Sequence
atgc intronic sequence ATGC exonic sequencegcaagtgtaacattttctttttgtttctggtgtattttttcatttttcttttctagtgtgtggttactcacatttttatcattgttctttctagGGAGAATTGTTTGAGATTCTTGAAGACGACAAGTGCCTCCCCGAAGCTCAAGTCCAGGCGATAGCAAAGCAACTGGTATGTATGTTAAGCCATCTT
Basic information
species | Selaginella moellendorffii |
transcript | EFJ37043 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ37043 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: AT1G50240.2 (Arabidopsis thaliana), 3'ss of exon 3
gcaagtgtaacattttc--tttttgtttctggtgtattttttcatttttctttt--ctagtgtgtggttactcacatttttatcattgttc-------tttctagGGAGAATTGTTTGAGATTCTTGAAGACGACAAGTGCCTCCCCGAAGCTCAAGTCCAGGCGATAGCAAAGCAACTGGTATGTATGTTAAGCCATCTT
| | | | || | | || | | ||| ||| | || || | | | |||| | | | | | | | ||| | | ||| |||| ||||||||||||||||||||||| ||||||||||| ||||||| ||||| || || || ||||||||| ||
gtacttttctcactgtagattgtagaatctaaagtactgatttatgaagcatatagctagacttatatgaaataaagaatcaccatggaacacccaattttacagGGTGAATTGTTTGAGATTCTTGAAGATGACAAGTGCCTTCCCGAAGAGCAAGTTCAAGCAATCGCAAAGCAATTG---------------------
upper sequence: EFJ37043 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv16s0039g02400.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------------------------------------------------gcaagtgtaacattttctttttgt-ttctggtgt---attttttcatttttcttttctagtgtgtggttactcacatttttatcattgttctttc-----tagGGAGAATTGTTTGAGATTCTTGAAGACGACAAGTGCCTCCCCGAAGCTCAAGTCCAGGCGATAGCAAAGCAACTGGTATGTATGTTAAGCCATCTT
||| || ||| || || || | | || | || | | || | | | | | ||| | || | |||||||| | |||||||||||||| || ||||||||||| || |||| ||||| || || || |||||||| ||
gtaattagctcttctctctctctctctctctctcttctctgttttgtacttacacatgcaaattcattccatgcgcatctatgcagcagaaagaatgtttcagagatgcaccctaacacaaaatatgcttggttattttgaccatagtttagatgcatgagtagttaatgaaaattttccatatgcagGGAGAACTCTTTGAGATTCTTGAGGATGACAAGTGCCTTCCTGAAGAACAAGTTCAAGCAATTGCAAAGCAGTTG--------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatttttcttttctagtgtgtggttactcacatttttatcattgttctttctagGGAGAATTGTTTGAGATTCTTGAAGACGACAAGTGCCTCCCCGAAGCTCAAGTCCAGGCGATAGCAAAGCAACTGGTATGTATGTTAAGCCATCTT
tactcac putative branch site (score: 1)
tcattgttctttct putative PPT
atttttatcattgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaagtgtaacattttctttttgtttctggtgtattttttcatttttcttttctagtgtgtggttactcacatttttatcattgttctttctagGGAGAATTGTTTGAGATTCTTGAAGACGACAAGTGCCTCCCCGAAGCTCAAGTCCAGGCGATAGCAAAGCAACTGGTATGTATGTTAAGCCATCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA