Sequence
atgc intronic sequence ATGC exonic sequencegtgaggagatttgtggtttattcttgttggtggatgtaagtgttgtgtgattttggcagGCTGGAGCAAGAATCTGGCTTCTTCTTCAACATGAAGTACCTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC
Basic information
species | Selaginella moellendorffii |
transcript | EFJ36405 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ36405 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 1
--------------------------------gtgaggagatttgtggtttattcttgttggtg-gatgtaa-------gtgttgtgtgattt-tggcagGCTGGAGCAAGAATCTGGCTTCTTCTTCAACATGAAGTACCTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC
|| | | |||| ||| | | | ||||| | | || | | | ||||| |||||||| || || ||||||||||||||||||||| ||||||| ||||||| |||||||||||| || ||||||| || | || || |||
aactaatgttctatttccttgtcacgactattatgttggattcaatggtacatttggtctagcaaggtgtaatttcctaatatggtacattctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAAGGTCCATGCTGGGGAGTGGGATGAAGTGGAGAAATATCTTTCAGGTTTC
upper sequence: EFJ36405 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os08g06480.1 (Oryza sativa), 3'ss of exon 1
----------------------------------------------------gtgagga-gatttgtggtttattcttgttggtggatgtaagtgttgtgtgattttggcagGCTGGAGCAAGAATCTGGCTTCTTCTTCAACATGAAGTACCTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC
|||| | | ||| || || ||| || || || | || | || ||| ||||||| || || | ||||| ||||||||||||| || ||||||| | ||| ||| |||||||||||||||||||||| |||| | || |||
gtaagcgtgtttttcggttgattggagtgagggattttgagccattttgttggtgaatatggtttttgattgtttcccattcgtttttggggttatttcggtcggtt--tagGTTGGAGCAGGAGTCGGCCTTCTACTTCAACATGAAGCACTTTGAAGACCTGGTGCAGGGAGGGGAGTGGGACGAGGTGGAGAAGTACCTCAGCGGGTTC
upper sequence: EFJ36405 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 1
----------------------------------gtgaggagatttgtggtttattcttgttggtggatgtaagtgttgtgtgattt--------tggcagGCTGGAGCAAGAATCTGGCTTCTTCTTCAACATGAAGTACCTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC
|| ||||| | | || | | |||||| || | || | | ||||| |||||||| || || ||||||||||| ||||||||| | || || ||||||| |||||||||||| ||||||||||| |||||||| || |||
aactgatgttgtaccacgttcttttatcccagaaatggaattgcctgtgggctgatatt-ctactacatgtaataattccctacttcacattgtgttgtagGCTTGAGCAAGAGTCAGGGTTCTTCTTCAATATGAAGTACTTCGAGGAGAAGGTCCATGCTGGGGAGTGGGATGAGGTGGAGAGATACTTGTCAGGATTC
upper sequence: EFJ36405 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G116506_T01 (Zea mays), 3'ss of exon 1
---------------------------------gtgaggagatttgtggtttattcttgttggtggatgtaagtgttgtgtgattt--------tggcagGCTGGAGCAAGAATCTGGCTTCTTCTTCAACATGAAGTACCTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC
|| || |||| || | || | ||||| || | || | | ||| | |||||||| || || ||||||||||| ||||||||| |||||| ||| ||| |||||| ||||| |||||||||| |||||||| || |||
actgatgttctcccacgttcttttatcccagaaatggaactatctgtgcgttgatattctactataatgtagtaattccctacttcacattgtgttgtagGTTTGAGCAAGAGTCGGGGTTCTTCTTCAATATGAAGTACTTTGAAGCGAAGGGCCATGCTGGGGACTGGGATGAGGTGGAGAAATACTTGTCAGGTTTC
upper sequence: EFJ36405 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA17G12110.2 (Glycine max), 3'ss of exon 2
--------------------------------------gtgaggagatttgtggttta-ttcttgttggtggatgtaagtgttgtgtgattttggcagGCTGGAGCAAGAATCTGGCTTCTTCTTCAACATGAAGTACCTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC
| | || | | |||| || || || | | | | || ||||| || ||| ||||||||||||| || || ||||| ||||||| ||| |||| ||| ||| ||||||||||||||| |||||||||| |||||||||||| ||
gtacgttagtttacgaaaaaaattaaatttattgcagtttttttatatatttaatttaattttttttattttgtatgtgaatt-tgtgaacgtga-agGTTGGAGCAAGAATCGGGATTTTTCTTTAACATGAGGTATTTTGAGGATATGGTGACGAATGGGGAGTGGGATGAGGTGGAGAAGTACTTGTCTGGTTTT
upper sequence: EFJ36405 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA13G22720.1 (Glycine max), 3'ss of exon 2
---------------------------------------------------------gtgaggagatttgtggtttattcttgttggtggatgtaagtgttgtgtgattttggcagGCTGGAGCAAGAATCTGGCTTCTTCTTCAACATGAAGTACCTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC
| | || | | |||| | ||||| | | | | || ||||| || ||| ||||||||||||| || || ||||| ||||||| ||| |||| ||| ||| ||||||||||||||| |||||||||| |||||||||||| ||
gtacgttagtttttgcgaaaaattaaatttttattccaggtttttgtttttgtttttttttttatatatttaatttaat-ttgttattatgtatctgaatt-tgtgaacgtga-agGTTGGAGCAAGAATCGGGATTTTTCTTTAACATGAGGTATTTTGAGGATATGGTGACGAATGGGGAGTGGGATGAGGTGGAGAAGTACTTGTCTGGTTTT
upper sequence: EFJ36405 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA10G29090.1 (Glycine max), 3'ss of exon 1
------------------------------------------gtgaggagatttgtggtttattcttgttggtggatgtaagtgttgtgtgattttggcagGCTGGAGCAAGAATCTGGCTTCTTCTTCAACATGAAGTACCTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC
| || | | | ||| ||| | | ||| || | | || | ||||||| ||| |||||||||| ||||| ||||||||||||||| |||| || | || ||| ||| |||||||| ||||| |||| |||||| || || ||
tctggttatttagggttttttttataaagaattttcattattatatggcatccactcgactgttcatgtcactcttt-taaatgcttcttaatgtgtgcagGCTTGAGAAAGAATCTGGGTTCTTTTTCAACATGAAGTACTTTGAGGAAAAAGTGCAGGCTGGCGAGTGGGAAGAGGTTGAGAAGTACTTATCAGGATTT
upper sequence: EFJ36405 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 1
------------------------------------------gtgaggagatttgtggtttattcttgttggtggatgtaagtgttgtgtgattttggcagGCTGGAGCAAGAATCTGGCTTCTTCTTCAACATGAAGTACCTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC
| || | | | ||| ||| | | ||| || | | || | ||||||| ||| |||||||||| ||||| || |||||||||||| |||| || | || ||| ||| |||||||| ||||| |||| |||||| || || ||
gcatagcgaagagcctctgggcaatggggtacgaagttttttatatggcatccactcgactgttcatgtcactcttt-taaatgcttcttaatgtgtgcagGCTTGAGAAAGAATCTGGGTTCTTTTTTAACATGAAGTACTTTGAGGAAAAAGTGCAGGCTGGCGAGTGGGAAGAGGTTGAGAAGTACTTATCAGGATTT
upper sequence: EFJ36405 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: AT3G16830.1 (Arabidopsis thaliana), 3'ss of exon 1
------------------------gtgaggagatttgtggtttattcttgttggtggatgtaagtgttgtgtgatt--ttggcagGCTGGAGCAAGAATCTGGCTTCTTCTTCAACATGAAGTACCTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC
||| | |||| | | | | | | ||| | ||| | || || | | ||||| ||||||||||||||||||||||| ||||| |||||| ||||||| | | | ||| |||||||| || ||||||| ||| | ||||| |||
gtaagtttgtgctttgtcgtttttgtgtgcttgtttggtttctctgcgtaattttgggtataatttggaattggttgatgtgtagGCTAGAGCAAGAATCTGGCTTCTTCTTTAACATTAAGTACTTTGAAGAGAAAGCTCTTGCTGGAGAGTGGGATGAAGTGGAGAAGTATCTTTCTGGTTTC
upper sequence: EFJ36405 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------gtgaggagatttgtggtttattc--ttgttggtggatgtaagtgttgtgtgattttggcagGCTGGAGCAAGAATCTGGCTTCTTCTTCAACATGAAGTACCTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC
| || ||||| || | | | | || || | | | | | |||| ||||||||||||| || ||||||||||| ||||||||| ||||||| || || || ||| |||||||| |||||||| | || || ||||| |||
tctgcgttacgtgaagctggtgtcattttcaaaatgtgcatacagacgtttgtttcttctgcaatctgtactgactggttttataataccttctaaccagGTTGGAGCAAGAATCAGGATTCTTCTTCAATATGAAGTACTTTGAAGACCAAGTTCAAGGTGGTGAGTGGGAGGAGGTGGAACGATATTTATCTGGGTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggagatttgtggtttattcttgttggtggatgtaagtgttgtgtgattttggcagGCTGGAGCAAGAATCTGGCTTCTTCTTCAACATGAAGTACCTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC
tttattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaggagatttgtggtttattcttgttggtggatgtaagtgttgtgtgattttggcagGCTGGAGCAAGAATCTGGCTTCTTCTTCAACATGAAGTACCTTGAAGATCAGGTCCAGAATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG