Sequence
atgc intronic sequence ATGC exonic sequencegtgaaagcgatgcgtttgcccacagacattttcttccaggcaagatatctttctttctttctttctatcttttgaatatgaatgagcatgtttatgttgaatccttgcgaagttcctggggatcaaacgagtttttagtttgctagtcttataaacttggactgattttatttttgcagCGACGATACGGCTGCCGAGCGATGATGCTCGAGACTGTCGCTGCGGTCCCGGGGATGGTCGGGGGGATGCTGCTGCACTGCCGCTCGCTTCGCCGGTTCG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ27318 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ27318 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os02g47200.1 (Oryza sativa), 3'ss of exon 2
gtgaaagcgatgcgtttgcccacagacattttcttccaggcaagatatctttctttctttctttctatcttttgaatatgaatgagcatgtttatgttgaatccttgcgaagttcc---tggggatcaaacgagtttttagtttgctagtctta-taaacttggactgattttat--ttttgcagCGACGATACGGCTGCCGAGCGATGATGCTCGAGACTGTCGCTGCGGTCCCGGGGATGGTCGGGGGGATGCTGCTGCACTGCCGCTCGCTTCGCCGGTTCG
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---------------------------------------------------------------------------------------------gtaaccaaccacaactaattttccatcaaagatcatgccaatctat--tttgctgatcgaaatggatgggaatcaatggaacgattttgcagAGGAGGTACGGGTGCCGCGCGATGATGCTGGAGACGGTGGCGGCGGTGCCGGGGATGGTGGGCGGCATGCTGCTGCACCTCCGGTCGCTCCGCCGCTTCG
upper sequence: EFJ27318 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os04g51150.1 (Oryza sativa), 3'ss of exon 2
gtgaaagcgatgcgtttgcccacagacattttcttccaggcaagatatctttctttctttctttctatcttttgaatatgaatgagcatgtttatgttgaatccttgcgaagttcctggggatcaaacgagtttttagtttgctagtcttataaact-tggactgattttatttttgcagCGACGATACGGCTGCCGAGCGATGATGCTCGAGACTGTCGCTGCGGTCCCGGGGATGGTCGGGGGGATGCTGCTGCACTGCCGCTCGCTTCGCCGGTTCG
| |||| | ||| | || || | || | || | | | | || | | | | ||| | || || | |||| | | || |||||||| ||||||||||| ||||| || || ||||| ||||||||||| || || |||||||| ||| ||| || || || || ||||
---------------------------------------------------------------------------acatga-tatccatttcta-gtagtatgtggaaatgatctctagtcggtcgctaattgctgtaactgtcaatggttaacactgcaaattgggttgggt---gcagAGGAGGTATGGCTGCCGCGCGATGATGCTGGAGACGGTGGCGGCGGTGCCGGGGATGGTGGGCGGCATGCTGCTCCACCTCCGGTCCCTCCGGCGCTTCG
upper sequence: EFJ27318 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os02g21300.1 (Oryza sativa), 3'ss of exon 2
gtgaaagcgatgcgtttgcccacagacattttcttccaggcaagatatctttctttctttctttctatcttttgaatatgaatgagcatgtttatgttgaatccttgcgaagttcctggggatcaaacgagtttttagtttgctagtcttataaacttggactgattttatttttg-cagCGACGATACGGCTGCCGAGCGATGATGCTCGAGACTGTCGCTGCGGTCCCGGGGATGGTCGGGGGGATGCTGCTGCACTGCCGCTCGCTTCGCCGGTTCG
||| || | | || ||| || | | | || | | ||| | || || | || | | | ||| ||| | | ||||| ||||| ||||||||||| ||||| || || ||||| ||||||||||| | || | ||||||| || ||||| || |||||||
-------------------------------------------------------------------------------gaagcgattaattcgtatcgagag-ttgataattgatcagattgctaatcaactagtagcagcaatgatgaatgaattctgatggtcaatttggttgtcagAGGAGGTACGGGTGCCGGGCGATGATGCTGGAGACGGTGGCGGCGGTGCCGGGGATGGTGGCCGGCGCGGTGCTGCATCTGCGTTCGCTGCGGCGGTTCG
upper sequence: EFJ27318 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AC233960.1_FGT002 (Zea mays), 3'ss of exon 2
gtgaaagcgatgcgtttgcccacagacattttcttccaggcaagatatctttctttctttctttctatcttttgaatatg-aatgagcatgtttatgttgaatccttgcgaagt--tcctggggatcaaacgagtttttagtttgctagtcttataaacttggactgattttatttttgcagCGACGATACGGCTGCCGAGCGATGATGCTCGAGACTGTCGCTGCGGTCCCGGGGATGGTCGGGGGGATGCTGCTGCACTGCCGCTCGCTTCGCCGGTTCG
| ||| | | | | | |||| || | | || | | || | || ||| |||| || || | |||| | || ||| | || ||| || || || ||| | ||| | | ||||||||||| || |||||||| || || || || ||||| ||||||||||| || || |||||||| ||| |||||||| ||||| ||||
-------------------------------------------gtgatccctgctcgccccaaccatttccctgaacatccagtctccaagactccaacaaaacggggcagagtcaccctgctgaagaattggattttccgattacta-ttttgctaacatga--cgagttaattgtctcagAGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGCCGGGGATGGTGGGCGGCATGCTGCTTCACCTGCGCTCGCTCCGCCGCTTCG
upper sequence: EFJ27318 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G125669_T01 (Zea mays), 3'ss of exon 2
gtgaaagcgatgcgtttgcccacagacattttcttccaggcaagatatctttctttctttctttctatcttttgaatatgaatgagcatgtttatgttgaatccttgcgaagttcctggggatcaaacgagt-ttttagtttgctagtcttataaacttggactgattttatttttgcagCGACGATACGGCTGCCGAGCGATGATGCTCGAGACTGTCGCTGCGGTCCCGGGGATGGTCGGGGGGATGCTGCTGCACTGCCGCTCGCTTCGCCGGTTCG
| | ||| |||| | |||| ||| || | | ||| | || ||||| | || | | || ||| | | | || |||| | ||| | ||||| | || || |||||||| ||||||||||| || || || |||||||| || |||||||| || || |||||||| ||| ||||| || ||||| ||||
------------------------------------------------------------------gcatgtcgaa-atga-tctgcatattt-tgaaggaaggttgaaaggtc------gatcattcatgtgctgttgtaagctgaccctgtgaa-ttgggcgaattgt----ctgcagAGGCGGTATGGCTGCCGGGCGATGATGCTGGAAACCGTGGCTGCGGTGCCTGGGATGGTGGGCGGCATGCTGCTCCACCTGCGCTCACTCCGCCGCTTCG
upper sequence: EFJ27318 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AT1G32350.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgaaagcgatgcgtttgcccacagacattttcttccaggcaagatatctttctttctttctttctatcttttgaatatgaatgagcatgtttatgttgaatccttgcgaagttcctggggatcaaacgagtttttagtttgctagtcttataaacttggactgattttatttttg----cagCGACGATACGGCTGCCGAGCGATGATGCTCGAGACTGTCGCTGCGGTCCCGGGGATGGTCGGGGGGATGCTGCTGCACTGCCGCTCGCTTCGCCGGTTCG
| | | ||| || | |||| | | ||| |||| | | ||| | |||| ||| | | ||| | || | |||| ||||||| || | || |||| |||||| |||| ||||| || |||||||| ||||| ||||||||||||||||| |||||| || || || ||||||
-------------------------------------------------------------------------gtaatttaatcagaaattttaaatc---ttcttcatttgttcttttatttttaacatgattttgtttt------ttcaaaaatt--gaataatttgatttttgagtatagAGGAAGCACATGTGCCATGCGATGTTGCTAGAGACGGTGGCTGCGGTGCCGGGAATGGTCGGGGGGATGCTTTTGCACTTGAAATCTCTCCGGAGGTTCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaacgagtttttagtttgctagtcttataaacttggactgattttatttttgcagCGACGATACGGCTGCCGAGCGATGATGCTCGAGACTGTCGCTGCGGTCCCGGGGATGGTCGGGGGGATGCTGCTGCACTGCCGCTCGCTTCGCCGGTTCG
gactgat putative branch site (score: 3)
ttttattttt CT-rich tract
actgattttattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaaagcgatgcgtttgcccacagacattttcttccaggcaagatatctttctttctttctttctatcttttgaatatgaatgagcatgtttatgttgaatccttgcgaagttcctggggatcaaacgagtttttagtttgctagtcttataaacttggactgattttatttttgcagCGACGATACGGCTGCCGAGCGATGATGCTCGAGACTGTCGCTGCGGTCCCGGGGATGGTCGGGGGGATGCTGCTGCACTGCCGCTCGCTTCGCCGGTTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC