Sequence
atgc intronic sequence ATGC exonic sequencegtttgtgatgctcgcgctttagttggtccttgacgacggagtgtgtttttttttttttttgctctccagGCGGTGTGCACGGAGGCTGGAATGTTTGCTCTGCGAGAGAGGCGCGTTCATGTCACCCAGGAAGACTTCGACATGCCGGTGGCCAAAGTGATGAAGAAGG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ04162 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ04162 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: LOC_Os06g39870.1 (Oryza sativa), 3'ss of exon 6
--------------------------------gtttgtgatgctcgcgctttagttggtccttgacgacggagtgtgtttttttttttttttgctctccagGCGGTGTGCACGGAGGCTGGAATGTTTGCTCTGCGAGAGAGGCGCGTTCATGTCACCCAGGAAGACTTCGACATGCCGGTGGCCAAAGTGATGAAGAAGG
|| || | || | | || | | || | || |||| ||| | | | || ||||||| |||||||| || ||||||||||| || || ||||| | |||||||||| |||||| || ||| ||| ||||||| || |||||||||||||
atgcactccattttgcatctgttgtgctccatattgatgctatcagctatatcactgtacataagttactcaccttgattttcacctttctgggtttc-agGCGGTCTGCACGGAAGCAGGAATGTTTGCCCTTCGCGAGAGAAGGGTTCATGTCAACCAGGAGGATTTCTTGATGGCGGTGGCGAAGGTGATGAAGAAGG
upper sequence: EFJ04162 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 8
----------------------------gtttgtgatgctcgcgctttagttggtccttgacgacg-gagtgtgtttttttttttttttgc--tctccagGCGGTGTGCACGGAGGCTGGAATGTTTGCTCTGCGAGAGAGGCGCGTTCATGTCACCCAGGAAGACTTCGACATGCCGGTGGCCAAAGTGATGAAGAAGG
| || || | | ||| | | | | | || ||| | ||| ||| |||||||| ||||| || ||||||||||||||||| || ||||| | || ||||| || || || ||||| || ||| | ||||| || ||||||||||| |
ttcaaaacaatgtgcatatatacacagcactatagaacgtcatagctcctataccttgtgatcatgcaactttattcactttctctttcatcatcttcagGCGGTCTGCACAGAAGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCATGTAACACAAGAGGACTTTGAGATGGCAGTGGCGAAGGTGATGAAGAAAG
upper sequence: EFJ04162 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 8
---------------------gtttgtgatgctcgcg----ctttag-ttggtccttg-acgacggagtgtgtttttttttttttttgctctc----cagGCGGTGTGCACGGAGGCTGGAATGTTTGCTCTGCGAGAGAGGCGCGTTCATGTCACCCAGGAAGACTTCGACATGCCGGTGGCCAAAGTGATGAAGAAGG
|||||||| | || ||| || || ||| | || | | | ||| |||||||| | | ||||| || ||||| |||||||||||||||||||| || ||||| | || || || |||||||| |||||||| ||| | |||||||| ||||||||||| |
tttcaatgcttattaccaagcatttgtgatcgttatagttcctatagctttgtgtttgtgtttcagactttttcctttcatttttttggtgttggttcagGCCGTCTGCACAGAGGCTGGAATGTTTGCTCTTCGTGAGAGAAGGGTGCACGTTACCCAGGAGGACTTCGAGATGGCAGTGGCCAAGGTGATGAAGAAAG
upper sequence: EFJ04162 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 8
------------------------------gtttgtgatgctcgcgctttagttggtccttga--cgacggagtgtgtt-tttttttttttttgctctccagGCGGTGTGCACGGAGGCTGGAATGTTTGCTCTGCGAGAGAGGCGCGTTCATGTCACCCAGGAAGACTTCGACATGCCGGTGGCCAAAGTGATGAAGAAGG
||||| ||| || || | | |||| ||| | | || | |||||||||| ||| | ||||| || || || |||||||||||||||||||| || ||||| | || || || || ||||| |||||||| ||| | |||||||| ||||||||||| |
gtttgttaaatccacttcatctgatgaactgtttgctgc-ctctcgtttcaatcttgtgttgattcgaagtaacgtttaacattttttttttggctgttcagGCCGTCTGTACAGAGGCTGGAATGTTTGCTCTCCGTGAGAGAAGGGTGCACGTTACACAGGAGGACTTCGAGATGGCAGTGGCCAAGGTGATGAAGAAAG
upper sequence: EFJ04162 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 8
--------gtttgtgatgctcgcgctttagttggtccttgacgacggagtgtgtttttttttt-tttttgctct------ccagGCGGTGTGCACGGAGGCTGGAATGTTTGCTCTGCGAGAGAGGCGCGTTCATGTCACCCAGGAAGACTTCGACATGCCGGTGGCCAAAGTGATGAAGAAGG
||| | | ||| | || | || || | || || | | | || | |||||| | ||||| |||||||||||||| ||||||||||||||||| |||||| | || || || || || |||||||| || ||| |||||||||| || |||||||| |
gtaaagtgttttctatttctctacttctatcttgttctct-ctacattttgcctctctcttatgtttttggttaatacggtcagGCTGTGTGCACGGAGGCGGGAATGTTTGCTCTGCGTGAGAGGAGAGTACACGTGACACAAGAAGACTTTGAGATGGCGGTGGCCAAGGTAATGAAGAAAG
upper sequence: EFJ04162 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: AT5G20000.1 (Arabidopsis thaliana), 3'ss of exon 8
------gtttgtgatgctcgcgctttagt-tggtccttgacgacggagtgtgtttttttttttttttgctctc-----cagGCGGTGTGCACGGAGGCTGGAATGTTTGCTCTGCGAGAGAGGCGCGTTCATGTCACCCAGGAAGACTTCGACATGCCGGTGGCCAAAGTGATGAAGAAGG
|||| | || | |||| || | || || | | || | | | | | ||||| | | | ||||| || ||||||||||| || |||||||| || || |||||| | || ||||| || ||||||||||| || ||| | ||||| || || |||||||| |
gtaagtgtttctc-tgtccctgcttctgtcttgttctctccaatct-gtctctctctaatgtttttggttattacggtcagGCTGTATGCACGGAGGCGGGCATGTTTGCACTTCGTGAGAGGAGAGTACATGTGACTCAGGAAGACTTTGAGATGGCTGTGGCGAAGGTAATGAAGAAAG
upper sequence: EFJ04162 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 8
---------------------------gtttgtgatgctcgcgctttagtt-----ggtccttgacgacggagtgtgtttttttttttttttgctctccagGCGGTGTGCACGGAGGCTGGAATGTTTGCTCTGCGAGAGAGGCGCGTTCATGTCACCCAGGAAGACTTCGACATGCCGGTGGCCAAAGTGATGAAGAAGG
| | | ||| | |||| || | || || | | || ||| ||||| | | |||||||| ||||| || || || ||||||||| || | |||||| | ||||| || || |||||||| ||||| ||| | || |||||||||||||||||||
ctgactttcctgccttcataggtttttgaatataatggaaaccatttacttgcatagatctgatacctctcggattgagcatttgaacttttgtt-tgcagGCGGTATGCACAGAAGCAGGGATGTTTGCTTTGAGGGAGAGGAGGGTTCACGTAACACAGGAAGATTTCGAGATGGCTGTAGCCAAAGTGATGAAGAAGG
upper sequence: EFJ04162 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: PP1S7016_1V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------------------gtttgtgatgctcgcgct---ttagttgg--tccttgacgacggagtgtgtttttttttttttttgctctccagGCGGTGTGCACGGAGGCTGGAATGTTTGCTCTGCGAGAGAGGCGCGTTCATGTCACCCAGGAAGACTTCGACATGCCGGTGGCCAAAGTGATGAAGAAGG
| | | | | | | ||| || | | | | | | | | |||||| || ||||| || ||||| |||||||| ||||||||||| || || |||| || ||||| || || || |||||||| ||| | ||||| || |||||||||||||
gtagctacaaacctacagtatctagggtttatttctggtagtgatacgaaggaagctgctagaggcttttgtattatgttatttaaaattttggctgttcgtttatactaattttttattgcttcaatcagGCTGTATGCACAGAGGCTGGCATGTTTGCTCTACGTGAACGGCGTGTACATGTGACACAAGAGGACTTCGAGATGGCTGTGGCTAAGGTGATGAAGAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgctttagttggtccttgacgacggagtgtgtttttttttttttttgctctccagGCGGTGTGCACGGAGGCTGGAATGTTTGCTCTGCGAGAGAGGCGCGTTCATGTCACCCAGGAAGACTTCGACATGCCGGTGGCCAAAGTGATGAAGAAGG
ccttgac putative branch site (score: 4)
tgtgtttttttttttt putative PPT
agtgtgtttttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtgatgctcgcgctttagttggtccttgacgacggagtgtgtttttttttttttttgctctccagGCGGTGTGCACGGAGGCTGGAATGTTTGCTCTGCGAGAGAGGCGCGTTCATGTCACCCAGGAAGACTTCGACATGCCGGTGGCCAAAGTGATGAAGAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG