Sequence
atgc intronic sequence ATGC exonic sequencegttattagactcttgccaatcactccggtgctgatgctctcgtgattttttcaggtggagcatgttagAGCAGAGCGTAATCTCCTAGCAGAGGTTGACAGTAATTGTATAGTGAAACTCTTTTGTTCCTTTCAAGACGATGAATATTTGTATCTCATCATGGAGTAT
Basic information
species | Selaginella moellendorffii |
transcript | EFJ29515 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA03G32160.1 (Glycine max), 3'ss of exon 3
------------------------------------------------gttattagactcttgccaa-tcactccggtgctgatgctctcgtgattttttcaggtggagcatgttagAGCAGAGCGTAATCTCCTAGCAGAGGTTGACAGTAATTGTATAGTGAAACTCTTTTGTTCCTTTCAAGACGATGAATATTTGTATCTCATCATGGAGTAT
| ||| | | || ||| | | || ||| | | | ||| ||| |||| || ||||||||||| || | ||||||||||||||||||||||| ||||| ||||| ||||| | |||||| |||||||| || |||||||||||||
gttagcaaccatttgtcttctacattatattctacaaactaatgtttttatgttaaaggataatgaagtcatcacacttctaatgttgt--taattattttagGTAGAACATGTTAGAGCTGAAAGGAATCTCCTAGCAGAGGTTGACAGCAATTGCATAGTTAAACTTTATTGTTCTTTTCAAGATGACGAATATTTGTATC--------------
upper sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA13G18670.1 (Glycine max), 3'ss of exon 3
------------------------------------------------------gttattagactcttgccaatcactccg--gtgctgatgc---tctcgtgattttttcaggtggagcatgttagAGCAGAGCGTAATCTCCTAGCAGAGGTTGACAGTAATTGTATAGTGAAACTCTTTTGTTCCTTTCAAGACGATGAATATTTGTATCTCATCATGGAGTAT
||| | || | | |||| | | | || || | | | | || ||||||||| |||||||||| ||| || | |||||||| |||||||||||||| ||||| ||||| || || | |||||| || ||||| ||||||||||||||||
gtttacaatcattgatcttgccagattatgttattccagtccagatattagtagtttaaatgcctatggtcaataaagtcatcatacttattcctatttgttaatattttcagGTTGAGCATGTTAAAGCTGAAAGGAATCTCCTCGCAGAGGTTGACAGAAATTGCATAGTCAAGCTTTATTGTTCTTTCCAAGATGATGAATATTTGTATC--------------
upper sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA10G04410.2 (Glycine max), 3'ss of exon 4
-------------------------------------------------------------------gttattagactcttgccaatcactccggtgctgatgctctcgtgattttttcaggtggagcatgttagAGCAGAGCGTAATCTCCTAGCAGAGGTTGACAGTAATTGTATAGTGAAACTCTTTTGTTCCTTTCAAGACGATGAATATTTGTATCTCATCATGGAGTAT
|| | || || | | | | | | | || | | || ||||||||| |||||||||| ||| || | |||||||| |||||||||||||| ||||| ||||| || || | |||||| || || || |||||| |||||||||
gttacaatcattgatcttgctagattatgttattccagtccagatattagtagtttaaatgcctatggtcaataaggtcatcatactttatact-tattcctgtttgt-taatattttcagGTTGAGCATGTTAAAGCCGAAAGGAATCTCCTTGCAGAGGTTGACAGCAATTGCATAGTCAAGCTTTATTGTTCTTTCCAGGATGATGAACATTTGTATC--------------
upper sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA19G34920.1 (Glycine max), 3'ss of exon 3
-------------------------------------------gttattagactcttg-ccaatcactccg--gtgctgatgctctcgt-gattttttcaggtggagcatgttagAGCAGAGCGTAATCTCCTAGCAGAGGTTGACAGTAATTGTATAGTGAAACTCTTTTGTTCCTTTCAAGACGATGAATATTTGTATCTCATCATGGAGTAT
||| ||| | | ||| | | | | || | | | || ||| ||| |||| || ||||||||||| || | ||||| || ||||||||||||| ||||| ||||| ||||| | |||||| |||||||| || |||||||||||||
gttagtaaccatttgtcttctacattatatcctacaaaaaatagtttttatgttaaaggttaatgaatacatcatacttctaattttgttaattattttagGTAGAACATGTTAGAGCTGAAAGGAATCTTCTGGCAGAGGTTGACAACAATTGCATAGTTAAACTTTATTGTTCTTTTCAAGATGACGAATATTTGTATC--------------
upper sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 3
-------------gttattagactcttgc--caatcactccggtgctg-atgctctcgtga---ttttttcaggtggagcatgttagAGCAGAGCGTAATCTCCTAGCAGAGGTTGACAGTAATTGTATAGTGAAACTCTTTTGTTCCTTTCAAGACGATGAATATTTGTATCTCATCATGGAGTAT
|| ||||| ||| || | | | | ||| | | | ||||||||||| || ||||| | ||| ||| | ||||| || || || |||||||| ||||| || || ||||| | ||||||||||||||| || || ||||| ||||
gtgaaattatcacattgttagagacttagagtaaatattgttttcttatatgtattggatacacttttttcagGTTGAACATGTCAAAGCTGAGAGAAATCTACTTGCTGAAGTTGACAGCAATTGCATTGTTAAACTTTATTGTTCCTTTCAAGATGAGGAGTATTTATATC--------------
upper sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 4
-----------------------gttattagactcttgccaatcact-ccggtgctgatgctctcgtgat--tttttcaggtggagcatgttagAGCAGAGCGTAATCTCCTAGCAGAGGTTGACAGTAATTGTATAGTGAAACTCTTTTGTTCCTTTCAAGACGATGAATATTTGTATCTCATCATGGAGTAT
|| || | ||| || | || | | |||| ||||||||||||||||||| | ||||||| | ||| | || |||||||||||||| ||||| || ||||| || | |||||| |||||||| || || ||||||||||
gtatctccttcaagctgcttttgtttgatatatctttgtttattatcgttcatgtttgttgaaatctgattctttttcagGTGGAGCATGTGAAAGCAGAGAGAAATTTACTTGCAGAGGTTGACAGCAATTGCATTGTGAAGCTGTATTGTTCTTTTCAAGATGAAGAGTATTTGTATC--------------
upper sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: AT1G03920.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------gttattagactcttg---ccaatcactccggtgctgatgctctcgtgattttttc--aggtggagcatgttagAGCAGAGCGTAATCTCCTAGCAGAGGTTGACAGTAATTGTATAGTGAAACTCTTTTGTTCCTTTCAAGACGATGAATATTTGTATCTCATCATGGAGTAT
||| | | | | | | | | | | | | |||| || ||||||||||||| ||||||||| | ||||| | ||||| || || ||||| ||||||||||| || | ||||| ||||||||| |||| ||| | ||||
gttacataatgtgacccacattgcattttcggttttacgaattttttttttttttttttgaaaatttctttgtagGTGGAGCATGTAAGAGCAGAGAGGAATCTATTGGCAGAAGTAGATAGTAACTGTATAGTGAAGCTTTACTGTTCTTTTCAAGACAATGAGTATCTTTATC--------------
upper sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S22_429V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------------------------------------------------------------------------------------gttattagactct--tgccaatcactccg--gtgctgatgctctcgtga---ttttttcaggtggagcatgttagAGCAGAGCGTAATCTCCTAGCAGAGGTTGACAGTAATTGTATAGTGAAACTCTTTTGTTCCTTTCAAGACGATGAATATTTGTATCTCATCATGGAGTAT
|| || | ||| | || ||| | | || | | | || |||||||||||||| | |||||| | ||| | || ||||||||||||||||| || |||||||| | | ||| |||||||||||||| | || |||||
gtacgtcacgtgtatatatgtggaagttgtttatagaattgtatctgtctttatttgccgtttgccaaaatcatataactctgaagaatcgactgaaggtcaaatctggagttattgttatgttttgttactcactttagtaatcgaaatctgaaggggattactttaccattttaatcaatggataaacactattgcagGTGGAGCATGTAAAGGCAGAGAGAAATTTGCTTGCAGAGGTTGACAGTAACTGCATAGTGAAGTTATATTGCTCCTTTCAAGACGAGAAGTACTTGTACT--------------
upper sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S86_100V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------------gttattag--actcttgccaatcactccggtgctga------tgctctc--------gtgattttttcaggtggagcatgttagAGCAGAGCGTAATCTCCTAGCAGAGGTTGACAGTAATTGTATAGTGAAACTCTTTTGTTCCTTTCAAGACGATGAATATTTGTATCTCATCATGGAGTAT
||| |||| | | | | ||| || || || | |||| || ||| | || ||||| |||||||||| ||||||| | ||||| || || || |||||||| || ||||| ||||| | | |||||| ||||||||||| || || |||||
ccgttgttttcatgcttgatatgcatacaagttcttagggagtttaccttatccttcttgtacttaaccatgtgctttcaacgcaacgtggtcttggcagGTAGAGCATGTTAAAGCAGAGAGAAATCTACTCGCTGAAGTTGACAGCAACTGTATTGTGAAGTTGTATTGTTCATTTCAAGACGAGGATTACTTGTACT-------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgccaatcactccggtgctgatgctctcgtgattttttcaggtggagcatgttagAGCAGAGCGTAATCTCCTAGCAGAGGTTGACAGTAATTGTATAGTGAAACTCTTTTGTTCCTTTCAAGACGATGAATATTTGTATCTCATCATGGAGTAT
tgctgat putative branch site (score: 3)
tgatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttattagactcttgccaatcactccggtgctgatgctctcgtgattttttcaggtggagcatgttagAGCAGAGCGTAATCTCCTAGCAGAGGTTGACAGTAATTGTATAGTGAAACTCTTTTGTTCCTTTCAAGACGATGAATATTTGTATCTCATCATGGAGTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA