Sequence
atgc intronic sequence ATGC exonic sequencegttctggagctcccttagtttttaactgcgtgagcttcatcctcttgtttggtagCATTGCTTGAATCGGTTTTCCAGGTCGTGGAAATCGCCAAAGGCAGCAAAGTCAAGTATGAGCTCGACAAGCAGAGTGGATTGATCAAG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ27171 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ27171 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os10g26600.1 (Oryza sativa), 3'ss of exon 3
---------gttctggagctcccttagtttttaact--gcgtgagcttcatcctcttgtttggta-gCATT---GCTTGAATCGGTTTTCC----AGGTCGTGGAAATCGCCAAAGGCAGCAAAGTCAAGTATGAGCTCGACAAGCAGAGTGGATTGATCAAG
|| | | || || | || | | | | | | || | | |||| | ||| | |||| |||| || || ||| | || || |||||||| ||||||||||| |||||| ||| |||| ||||||||
gtaagcatcgtgttcataatatatttgtcatcaaattgaagcaaacactgcgatttatttcaggatgcatctggacctgacatgtttttttttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAGACTGGAATGATCAAG
upper sequence: EFJ27171 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 2
------------------gttctggagctcccttagtttttaactg-cgtgagcttcatcctcttgttt---ggtagCATTGCTTGAATCGGTTTTCCAGGTCGTGGAAATCGCCAAAGGCAGCAAAGTCAAGTATGAGCTCGACAAGCAGAGTGGATTGATCAAG
| | || | | | | || || || | ||| || ||| |||||| | ||||| ||||| ||| | ||||| ||||| ||||||||||| || |||||| ||| ||||||||| |||
tatagcaattgcatgatgacaccacacctatataattccattcttgatttgcatttagttttctagtaaaagggtgtttctgcttgttcaatggctgcagGTTGTGGAGATCACTAAAGGAAGCAAGGTCAAGTATGAACTTGACAAGAAGACTGGATTGATTAAG
upper sequence: EFJ27171 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S142_132V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------gttctggagctcccttagttttta--actgcgtgagcttcatcctcttgtttggtagCATTGCTT---GAATCGGTTTTCCAGGTCGTGGAAATCGCCAAAGGCAGCAAAGTCAAGTATGAGCTCGACAAGCAGAGTGGATTGATCAAG----------------------------------
|| ||| | || ||| || || ||| ||| | | |||| || |||| | | ||||| | || || | ||| || |||||||| |||||||||||||||||| ||||||| |||||||||
atctagcaatggttgacattatgggttacatccagccattaggacaagtagattttctgggaattgatccctgagattgatttgggaatttgctgaacagGTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAGAGTGGTTTGATCAAGGTTGATCGTATTCTGTATTCATCTGTTGTGTACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttctggagctcccttagtttttaactgcgtgagcttcatcctcttgtttggtagCATTGCTTGAATCGGTTTTCCAGGTCGTGGAAATCGCCAAAGGCAGCAAAGTCAAGTATGAGCTCGACAAGCAGAGTGGATTGATCAAG
ttttaac putative branch site (score: 2)
cttcatcctcttgttt putative PPT
ttagtttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttctggagctcccttagtttttaactgcgtgagcttcatcctcttgtttggtagCATTGCTTGAATCGGTTTTCCAGGTCGTGGAAATCGCCAAAGGCAGCAAAGTCAAGTATGAGCTCGACAAGCAGAGTGGATTGATCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA