Sequence
atgc intronic sequence ATGC exonic sequencegtattttaaaaggtttcttaagctgaacctaattcactgaactgattgacagAACAATCTACACGAGTTATGGGCTCTTCTTAACTTTCTGCTGCCGGAGATTTTCAGCTCTGCTGAAACATTCGACGAATGGTTTCAAATATCTGGCGAAA
Basic information
species | Selaginella moellendorffii |
transcript | EFJ15818 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ15818 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 7
------------------------------------------------------------------gtattttaaaaggtttcttaagctgaacc----taattcactgaac---tgattga------cagAACAATCTACACGAGTTATGGGCTCTTCTTAACTTTCTGCTGCCGGAGATTTTCAGCTCTGCTGAAACATTCGACGAATGGTTTCAAATATCTGGCGAAA
|| | || ||| || | | |||||| ||| ||||||| ||||| ||||| || ||| | ||| |||| || ||||| || |||| || || || ||||||||||||||||| || |||||||||||||| ||||| ||||
gtaggtctcccctggctgtgctctttttttggactgtagccatggtcaaagtaattatgttggtttacatcctcaagcatttttttgcttttattctgataattcgttgatgctatgattgatgtttgcagAATAATCTCCATGAGCTTTGGTCTCTCCTCAACTTCTTGTTGCCTGAAATATTTAGCTCTGCTGAAACATTTGATGAATGGTTTCAAATTTCTGGTGAAA
upper sequence: EFJ15818 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 7
--------------------------------------------------------------------gtattttaaaaggtttcttaagctgaacct---aattcactgaac---tgattga------cagAACAATCTACACGAGTTATGGGCTCTTCTTAACTTTCTGCTGCCGGAGATTTTCAGCTCTGCTGAAACATTCGACGAATGGTTTCAAATATCTGGCGAAA
| | || ||| || | | || ||||| ||| ||||||| ||||| ||||| || ||| | ||| |||| || ||||| || |||| || || || ||||||||||||||||| || |||||||||||||| ||||| ||||
gtaggtctcccctggctgtgctctttttttggactgtagccatggtcaaagtaattatgttggtttacattcctcaagcatttttttgcttttattctgataattcgttgatgctatgattgatgtttgcagAATAATCTCCATGAGCTTTGGTCTCTCCTCAACTTCTTGTTGCCTGAAATATTTAGCTCTGCTGAAACATTTGATGAATGGTTTCAAATTTCTGGTGAAA
upper sequence: EFJ15818 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 7
-----------------------------------------------gtattttaaaaggtttcttaagctgaacctaattcactgaactgat-tgacagAACAATCTACACGAGTTATGGGCTCTTCTTAACTTTCTGCTGCCGGAGATTTTCAGCTCTGCTGAAACATTCGACGAATGGTTTCAAATATCTGGCGAAA
|| |||| | || | | | | || | |||| | ||||||||||| ||||| | ||||||||||| |||||||| |||| || || || || ||||||||||| || || |||||||||||||| ||||| ||||
tgaaatctgaatcttatttccctttcattggttgcatgtgtaagcgataatgttaatacacttaagtaattaatgtgatttgtttcttttgatattgcagAACAATCTTCACGAACTCTGGGCTCTTCTCAACTTTCTTTTGCCTGAAATATTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA
upper sequence: EFJ15818 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 7
----------------------------------------------------gtattttaaaaggtttcttaagctgaacctaattcactgaactgattgacagAACAATCTACACGAGTTATGGGCTCTTCTTAACTTTCTGCTGCCGGAGATTTTCAGCTCTGCTGAAACATTCGACGAATGGTTTCAAATATCTGGCGAAA
| || | ||| ||| | || | || || | || | |||||| ||||| || || | ||| ||||||| |||||||| ||||| || ||||| || ||||||||||| || || |||||||||||||| ||||| ||||
tatgcttttctagcttattttgaaatctgaactattatttttttgtttgtatgcatcctcaaatatttactggtgtgtat-tatctctttcaatggc---acagAATAATCTTCATGAACTCTGGTCTCTTCTCAACTTTCTTCTGCCCGAAATTTTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA
upper sequence: EFJ15818 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 7
----------------------------------------------------gtattttaaaaggtttcttaagctgaacctaattcactgaactgattgacagAACAATCTACACGAGTTATGGGCTCTTCTTAACTTTCTGCTGCCGGAGATTTTCAGCTCTGCTGAAACATTCGACGAATGGTTTCAAATATCTGGCGAAA
| || | ||| ||| || || | || | | || |||||| || || || || | ||| ||||||| |||||||| ||||| || ||||| || ||||||||||| || || |||||||||||||| ||||| ||||
tgcttttctaccttgttttgaaatcttaattattttttttgtttgtttgtatgcatcctcaaatatttactag--tgtctattatcacttttattggc--acagAATAACCTTCATGAACTCTGGTCTCTTCTCAACTTTCTTCTGCCCGAAATTTTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA
upper sequence: EFJ15818 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 7
---------------------------------------gtattttaaaaggttt-----cttaagc--tgaacctaattcactgaactgattg--acagAACAATCTACACGAGTTATGGGCTCTTCTTAACTTTCTGCTGCCGGAGATTTTCAGCTCTGCTGAAACATTCGACGAATGGTTTCAAATATCTGGCGAAA
||| | | || ||| |||||| | || | ||| | | | ||||||||||| || || | ||||||||||| |||||||| |||| || || || || ||||||||||| || || |||||||||||||| ||||| ||||
ttgaaatctgaatttttttccttttcatttgttgcataggtaagtgataatgttaatacacttaagtaattaatgtgatttgtttcttttgacgttgcagAACAATCTTCATGAACTCTGGGCTCTTCTCAACTTTCTTTTGCCTGAAATATTTAGTTCTGCTGAAACTTTTGATGAATGGTTTCAAATCTCTGGTGAAA
upper sequence: EFJ15818 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 7
---------------------------------------------------------------------------------------------------------------------------------------------gtattttaaaaggtttcttaagctgaacctaatt-cactgaactgattga--cagAACAATCTACACGAGTTATGGGCTCTTCTTAACTTTCTGCTGCCGGAGATTTTCAGCTCTGCTGAAACATTCGACGAATGGTTTCAAATATCTGGCGAAA
|| || || | | | ||| || | | || || || | ||||| ||||| || || | ||||||||||| || ||||| ||||| |||||||| || || || || || || || |||||||||||||| ||||| || |
gtgtttgctctatcttattcttgaatatttggacattgaagttttctttgttaagttgcttctaattgaatgttgaaacaacctttcttgtacggctctgtttgcactcttaacttttgcttttccgggcacttttaatatttaccgtataatgactgtgtagcctgctgtactcatattgtcctcatatatgcagAATAATCTCCATGAACTGTGGGCTCTTCTAAATTTTCTTCTGCCTGAGATTTTTAGTTCAGCAGAGACTTTTGATGAATGGTTTCAAATTTCTGGTGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtattttaaaaggtttcttaagctgaacctaattcactgaactgattgacagAACAATCTACACGAGTTATGGGCTCTTCTTAACTTTCTGCTGCCGGAGATTTTCAGCTCTGCTGAAACATTCGACGAATGGTTTCAAATATCTGGCGAAA
aactgat putative branch site (score: 3)
attttaaaaggttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttaaaaggtttcttaagctgaacctaattcactgaactgattgacagAACAATCTACACGAGTTATGGGCTCTTCTTAACTTTCTGCTGCCGGAGATTTTCAGCTCTGCTGAAACATTCGACGAATGGTTTCAAATATCTGGCGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC