Sequence
atgc intronic sequence ATGC exonic sequencegtaagcgcttctttcttgctcgatcgtcgaaatattttgcccgggtttctcacacccctcgttctttctttctttgcccagGTTGATCTAGTCGGCGGCTACTACGACGCCGGCGACAATGTCAAGTTTGGCCTCCCAATGGCCTTCACGATCACAATGCTGTCTTGGAGCGCCATCGAGT
Basic information
species | Selaginella moellendorffii |
transcript | EFJ14373 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ14373 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os01g12070.1 (Oryza sativa), 3'ss of exon 1
-------------gtaagcgcttctttcttgctcgatcgtcgaaatattttgcccgggtttct-cacacccctcgtt--ctttctttctttgcccagGTTGATCTAGTCGGCGGCTACTACGACGCCGGCGACAATGTCAAGTTTGGCCTCCCAATGGCCTTCACGATCACAATGCTGTCTTGGAGCGCCATCGAGT
| | | || | | | || || | || | || | | | | || ||| ||| ||||||| ||||| ||||| || || || |||||||||||||||||||| |||||||| || || || ||||| |||||| | || ||| || | ||||||| ||||||||
gtacgtggagtcgttcaccattttctccgttcttgaattgcaggatgtgttctacagctccatgcatctgatctgttgattttttttcttttttcagGTGGATCTTGTTGGTGGGTACTACGACGCCGGCGACAACGTCAAGTTCGGGCTGCCGATGGCGTTCACGGTGACCATGATGGCGTGGAGCGTCATCGAGT
upper sequence: EFJ14373 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os01g12030.1 (Oryza sativa), 3'ss of exon 1
--------------------------------gtaagcgcttctttcttgctc--gatcgtcgaaatattttgcccgggtttctcacacccctcgttctttctttctttgc---ccagGTTGATCTAGTCGGCGGCTACTACGACGCCGGCGACAATGTCAAGTTTGGCCTCCCAATGGCCTTCACGATCACAATGCTGTCTTGGAGCGCCATCGAGT
|| | || ||||| |||| | || | | || | || | | | | | | | ||||| ||||| || || ||||||||||||||||| ||||| |||||||| || |||| ||||| |||||| | || ||| || | ||||||| | ||||||
gtacgtgctcccgccattgtggcagctagcaaacctgcaatctttctctgctcttgatc-ttgatcagtacggtttaatttgcaagaacgtgttctattctacacatctacatttcagGTGGATCTTGTTGGTGGCTACTACGACGCCGGAGACAACGTCAAGTTCGGGTTCCCGATGGCGTTCACGGTGACCATGATGGCGTGGAGCGTCCTCGAGT
upper sequence: EFJ14373 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G453565_T01 (Zea mays), 3'ss of exon 1
-------gtaagcgcttctttcttgctcgatcgtcgaaat---attttgcccgggtttctcacacccctcgttctttctttc---tttg------cccagGTTGATCTAGTCGGCGGCTACTACGACGCCGGCGACAATGTCAAGTTTGGCCTCCCAATGGCCTTCACGATCACAATGCTGTCTTGGAGCGCCATCGAGT
| ||| | | || | ||| || ||||| || | || || | || | || |||||| ||||| || |||||||||||||||||||||||||| |||||||| ||||| || ||||| |||||| |||| ||| |||| ||||||| ||||||||
gtctcagctgtatatttcatacatggataactaataaaaaccggcatttattttgtttccttcatcaatcaatcaataaatcaaatgtggtccactccagGTGGATCTGGTGGGCGGCTACTACGACGCCGGCGACAACGTCAAGTTCGGCCTGCCGATGGCGTTCACGGTCACCATGATGTCCTGGAGCGTCATCGAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgaaatattttgcccgggtttctcacacccctcgttctttctttctttgcccagGTTGATCTAGTCGGCGGCTACTACGACGCCGGCGACAATGTCAAGTTTGGCCTCCCAATGGCCTTCACGATCACAATGCTGTCTTGGAGCGCCATCGAGT
ttctcac putative branch site (score: 2)
tttctcacacccctcg CT-rich tract
atatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcgcttctttcttgctcgatcgtcgaaatattttgcccgggtttctcacacccctcgttctttctttctttgcccagGTTGATCTAGTCGGCGGCTACTACGACGCCGGCGACAATGTCAAGTTTGGCCTCCCAATGGCCTTCACGATCACAATGCTGTCTTGGAGCGCCATCGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG