Sequence
atgc intronic sequence ATGC exonic sequencegtaactctcaagaaaaaaccagaaacttccgtaactttcttcatgcttctcgtactcgacagAGGAAATGGATTGGGACAAGAATGGGATGATCACGTTTAAGGAGTTTCTGTTTGCTTTTACTGATTGGGTTGGGATCGAAGAAGAAGAAGATGCAGACGA
Basic information
species | Selaginella moellendorffii |
transcript | EFJ07984 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ07984 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os02g10470.1 (Oryza sativa), 3'ss of exon 4
-----------------------------gtaactctcaagaaaaaaccagaaacttccg-taactttcttcatgc-ttctcgtactcgac--agAGGAAATGGATTGGGACAAGAATGGGATGATCACGTTTAAGGAGTTTCTGTTTGCTTTTACTGATTGGGTTGGGATCGAAGAAGAAGAAGATGCAGACGA
| ||| || ||| | | | | ||| | | | || | || | ||| | | | | ||||||||||||||||||||||||||| | | | || || |||||||| || || ||||||||| |||||| ||||| || || | ||||||| |||||
gtaagttttcttttttgtggtatcgtcacaaatctcacatgaacacagtacacactgacaatgatggtcctaatacactcttttggtggtcccagAGGAAATGGATTGGGACAAGAATGGAACGGTGACCTTCAAGGAGTTCCTCTTCGCTTTTACTCGTTGGGTGGGGATTGATGATAACGAAGATGACGACGA
upper sequence: EFJ07984 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os06g40720.1 (Oryza sativa), 3'ss of exon 4
----------------------------------gtaactctcaagaa----aaaaccagaaacttccgtaactttcttcatgcttctcgtactcgacagAGGAAATGGATTGGGACAAGAATGGGATGATCACGTTTAAGGAGTTTCTGTTTGCTTTTACTGATTGGGTTGGGATCGAAGAAGAAGAAGATGCAGACGA
|| || || | | || | || | | ||| | || | | ||||||||||||| |||||||||||||| ||| | || || || || ||||||||||| || ||| ||||||||||| || ||| | || || | | ||
atttctctatagtaatctaaaaatttctagattgacaattcccatcagtttcagaattaagtcctaacatgtaacactttctttttttgcatggcaccagAGGAAATGGACTGGGACAAGAATGGAATGGTGACCTTCAAAGAATTTCTGTTTGCATTCACTCGCTGGGTTGGGATTGACGAAAATGAGGACGACAATGA
upper sequence: EFJ07984 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G142693_T02 (Zea mays), 3'ss of exon 4
-------------------------------gtaactctcaagaaaaaaccagaaacttccgtaacttt--cttcatgcttctcgtactcg-----acagAGGAAATGGATTGGGACAAGAATGGGATGATCACGTTTAAGGAGTTTCTGTTTGCTTTTACTGATTGGGTTGGGATCGAAGAAGAAGAAGATGCAGACGA
| || | | | | || | | || ||| | | || || | | ||||||||||||||||||||||||||||| | | || || ||||| || || |||||||||||| ||||| |||||||| | ||||| |||| || ||
cgtcggtacgttttccttcttatgccctgtgggtacccgattgccatccctggatatgtttatatgtttgccctgatatttactactttggtgaatacagAGGAAATGGATTGGGACAAGAATGGCACAGTGACCTTCAAGGAATTCCTTTTTGCTTTTACTCGCTGGGTGGGGATCGATAATGAAGACGATGATGATGA
upper sequence: EFJ07984 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G006790_T01 (Zea mays), 3'ss of exon 3
--------------------------------gtaactctcaagaaa---aaaccagaaacttccgtaactttcttcatgcttctcgtactcgaca---gAGGAAATGGATTGGGACAAGAATGGGATGATCACGTTTAAGGAGTTTCTGTTTGCTTTTACTGATTGGGTTGGGATCGAAGAAGAAGAAGATGCAGACGA
|| ||| | |||| | | | || || | | ||| ||| | || ||||||||||| ||||||||||| || ||| | || || |||||||| |||||||| || ||| ||||| || || || ||| | || |||| ||| ||
gaagtataaaaacttgcacactcataattcctgttactgttttgaaacttgcgtcccatcttcccagtcctgacgtttacctttctttacatggcactagAGGAAATGGACTGGGACAAGAACGGAATGGTGACATTCAAGGAGTTCCTGTTTGCCTTCACTCGCTGGGTAGGAATTGATGAAAATGAGGATGAAGATGA
upper sequence: EFJ07984 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S197_126V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------------------------------------------------gtaactctcaagaaaaaaccagaaacttccgtaactttcttcatgcttctcgtactcgacagAGGAAATGGATTGGGACAAGAATGGGATGATCACGTTTAAGGAGTTTCTGTTTGCTTTTACTGATTGGGTTGGGATCGAAGAAGAAGAAGATGCAGACGA
| || || | ||| || ||| | ||| | | | | ||||||||||||||||||| || | || |||||||| || ||||||||| | || |||||||| || ||||| || | || | || ||||| | | |
gtatgttactctttcccacctcactgtcatgcatcaaattatttctgcaaccgttttcaattgccattgcctttcctgtaaatgt--gacactgactaaacgaatgcgaaccccaacatgt---gcagAGGAAATGGATTGGGATAAAGACGGCATGATCACATTCAAGGAGTTTTTATTCGCTTTTACGGACTGGGTAGGACTTGAGAATGACGAAGAAGAAACAGG
upper sequence: EFJ07984 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S429_31V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------------gta-actctcaagaaaaaaccagaaacttccgtaactttcttcatgcttctcgtactcgacagAGGAAATGGATTGGGACAAGAATGGGATGATCACGTTTAAGGAGTTTCTGTTTGCTTTTACTGATTGGGTTGGGATCGAAGAAGAAGAAGATGCAGACGA
|| |||| | || || ||| || || | | | || || | || ||||||||||||| |||||||| | || |||||||| || ||||||||| |||| ||||| || || ||||| || | || | || ||||| | | |
gtccgtttctcgtactttcatcatccattgaattgcgtacaccactctattcaaactcgtgtgttctcttgcaagtgt--gatactgacgaaa---tgtacgtgagtcgcaatctgttcagAGGAAATGGACTGGGACAAAGACGGTATGATCACATTCAAGGAGTTTTTGTTCGCTTTCACCGACTGGGTAGGACTTGAGAACGACGAAGAAGAAACAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaagaaaaaaccagaaacttccgtaactttcttcatgcttctcgtactcgacagAGGAAATGGATTGGGACAAGAATGGGATGATCACGTTTAAGGAGTTTCTGTTTGCTTTTACTGATTGGGTTGGGATCGAAGAAGAAGAAGATGCAGACGA
ccgtaac putative branch site (score: 3)
cttctcgt putative PPT
aaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactctcaagaaaaaaccagaaacttccgtaactttcttcatgcttctcgtactcgacagAGGAAATGGATTGGGACAAGAATGGGATGATCACGTTTAAGGAGTTTCTGTTTGCTTTTACTGATTGGGTTGGGATCGAAGAAGAAGAAGATGCAGACGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG