Sequence
atgc intronic sequence ATGC exonic sequencegtacttatccagcatttataaatcaaccatgagtaacactttttctcagGTCTTACGCCCATTTCTCTTAAGACGTCTCAAGTCGGATGTTGAAAGAGGATTACCCCCAAAGAAGGAGACAATCCTCAAAGTTGGGATGTCTCAGATGC
Basic information
species | Selaginella moellendorffii |
transcript | EFJ06565 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 8
-----------------------------------------gtactt--atccagcatttataaatcaaccatgagtaacactttttctcagGTCTTACGCCCATTTCTCTTAAGACGTCTCAAGTCGGATGTTGAAAGAGGATTACCCCCAAAGAAGGAGACAATCCTCAAAGTTGGGATGTCTCAGATGC
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gtgagtaatataactcccatgctcaatggctcattatgctaataatttgggacaacctgcatagttcattcatgta-aattcttctatgaagGTTCTTCGCCCATTTCTTCTTCGAAGGCTTAAATCTGATGTTGAAAAGGGATTACCCCCCAAAAAGGAAACTATCCTTAAGGTTGGAATGTCTCAGATGC
upper sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 5
---------------------gtacttatcc-agcatttataaatcaaccatgagtaac-----------actttttctcagGTCTTACGCCCATTTCTCTTAAGACGTCTCAAGTCGGATGTTGAAAGAGGATTACCCCCAAAGAAGGAGACAATCCTCAAAGTTGGGATGTCTCAGATGC
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gttgggatatagttttcgtgatcaccaattttagtaccttaaaatgaactctttataattgtttctcgcaacttttgcaaagGTTCTTCGCCCATTCCTTCTTAGGAGGCTCAAGTCTGATGTAGAAAAGGGCCTACCTCCAAAGAAAGAAACAATTCTTAAAGTTGGAATGTCTCAGATGC
upper sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 8
-----------------------gtacttatccagcatttataaatcaaccatgagtaacactttttctcagGTCTTACGCCCATTTCTCTTAAGACGTCTCAAGTCGGATGTTGAAAGAGGATTACCCCCAAAGAAGGAGACAATCCTCAAAGTTGGGATGTCTCAGATGC
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gtatgtactcatattttatcaaggttattctctaa-gttcttatgctaatcatt--tacctcatctttgtagGTTCTGCGACCATTTCTTCTTCGGAGGTTAAAATCAGATGTAGAGAAAGGCTTACCTCCAAAAAAGGAGACAATACTCAAAGTTGGCATGTCTCAAATGC
upper sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 8
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 8
--------------------------gtacttatccagcatt-tataaatcaaccatgagtaacact------ttttctcagGTCTTACGCCCATTTCTCTTAAGACGTCTCAAGTCGGATGTTGAAAGAGGATTACCCCCAAAGAAGGAGACAATCCTCAAAGTTGGGATGTCTCAGATGC
| |||| | | | | | | || | | | | | | || | |||| | || |||||||| | || | || ||||| |||||||| | ||| || || || ||||||||||| || || |||||||| |||||||||||||
gtatggatgcacccattccttgcattgagtttattctgttctgtgtgagtcgtaggttaattgctttcatgtatctttttagGTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAGATGTTGAGAAAGGTTTGCCACCGAAGAAGGAGACCATACTTAAAGTTGGTATGTCTCAGATGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtacttatccagcatttataaatcaaccatgagtaacactttttctcagGTCTTACGCCCATTTCTCTTAAGACGTCTCAAGTCGGATGTTGAAAGAGGATTACCCCCAAAGAAGGAGACAATCCTCAAAGTTGGGATGTCTCAGATGC
gagtaac putative branch site (score: 2)
cactttttctc CT-rich tract
atttataaatcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttatccagcatttataaatcaaccatgagtaacactttttctcagGTCTTACGCCCATTTCTCTTAAGACGTCTCAAGTCGGATGTTGAAAGAGGATTACCCCCAAAGAAGGAGACAATCCTCAAAGTTGGGATGTCTCAGATGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG