Sequence
atgc intronic sequence ATGC exonic sequencegtacttgggagaagttttcgctttgcttgctaatgttcttgctggtgatcgcagGGATATCAAGGCTACCAGCATTCTTCTCGATGACAAGTTTGAAGTGAGGCTTGGAAGCTTGAGCGAGGCTCGGATTCAAGATGGAGGAGTTCATCCAAAT
Basic information
species | Selaginella moellendorffii |
transcript | EFJ09880 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ09880 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S45_80V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------gta-cttgggagaagttttcgct--ttgcttgctaatgttcttgctggtgatcgcagGGATATCAAGGCTACCAGCATTCTTCTCGATGACAAGTTTGAAGTGAGGCTTGGAAGCTTGAGCGAGGCTCGGATTCAAGATGGAGGAGTTCATCCAAAT
| | ||| ||| || | | || | | | ||| ||| || | |||| ||| | ||||| | |||||| ||||| |||||||||||||| || ||||| || ||||||||||| ||| || | ||||||||| |||||| | |
tgatgcagctacagtcatgttcaatgcactaattggcactgttgcagcttcaatttagtgttgagtgttcaattccgatttctctcgcttgttttggcagAGATGTGAAGGCAAGCAGCATCCTTCTGGATGACAAGTTTGAGGTCAGGCTCGGGAGCTTGAGCGATGCTAGGGTGCAAGATGGAAACTCTCATCCTAGT
upper sequence: EFJ09880 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S2_806V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------------------------gtacttgggagaagttttcgctttgcttgctaatgttcttgctggtgatcgcagGGATATCAAGGCTACCAGCATTCTTCTCGATGACAAGTTTGAAGTGAGGCTTGGAAGCTTGAGCGAGGCTCGGATTCAAGATGGAGGAGTTCATCCAAAT
| || | | | | || || || | |||| | | | | |||||||| | ||||| | ||| || ||||| |||||||||||||| || ||||||| ||||||||||| || ||| | |||||||| | ||||| |
gtacgtgttctctttcctcgtttacatcagtattgggtaatttcgtatcttcaggactagcctcagatccattttcggggaatcctcagttcattttttt---ttctggttaattct-gcagGGATGTGAAGGCAAGCAGTATCCTTCTGGATGACAAGTTTGAGGTTCGGCTTGGGAGCTTGAGCGATGCCCGGGTGCAAGATGGGGACCCACATCCTAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtacttgggagaagttttcgctttgcttgctaatgttcttgctggtgatcgcagGGATATCAAGGCTACCAGCATTCTTCTCGATGACAAGTTTGAAGTGAGGCTTGGAAGCTTGAGCGAGGCTCGGATTCAAGATGGAGGAGTTCATCCAAAT
tgctaat putative branch site (score: 2)
aagtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttgggagaagttttcgctttgcttgctaatgttcttgctggtgatcgcagGGATATCAAGGCTACCAGCATTCTTCTCGATGACAAGTTTGAAGTGAGGCTTGGAAGCTTGAGCGAGGCTCGGATTCAAGATGGAGGAGTTCATCCAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG