Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcttcttttctacgcccatacgcttgcttctacaagcgagcctctattgacaagattgatagatgttggatccacaaccgaaagaaagaagaagcatggaatcgtttatgcttattttttcttcgccttctaatttctacgcgttcttccagGAAGATGACAAGGCACGTCTTGTCCAGGAGACCGGATTGGAGCTCAAGCAGATCAACAATTGGTTTATAAACCAGAGGAAGCGAAACTGGCACAGCAATC
Basic information
species | Selaginella moellendorffii |
transcript | EFJ30263 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: EFJ30264 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os08g19650.1 (Oryza sativa), 3'ss of exon 4
gtaagttcttcttttctacgcccatacgcttgcttctacaagcgagcctctattgacaagattgatagatgttggatccacaaccgaaagaaagaagaagcatggaatcgtttatgcttattttttcttcgccttctaatttctacgcgttcttccagGAAGATGACAAGGCACGTCTTGTCCAGGAGACCGGATTGGAGCTCAAGCAGATCAACAATTGGTTTATAAACCAGAGGAAGCGAAACTGGCACAGCAATC
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-------------------------------------------------atgccgtttggccacttgtgccctctcttttcatccattttgggtgttcatcacaggat-gtacataactgaattcctctcccttttt--tttcgtcatgt------agGAGGAAGACAAGGCACGGCTAGTCCAAGAAACAGGGCTACAGCTAAAGCAGATCAACAACTGGTTCATCAACCAAAGGAAAAGAAACTGGCACAGTAACC
upper sequence: EFJ30264 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G370332_T01 (Zea mays), 3'ss of exon 4
gtaagttcttcttttctacgcccatacgcttgcttctacaagcgagcctctattgacaagattgatagatgttggatccacaaccgaaagaaagaagaagcatggaatcgtttatgcttatttt---ttcttcgcct-tctaatttctacgcgttcttccagGAAGATGACAAGGCACGTCTTGTCCAGGAGACCGGATTGGAGCTCAAGCAGATCAACAATTGGTTTATAAACCAGAGGAAGCGAAACTGGCACAGCAATC
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----------------------------------------------------------------------gtatgtgacactacggcgacatataattccctcgtcaacttttgctatcagcttgggttcattgctgatccactctttgcttattcatccagGAAGACGACAAGGCACGACTGGTGCAGGAAACGGGATTGCAGCTAAAGCAGATTAACAACTGGTTCATCAACCAACGCAAACGGAACTGGCACAGCAACC
upper sequence: EFJ30264 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G433591_T02 (Zea mays), 3'ss of exon 5
gtaagttcttcttttctacgcccatacgcttgcttctacaagcgagcctctattgacaagattgatagatgttggatccacaaccgaaagaaagaagaagcatggaatcgtttatgcttattttttcttcgccttctaatttctacgcgttcttccagGAAGATGACAAGGCACGTCTTGTCCAGGAGACCGGATTGGAGCTCAAGCAGATCAACAATTGGTTTATAAACCAGAGGAAGCGAAACTGGCACAGCAATC
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----------------------------------------------------------------gtacgtgacaccgcgtcaacttaattccctcgttagctt----ctgctatcaggttcggctcattgatgagcaactctttgcttactcgtccagGAAGACGACAAGGCCAGACTGGTGCAGGAAACGGGGTTGCAGCTAAAGCAAATCAACAACTGGTTCATTAACCAACGCAAGCGGAACTGGCACAGCAACC
upper sequence: EFJ30264 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G055243_T01 (Zea mays), 3'ss of exon 4
gtaagttcttcttttctacgcccatacgcttgcttctacaagcgagcctctattgacaagattgatagatgttggatccacaaccgaaagaaagaagaagcatggaatcgtttatgcttattttttcttcgccttctaatttctacgcgttcttccagGAAGATGACAAGGCACGTCTTGTCCAGGAGACCGGATTGGAGCTCAAGCAGATCAACAATTGGTTTATAAACCAGAGGAAGCGAAACTGGCACAGCAATC
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gtaagtgaacacattg-atcctatcactcccagcaccattc-ctagttactcatgagcatattatta--cgttgaacacatggatcctatcact------cccagcaccatt----cctatttactcatgagtatattatcgtggaccacttgtttagGAGGAAGACAAGGCTCGACTGGTGCAGGAAACAGGGCTACAACTGAAGCAGATCAATAACTGGTTTATCAACCAGCGTAAGCGGAACTGGCACAACAATT
upper sequence: EFJ30264 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA04G06810.1 (Glycine max), 3'ss of exon 5
gtaagttcttcttttctacgcccatacgcttgcttctacaagcgagcctctattgacaagattgatagatgttggatccacaaccgaaagaaagaagaagcatggaatcgtttatgcttattttttcttcgccttctaatttctacgcgttcttccagGAAGATGACAAGGCACGTCTTGTCCAGGAGACCGGATTGGAGCTCAAGCAGATCAACAATTGGTTTATAAACCAGAGGAAGCGAAACTGGCACAGCAATC
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----------------------------------------------------------aagctactccaaattgaagctactccaggagaattttacaattgacattttgaagattaataaatgctgtctcacaatttgttcttcaatgttttttcagGAGGAGGATAAGGCACGGTTGGTGCAGGAAACGGGTTTGCAGCTAAAGCAGATCAATAATTGGTTTATCAATCAAAGGAAGAGGAACTGGCATAGCAACC
upper sequence: EFJ30264 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv04s0008g06130.t01 (Vitis vinifera), 3'ss of exon 4
gtaagttcttcttttctacgcccatacgcttgcttctacaagcgagcctctattgacaagattgatagatgttggatccacaaccgaaagaaagaagaagcatggaatcgtttatgcttattttttcttcgccttctaatttctacgcgttcttccagGAAGATGACAAGGCACGTCTTGTCCAGGAGACCGGATTGGAGCTCAAGCAGATCAACAATTGGTTTATAAACCAGAGGAAGCGAAACTGGCACAGCAATC
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------------------------------------------------------tacacaacacatacacagtgtgttcatatgtgaaatatattag--gtgagatgtgccttgagtatgatacctaagcaaatgctgattttgatatcttctt--agGAGGAGGACAAGGCAAAGTTGGTACAAGAAACAGGCTTGCAACTAAAGCAGATAAACAATTGGTTCATCAATCAGAGGAAGAGAAACTGGCACAGTAACC
upper sequence: EFJ30264 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S77_59V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaagttcttcttttctacgcccatacgcttgcttctacaagcgagcctctattgacaagattgataga---tgttggatccacaaccgaaagaaagaagaagcatggaatcgtttatgcttattttttcttcgccttctaatttctacgcgttcttccagGAAGATGACAAGGCACGTCTTGTCCAGGAGACCGGATTGGAGCTCAAGCAGATCAACAATTGGTTTATAAACCAGAGGAAGCGAAACTGGCACAGCAATC
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------------------------------------------------------tgcataaccggtagactcttctgaatgcgtggcttat-gacgtttctagcatatcatcaaa-acgcccagtaacattttgt-tccgggacacaatgcaatc----agGAGGATGAGAAAGAACAATTAATACAGGAGACAGGATTGGAGCTCAAGCAAGTCAACAACTGGTTTATAAACCAGCGAAAGCGAAACTGGCATAGCAACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggaatcgtttatgcttattttttcttcgccttctaatttctacgcgttcttccagGAAGATGACAAGGCACGTCTTGTCCAGGAGACCGGATTGGAGCTCAAGCAGATCAACAATTGGTTTATAAACCAGAGGAAGCGAAACTGGCACAGCAATC
ttctaat putative branch site (score: 2)
cgttcttcc putative PPT
tttatgcttatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcttcttttctacgcccatacgcttgcttctacaagcgagcctctattgacaagattgatagatgttggatccacaaccgaaagaaagaagaagcatggaatcgtttatgcttattttttcttcgccttctaatttctacgcgttcttccagGAAGATGACAAGGCACGTCTTGTCCAGGAGACCGGATTGGAGCTCAAGCAGATCAACAATTGGTTTATAAACCAGAGGAAGCGAAACTGGCACAGCAATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA