Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgattcccctcccctcgctctcgatcgattcgtgcttcttcctgtggtggattgattggttttctctcttttttttttgtgtgtgttcttcgtgttcttcgtgctgtttagAGGACAAGTACCCCTCCGAGGTGGTCCGCGCGGAGCTCTCCACGAAATTGAGCCTCACGGACAGGCAGCTCCAGATGTGGTTCTGCCACCGGCGGCTCAA
Basic information
species | Selaginella moellendorffii |
transcript | EFJ11318 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ11353 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os05g48820.1 (Oryza sativa), 3'ss of exon 1
----gtgagtgattcccctcccctcgctctcgatc-----gattcgtgcttct-tcctgtggtggattgattggttttc---------tctcttttttttttgtgtgtgttcttcgtgttcttcgtgctgtt-tagAGGACAAGTACCCCTCCGAGGTGGTCCGCGCGGAGCTCTCCACGAAATTGAGCCTCACGGACAGGCAGCTCCAGATGTGGTTCTGCCACCGGCGGCTCAA
||| |||| || || ||| ||| | || | ||| | |||| | | |||| | | | ||| |||| | ||| || || | ||| || | |||||| ||| || ||| | | | |||||| | || ||| || | || |||||||||||||| |||||||||||||||||||||||| | ||
gttcgtggatgatggcctatgggggactggggattctggaaatttttagggctatttcgtgtttgatttgtcgatttttcgatcgaaacagccctgtgatttctgtgcttacttggttttgtctgtgttgctgcagAGGATCCGTATCCAAATGAGACGATGAGAGCGGAGTTGTCTGTGAAGTTAGGGCTGACGGACAGGCAGCTGCAGATGTGGTTCTGCCACCGGCGGTTGAA
upper sequence: EFJ11353 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os01g48170.1 (Oryza sativa), 3'ss of exon 1
gtgagtg-attcccctcccctcgc---tctcgatcgattcgtgcttcttcctgtggtggattgattggttttctctcttttttttttgtgtgtgttcttcgtgttcttcgtgctgtttagAGGACAAGTACCCCTCCGAGGTGGTCCGCGCGGAGCTCTCCACGAAATTGAGCCTCACGGACAGGCAGCTCCAGATGTGGTTCTGCCACCGGCGGCTCAA
||| ||| |||| | | || || || | || | ||| ||||| |||| | | |||| |||| || | ||| | || || || || ||| ||||||| || ||| | || |||||||| ||| |||| | || | | ||||||||||| || ||||||||||| ||||||||||| ||
gtgcgtggattctgatggttttgcgaggctttggaagtttggagaattttttttggaggattt-ttgggtggggaattgaggttttggtgtttggggat-gtgattttggtttggtgcagTGGAGCAGTACCCGTCGGAGACCTTGCGGGCGGAGCTGTCCGCGAAGATAGGCTTGTCAGACAGGCAGCTGCAAATGTGGTTCTGTCACCGGCGGCTGAA
upper sequence: EFJ11353 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G122750_T01 (Zea mays), 3'ss of exon 1
gtgagtgattcccctcccctcgctctcgatcgattcgtgcttcttcctgtggtggattgattggttttctctcttttttttttgtgtgtgttcttcgtgttcttcgtgctgtttagAGGACAAGTACCCCTCCGAGGTGGTCCGCGCGGAGCTCTCCACGAAATTGAGCCTCACGGACAGGCAGCTCCAGATGTGGTTCTGCCACCGGCGGCTCAA
| | || ||| || || | || | | | | || || ||| || | ||||| || | | ||||| || |||||| |||||| |||| | || |||||||| || | | || | |||||||||||||||||| |||||||||||||||||||| ||||||||
-------------gttcgtcgactactgat-gactctgaatgttttgggggtttgtttttgcgggcctctgatcgaattgtgcttgtgtttttcatggggatttcgt-ttgcgcagAGGATTCGTACCCAAACGAGACGAAGCGGGCGGAGCTATCGGTGCAGTTAAACCTCACGGACAGGCAGCTGCAGATGTGGTTCTGCCACCGCCGGCTCAA
upper sequence: EFJ11353 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G125294_T01 (Zea mays), 3'ss of exon 1
gtgagtgattcccctcccctcgctctcgatcgattcgtgcttcttcctgtggtggattgattggttttctctcttttttttttgtgtgtgttcttcgtgtt--cttcgtgctgtttagAGGACAAGTACCCCTCCGAGGTGGTCCGCGCGGAGCTCTCCACGAAATTGAGCCTCACGGACAGGCAGCTCCAGATGTGGTTCTGCCACCGGCGGCTCAA
| | ||| | ||| ||||| || |||| || ||| | | | | || ||||| | ||| || | || || ||||||| ||| ||| |||| | || |||||||| || | | |||| |||||| ||||||||||| |||||||||||||||||||| ||||||||
-------------gttcgtcggctattgat-gattctgaaacgttttgatggtttgttt-ttgcgagcttttgatcgaactgtgcgtgtggttttcatggggattctgttttgcgcagAGGACTCGTATCCCAACGAGACGAAGCGGGCGGAGCTGTCGGTGCAGTTGAACCTCACAGACAGGCAGCTTCAGATGTGGTTCTGCCACCGCCGGCTCAA
upper sequence: EFJ11353 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G060541_T01 (Zea mays), 3'ss of exon 1
--gtgagtgattcccctcccctcgctctcgatcgattcgtgcttcttcctgtggtggatt---gattggttttctctcttttttttttgtgtgtgttcttcgtgttcttcgtgctgtttagAGGACAAGTACCCCTCCGAGGTGGTCCGCGCGGAGCTCTCCACGAAATTGAGCCTCACGGACAGGCAGCTCCAGATGTGGTTCTGCCACCGGCGGCTCAA
|| | || | | | || | | || || || ||| | | | | | |||| | | |||| | | || | ||| | | | ||||| || ||| | || || ||||| | || |||||| || |||| | | || ||||||||||||| || ||||||||||||||||| || |||||
gtttgtggaatgaggattttgatgaatccattcaaat-gtttttttttgtgttcttcctccccgctggtttttttgggtgcttttatcgattgagcatttctgggtggtt-tgctgc--agTGGAGCATTATCCGTCCGAAGCTAAGCGGCTGGAGCTGTCAGCGAAGATAGGGCTTTCGGACAGGCAGCTGCAAATGTGGTTCTGCCACCGCCGCCTCAA
upper sequence: EFJ11353 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G159357_T01 (Zea mays), 3'ss of exon 1
gtgagtgattcccctcccctcgctctcgatcga----ttcgtgcttcttcctgtggtggattgattggttttctctcttttttttttgtgtgtgttcttcgtgttcttcgtgctgtttagAGGACAAGTACCCCTCCGAGGTGGTCCGCGCGGAGCTCTCCACGAAATTGAGCCTCACGGACAGGCAGCTCCAGATGTGGTTCTGCCACCGGCGGCTCAA
| | | | ||||| | || ||| | | || |||||| | ||| |||| | ||| | | ||| | ||| || || | || ||| ||||||| || || | | || |||||| || |||| | | || ||||||||||||| || ||||||||||||||||| || |||||
--------------gttcgtggatttcgatgaagtgttttgtgttcttccccaccctggatttttgggtg------ctttatcgattgagcat-ttccgggggtttttggtttgctgcagTGGAGCAGTACCCGTCGGAAGCTATGCGGCTGGAGCTGTCGGCGAAGATAGGGCTGTCGGACAGGCAGCTGCAAATGTGGTTCTGCCACCGCCGCCTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggttttctctcttttttttttgtgtgtgttcttcgtgttcttcgtgctgtttagAGGACAAGTACCCCTCCGAGGTGGTCCGCGCGGAGCTCTCCACGAAATTGAGCCTCACGGACAGGCAGCTCCAGATGTGGTTCTGCCACCGGCGGCTCAA
ttcttcgt CT-rich tract
tctctttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgattcccctcccctcgctctcgatcgattcgtgcttcttcctgtggtggattgattggttttctctcttttttttttgtgtgtgttcttcgtgttcttcgtgctgtttagAGGACAAGTACCCCTCCGAGGTGGTCCGCGCGGAGCTCTCCACGAAATTGAGCCTCACGGACAGGCAGCTCCAGATGTGGTTCTGCCACCGGCGGCTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG