Sequence
atgc intronic sequence ATGC exonic sequence...ttttaattgacgggggaagcatgacaggagcgaggcaatgagtattttctgttactgttcggtgcaacttgacatagtattctgatcgtttttgtggcagGAGTGGGGGGTTACTCGTATCTATATGAACCGCTATGGTGGTCCGGCATGATCACAA
Basic information
species | Physcomitrella patens |
transcript | PP1S49_181V6.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S49_181V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ16080 (Selaginella moellendorffii), 3'ss of exon 1
ttttaattgacgggggaagcatgacaggagcgaggcaatgagtattttctgttactgttcggtgcaacttgacatagtattctgatcgtttttgtg-----gcagGAGTGGGGGGTTACTCGTATCTATATGAACCGCTATGGTGGTCCGGCATGATCACAA
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--------------gtaggcatggttttaa------attcttttttttttttttttttttgttgcaatgtcgtgctctagtcacagctttttcgtgtttttgtagGTGTTGGGGGCTACTCCTATCTGTATGAACCGCTTTGGTGGGCAGGCATGATCACAA
upper sequence: PP1S49_181V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ22449 (Selaginella moellendorffii), 3'ss of exon 1
ttttaattgacgggggaagcatgacaggagcgaggcaatgagtattttctgttactgttcggtgcaacttgacatagtattctgatcgtttttgtggcagGAGTGGGGGGTTACTCGTATCTATATGAACCGCTATGGTGGTCCGGCATGATCACAA
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------------------gtacctccatggttttatctttagttttcttcgatcatg---gattgaattt-acatt-cgatctaaaaccaaatcttgcagGAGTGGGAGGTTATTCTTATTTATTGGAGCCGCTATGGTGGTCTGGCATGATCACGA
upper sequence: PP1S49_181V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ15113 (Selaginella moellendorffii), 3'ss of exon 1
ttttaattgacgggggaagcatgacaggagcgaggcaatgagtattttctgttactgttcggtgcaacttgacatagtattctgatcgtttttgtggcagGAGTGGGGGGTTACTCGTATCTATATGAACCGCTATGGTGGTCCGGCATGATCACAA
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--------------gtaggcatggttttaa------attccttttttttagttgcaatgtcgtgct-ctagtcacagctttttcgt-gtttttgt---agGTGTTGGGGGCTACTCCTATCTGTATGAACCGCTTTGGTGGGCAGGCATGATCACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctgttactgttcggtgcaacttgacatagtattctgatcgtttttgtggcagGAGTGGGGGGTTACTCGTATCTATATGAACCGCTATGGTGGTCCGGCATGATCACAA
ttctgat putative branch site (score: 3)
tcgttttt CT-rich tract
atagtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttaattgacgggggaagcatgacaggagcgaggcaatgagtattttctgttactgttcggtgcaacttgacatagtattctgatcgtttttgtggcagGAGTGGGGGGTTACTCGTATCTATATGAACCGCTATGGTGGTCCGGCATGATCACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG