Sequence
atgc intronic sequence ATGC exonic sequencegtctccaaggcaaagcacaaaacccatgatcaaacttgcggattctttgcttaactcttgtgcttgcgtttcagGCTTCCAGATCTCCCACTCCATGGGAGGCGGGACAGGGTCGGGGATGGGGACGCTGCTCATCTCCAAGATCCGCGAGGAATACCCCGACCGCATGATGCT
Basic information
species | Selaginella moellendorffii |
transcript | EFJ05935 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ05935 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: EDP02933 (Chlamydomonas reinhardtii), 3'ss of exon 3
---------------------------------------------------------------gtctccaaggcaaagcacaaaacccatgatcaaac-ttgcggattctttgcttaactcttgtgcttgcgtttcagGCTTCCAGATCTCCCACTCCATGGGAGGCGGGACAGGGTCGGGGATGGGGACGCTGCTCATCTCCAAGATCCGCGAGGAATACCCCGACCGCATGATGCT
| ||| || | | | ||| || |||| || | | || || || | | |||||||||||| ||| |||||| |||| ||||| || || || || ||||| || ||||| |||||||||||||| ||||| ||||||||||||||||||||
gtgagcagttctgcacgggccgtcgggtgtcagtgtatggaccgcagggctcggcatgacgggctgctttgggctgtgcgcccc-ttcgtcttcacacgttgctgacttctctctcccctgttcttccctaccctcagGCTTCCAGGTCTGCCACTCTCTGGGTGGCGGCACCGGCTCCGGCATGGGCACCCTGCTGATCTCCAAGATCCGTGAGGAGTACCCCGACCGCATGATGCT
upper sequence: EFJ05935 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: EDP03008 (Chlamydomonas reinhardtii), 3'ss of exon 3
--------------------------------------------------------------gtctccaaggcaaagcacaaaacccatgatcaaacttgcggattctttgcttaactcttgtgcttgcgtttcagGCTTCCAGATCTCCCACTCCATGGGAGGCGGGACAGGGTCGGGGATGGGGACGCTGCTCATCTCCAAGATCCGCGAGGAATACCCCGACCGCATGATGCT
| | | | || | | | |||| || | | | | | |||| | |||||||||||| | | |||||| |||| || || || || || || ||||| || ||||| |||||||||||||| ||||| ||||||||||||||||||||
gtgagcagttttgcacgggccgccgggtgtcggggtgtggaccgcagggcttggcatgacgggctgctgggtctgtgctcctcgtcgtcttcaacggttgctgacttctctcctc-ttgttgttcccttccctcagGCTTCCAGGTTTGCCACTCTCTGGGTGGTGGCACTGGCTCCGGCATGGGCACCCTGCTGATCTCCAAGATCCGTGAGGAGTACCCCGACCGCATGATGCT
upper sequence: EFJ05935 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S35_125V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------gtctccaaggcaaagcacaaaacccatgatcaaacttgc-ggattctttgcttaactcttgtgcttgcgtttcagGCTTCCAGATCTCCCACTCCATGGGAGGCGGGACAGGGTCGGGGATGGGGACGCTGCTCATCTCCAAGATCCGCGAGGAATACCCCGACCGCATGATGCT
| || || | || | ||| | | | || ||| | | | || | ||| |||| || ||||| | || ||||||||||| || || || || || ||||||||||| |||||||| ||||| | |||||||| || || ||||||||| |
caacggtttcacagaacaatttttttattattcagtcacaatttcgaagggaccatctgagatactatatgagttgttgtattgtttgattggcgaa-cagGATTTCAGATTTGTCATTCCATGGGAGGTGGAACGGGATCAGGCATGGGGACGCTTCTCATCTCAAAGATTAGGGAGGAATATCCGGATCGCATGATGGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaacccatgatcaaacttgcggattctttgcttaactcttgtgcttgcgtttcagGCTTCCAGATCTCCCACTCCATGGGAGGCGGGACAGGGTCGGGGATGGGGACGCTGCTCATCTCCAAGATCCGCGAGGAATACCCCGACCGCATGATGCT
gcttaac putative branch site (score: 3)
attcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctccaaggcaaagcacaaaacccatgatcaaacttgcggattctttgcttaactcttgtgcttgcgtttcagGCTTCCAGATCTCCCACTCCATGGGAGGCGGGACAGGGTCGGGGATGGGGACGCTGCTCATCTCCAAGATCCGCGAGGAATACCCCGACCGCATGATGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT