Sequence
atgc intronic sequence ATGC exonic sequencegtaaagactttgaaaattttgctctccagatactgatatcaagacgattatcagCCCTGTTCAATTGGTTTTGCGACCGGTGGAAGAACTTTCTTTTTGTGGGGCGGATGCATGATG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ38341 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ38341 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: LOC_Os01g67870.1 (Oryza sativa), 3'ss of exon 7
---------------------------------------------gtaaagactttgaaaattttgctctccagatactgatatcaagacgattat-cagCCCTGTTCAATTGGTTTTGCGACCGGTGGAAGAACTTTCTTTTTGTGGGGCGGATGCATGATG
| | ||| | ||| | ||| || ||||| || | ||||| ||||||||||| ||||| || ||||| | ||||||||||||||||| || |||||||||
ctgttttcgtaagctagttatttagttctgtatctccctatttttatttttatttttattttttactcttttcgatttactaataaagaccatattgcagCCTTGTTCAATTGGATTTGCAACTGGTGGGAAGACTTTCTTTTTGTGGGGTGGCTGCATGATG
upper sequence: EFJ38341 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA16G08510.1 (Glycine max), 3'ss of exon 6
---------------------------------------------gtaaagactt-tgaaaattttgctctccagatactgatatcaagacgattatcagCCCTGTTCAATTGGTTTTGCGACCGGTGGAAGAACTTTCTTTTTGTGGGGCGGATGCATGATG----
| || || | | | | || | | | | | | | | ||||| |||||||| || ||||| || |||||| ||| |||||||||||||| || |||||||||
ttggatctgatgacttctattaatggtttttgataatatatcaatattctgatttgtacatactcaattcacttattcccatttttattttgttctacagCCTTGTTCAATGGGCTTTGCCACTGGTGGACAAACATTCTTTTTGTGGGGAGGGTGCATGATGGCAA
upper sequence: EFJ38341 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA01G01130.1 (Glycine max), 3'ss of exon 6
--------------------------------------------gtaaagactttga--aaattttgctctccagatactgatatcaagacgattatcagCCCTGTTCAATTGGTTTTGCGACCGGTGGAAGAACTTTCTTTTTGTGGGGCGGATGCATGATG----
| || | | ||| | || || | | || | | | | | ||||| |||||||| || ||||| || |||||| ||| |||||||||||||| || |||||||||
tagcgatggatctgatgacttctattaagggtttttgataatatatcaatattctgattgtacttaattcacttattcctatttttattttgttctacagCCTTGTTCAATGGGCTTTGCCACTGGTGGACAAACATTCTTTTTGTGGGGAGGGTGCATGATGGCAA
upper sequence: EFJ38341 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 7
--------------------------------------gtaaagactttgaaaattttgc--tctccagat----actgatatcaaga-----cgattatcagCCCTGTTCAATTGGTTTTGCGACCGGTGGAAGAACTTTCTTTTTGTGGGGCGGATGCATGATG
|| | | || | |||| | | || || || |||| | | || ||||| || ||||| || |||||||| ||||||||||| |||||||||||||| ||||| ||||||
gtacggtagatataatcactggttacttttatcaagttgttaggttgtttataattgtagcatatcgtaatttgagctaatatttggcatgttcactttccagCCTTGCTCAATGGGATTTGCGACTGGTGGAAGAACATTCTTTTTGTGGGGAGGATGTATGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaaagactttgaaaattttgctctccagatactgatatcaagacgattatcagCCCTGTTCAATTGGTTTTGCGACCGGTGGAAGAACTTTCTTTTTGTGGGGCGGATGCATGATG
tactgat putative branch site (score: 2)
actttgaaaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagactttgaaaattttgctctccagatactgatatcaagacgattatcagCCCTGTTCAATTGGTTTTGCGACCGGTGGAAGAACTTTCTTTTTGTGGGGCGGATGCATGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC