Sequence
atgc intronic sequence ATGC exonic sequencegtatgcgtttctaagatcctgctcgttttgtaacaagctctacttgatctctttggttgttctcttcaagGTGGTTCTCCGAGGAGGCTACATCGACTCTGGAGACAACGTAAAGTTTGGATTCCCCATGGCATTCACGATCACCATGCTTTCATGGAGCGTGATAGAAT
Basic information
species | Selaginella moellendorffii |
transcript | EFJ21535 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ21535 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA02G01990.1 (Glycine max), 3'ss of exon 1
gtatgcgt-ttctaagat-cctgctcgttttgtaacaagctctacttgatctctttggttgttctcttcaagGTGGTTCTCCGA-----------------GGAGGCTACATCGACTCTGGAGACAACGTAAAGTTTGGATTCCCCATGGCATTCACGATCACCATGCTTTCATGGAGCGTGATAGAAT
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gtatgtatataccaagttaccaactctcacattaccatgctatttgtgtttttttggtttgcttatttatgtgtgaatgtgcaatgcagGTTGATTTGGTTGGAGGGTACTATGATGCTGGGGACAATGTGAAATTTGGTTTTCCCATGGCATTCACCACCACCATGCTTTCATGGAGCGTTATTGAGT
upper sequence: EFJ21535 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA10G02130.1 (Glycine max), 3'ss of exon 1
----------------gtatgcgtttctaagatcctgctcgttttgtaacaagctctacttgatc-tctttggttgttctcttcaagGTGGTTCTCCGAGGAGGCTACATCGACTCTGGAGACAACGTAAAGTTTGGATTCCCCATGGCATTCACGATCACCATGCTTTCATGGAGCGTGATAGAAT
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gtatgcatataccaactctcacattaccatgtttt--ctggtttttgtttttggtttgcttatttatgtgtgaatgtgcaatgcagGTTGATTTAGTT-GGAGGGTACTATGATGCTGGGGACAATGTAAAATTTGGTTTTCCCATGGCCTTCACCACCACCATGCTTTCATGGAGCGTTATTGAGT
upper sequence: EFJ21535 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA03G37420.1 (Glycine max), 3'ss of exon 1
------------------------------------------gtatgcgtttctaagatcctgctcgttttgtaacaagctctacttgatctctttggttgttctcttcaagGTGGTTCTCCGAGGAGGCTACATCGACTCTGGAGACAACGTAAAGTTTGGATTCCCCATGGCATTCACGATCACCATGCTTTCATGGAGCGTGATAGAAT
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gtatgataatataataatattaatacaacattcttagtctcagtctcagtttttgtgttct--ctggcttgtgcacatggcttattt--ctgcattgaatgtacaatgcagGTTGATTTGGTT-GGAGGGTACTATGATGCTGGGGACAATGTCAAGTTTGGTTTTCCCATGGCCTTCACCACCACCATGCTTTCGTGGAGTGTTATTGAGT
upper sequence: EFJ21535 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT1G02800.1 (Arabidopsis thaliana), 3'ss of exon 1
---------------------------------gtatgcgtttctaagatcctgctcgttttgtaacaagctctacttgatctctttggttgttctcttcaagGTGGTTCTCCGAGGAGGCTACATCGACTCTGGAGACAACGTAAAGTTTGGATTCCCCATGGCATTCACGATCACCATGCTTTCATGGAGCGTGATAGAAT
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accctaattttgttattatgctttttaggttaaaacagagaaactaagttacatattttcttggaa--agcctaatttgtgtgaattggtt-taattttgtagGTGGATTTGGTGGGAGGATACTACGATGCAGGGGACAATATGAAGTTTGGATTCCCAATGGCATTCACAACCACAATGCTCTCATGGAGTTTAATTGAGT
upper sequence: EFJ21535 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv07s0005g00740.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------------gtatgcgtttctaagatcctgctcgttttgtaacaagctctacttgatctc--tttggttgttctcttcaagGTGGTTCTCCGAGGAGGCTACATCGACTCTGGAGACAACGTAAAGTTTGGATTCCCCATGGCATTCACGATCACCATGCTTTCATGGAGCGTGATAGAAT
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gtatgtgtaaatgtgtatgctctgtttcttcaattacttgttttagatttttcatcttttgaagttggttttg-ttaatttgggcgtggaaatggaaatgcagGTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGGTTCCCAATGGCCTTCACCACCACCATGCTTTCATGGAGTGTGATCGAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcctgctcgttttgtaacaagctctacttgatctctttggttgttctcttcaagGTGGTTCTCCGAGGAGGCTACATCGACTCTGGAGACAACGTAAAGTTTGGATTCCCCATGGCATTCACGATCACCATGCTTTCATGGAGCGTGATAGAAT
ttgttctcttc CT-rich tract
ttttgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcgtttctaagatcctgctcgttttgtaacaagctctacttgatctctttggttgttctcttcaagGTGGTTCTCCGAGGAGGCTACATCGACTCTGGAGACAACGTAAAGTTTGGATTCCCCATGGCATTCACGATCACCATGCTTTCATGGAGCGTGATAGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA