Sequence
atgc intronic sequence ATGC exonic sequencegttcgtgctcttcttctttcttgtgctggattgaaaactcgttaaatcgttgtcgcttgatctgtatggaatgaaaaaaaaggtgatagctttgttgggtggttgtggtggtgttggtggatgctagctaagctaatctttggctgatttcctcgagattttctttgcttcctctggcttttgcttttgttgcagGCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAG
Basic information
species | Selaginella moellendorffii |
transcript | EFJ14702 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ14702 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os07g26720.2 (Oryza sativa), 3'ss of exon 2
gttcgtgctcttcttctttcttgtgctggattgaaaactcgttaaatcgttgtcgcttgatctgtatggaatgaaaaaaaaggtgatagctttgttgggtggttgtggtggtgttggtggatgctagctaagctaatctttggctgatttcctcgagattttctttgcttcctctggcttttgcttttgttgcagGCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAG
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-----------------------------------------------------------------------------------------------------------gtatcttctgtcattcttctccatttttattcttttatcagattattaagccctagtttctaaaaaaatgttgatgtgtttaat-cagGAACCTAATGTGAGCATGATCATCACGGACTACTGGATGCCGGAGATGACCGGGTACGACCTGCTCAAGAAGATCAAG
upper sequence: EFJ14702 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os02g58350.1 (Oryza sativa), 3'ss of exon 2
gttcgtgctcttcttctttcttgtgctggattgaaaactcgttaaatcgttgtcgcttgatctgtatggaatgaaaaaaaaggtgatagctttgttgggtggttgtggtggtgttggtggatgctagctaagctaatctttggctgatttcctcgagattttctttgcttcctctggcttttgcttttgttgcagGCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAG
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-----------------------------------------------------------------------------------------gtatgttctttgatccctatg---cctgtggatgtcagtcag-------ttttgaagaattgctagaaatgaatgtaaaat----tagtttgtg-ttatgatgcagGATCGGAATGTGCATATGATCATCACGGATTACTGCATGCCGGAGATGACAGGGTTCGATCTCCTCAAGAGGGTCAAG
upper sequence: EFJ14702 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G129954_T01 (Zea mays), 3'ss of exon 2
gttcgtgctcttcttctttcttgtgctggattgaaaactcgttaaatcgttgtcgcttgatctgtatggaatgaaaaaaaaggt--gatagctttgttgggtggttgtggtggtgttggtggatgctagctaagctaatctttggctgatttcctcga-gattttctttgcttcctctggcttttgcttttgttgcagGCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAG
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----------------------------------------gtaagaagaagatggcttcctcttcctagctcctacgagttggttggtcaaccgtgttgtgcact---gcttgtattgtcttctcctagc-------gtcactagctagtcctcaagaagaggtttctggtgtaatcagGATGTGGCTGCCAAT-CAGGATGTGGCTGTGAACCTGATCATCACAGACTACTGCATGCCTGGCATGACAGGATATGACCTGCTCAAGAAGATCAAG
upper sequence: EFJ14702 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA04G29250.1 (Glycine max), 3'ss of exon 2
gttcgtgctcttcttctttcttgtgctggattgaaaactcgttaaatcgttgtcgcttgatctgtatggaatgaaaaaaaaggtgatagctttgttgggtggttgtggtggtgttggtggatgctagctaagctaatctttggctgatttcctcgagattttctttgcttcctctggcttttgcttttg-ttgcagGCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAG
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--------------------------------------------------------------------------------------------------------------gtacaataatcctctagcaaagtcaacaaata-ctgatacgtac---atattttaaactttctaatcatgttacttctgattgcagGATGTAGAAGTAAACCTGATCATAACTGATTACTGTATGCCAGAAATGACAGGCTATGATCTGCTGAAAAAGATCAAG
upper sequence: EFJ14702 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA11G21650.1 (Glycine max), 3'ss of exon 2
gttcgtgctcttcttctttcttgtgctggattgaaaactcgttaaatcgttgtcgcttgatctgtatggaatgaaaaaaaaggtgatagctttgttgggtggttgtggtggtgttggtggatgctagctaagctaatctttggctgatttcctcgagattttctttgcttcctctggcttttgcttttgttgcagGCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAG
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------------------------------------------------------------------------------------------ttgattactaaatgctactcatacttacatatttta---aacttttttattgggcaagttagaaagatgcataatctaatcattttacttctgatt--gctgcagGATGTAGAAGTAAACCTGATCATAACTGATTACTGTATGCCAGAAATGACTGGCTATGATCTGCTGAGAAAGATCAAG
upper sequence: EFJ14702 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv13s0067g03070.t01 (Vitis vinifera), 3'ss of exon 2
gttcgtgctcttcttctttcttgtgctggattgaaaactcgttaaatcgttgtcgcttgatctgtatggaatgaaaaaaaaggtgatagctttgttgggtggttgtggtggtgttggtggatgctagctaagctaatctttggctgatttcctcgagattttctttgcttcctctggcttttgcttttgttgcagGCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAG
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----------------------------gtatgtcaccttcttt--tctctccccatgaatgtctttaattttaagaaaaagttttcagaatttt---atcatttc--tccttttggaagat--caacaaagaatgtaactaagaaagcctttttgggttatagtaatccatagttgttactaattctat-gcagGTTTCAAAGGTGAATTTGATAATTACAGACTACTGTATGCCAGGAATGACAGGCTATGAGCTGCTCAAGAGAGTCAAG
upper sequence: EFJ14702 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv17s0000g07580.t01 (Vitis vinifera), 3'ss of exon 2
gttcgtgctcttcttctttcttgtgctggattgaaaactcgttaaatcgttgtcgcttgatctgtatggaatgaaaaaaaaggtgatagctttgttgggtggttgtggtggtgttggtggatgctagctaagctaatctttggctgatttcctcgagattttctttgcttcctctggcttt-tgcttttgttgcagGCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAG
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----------------------------------------------------------------------------------------------gcaaataaacagaggtctttttgtttttccttttttgattaaattcaaa--gatttctttaatactgtttggatgattgatatctcaatggtttccttgaagGGTTTGAAGGTGAATCTGATCATGACGGACTATTCTATGCCTGGGATGACAGGGTATGAGTTGCTCAAGAAGATCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggctgatttcctcgagattttctttgcttcctctggcttttgcttttgttgcagGCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAG
ggctgat putative branch site (score: 4)
ttttctttgcttcctc putative PPT
attttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcgtgctcttcttctttcttgtgctggattgaaaactcgttaaatcgttgtcgcttgatctgtatggaatgaaaaaaaaggtgatagctttgttgggtggttgtggtggtgttggtggatgctagctaagctaatctttggctgatttcctcgagattttctttgcttcctctggcttttgcttttgttgcagGCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG