTGAAACTTTAGGATTTGTGGTTTTAGAAGC
|| | ||| | ||| | | || || || | | ||| |||||| || |||| | | || ||||| || ||||| ||| |||||||||||||||||||||||||| | || | ||
gtaagtcactgaatttcatggctaaacttgttctagc--gagtccacatcgttgcagGAAGGACTTGGAGGAATTGTTCGCGGATTTGCCAGTGGTTTTCACTGGAATGCTTCAAGGAGAAGAGCTCTCACAAGCCTATGCCAGTGCGGACGTGTTC-----------------------------------------------Mapped 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|67692569|gb|BJ952802.1|BJ952802EST: GAGAGAATTTCTGAAGCAAGACTTGTCTTTGTGGGTGATGGACCTTACAA GCATGCTGTCAGGCGAAGAGCTCTCACAAGCCTATGCCAGCGGTGATATAT
genomic: GAGAGAATTTCTGAAGCAAGACTTGTCTTTGTGGGTGATGGACCTTACAAgtatgtcaac ... cacttcacagGCATGCTGTCAGGCGAAGAGCTCTCACAAGCCTATGCCAGCGGTGATATAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaaataggccaacattggagaaactgtttgaaggcaaaaatgtccacttcacagGCATGCTGTCAGGCGAAGAGCTCTCACAAGCCTATGCCAGCGGTGATATATTTATCACACCATCAGAGTCTGAAACTTTAGGATTTGTGGTTTTAGAAGC
tccacttc CT-rich tract
aaaaatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agatttcaacttttgtatgggccttacttttgcatgattctggaccaaaataggccaacattggagaaactgtttgaaggcaaaaatgtccacttcacagGCATGCTGTCAGGCGAAGAGCTCTCACAAGCCTATGCCAGCGGTGATATATTTATCACACCATCAGAGTCTGAAACTTTAGGATTTGTGGTTTTAGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC