Sequence
atgc intronic sequence ATGC exonic sequencegtaagcactttcttacagtacttctatggttggtccaaaattgaattctatgattttgtgggcaatttttttgtgtgtatttttggagatagggggtgggatgttgacatcaaacgaaaccgtttatcatttcttatcttttatccatgattgctaagtggtgcaacttctttcgtttgtagTCGAGAGTCGTACAGCAAGCAGAAGGTGAAAGGTCATATCACGTTTTTTATCAACTGTGTGCTGGAGCTGATGAATCTTTACGAG
Basic information
species | Physcomitrella patens |
transcript | PP1S104_215V6.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S104_215V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA13G35790.1 (Glycine max), 3'ss of exon 10
gtaagcactttcttacagtacttctatggttggtccaaaattgaattctatgattttgtgggcaatttttttgtgtgtatttttggagatagggggtgggatgttgacatcaaacgaaaccgtttatcatttcttatcttttatccatgattgctaagtggtgcaacttctttcgtttgtagTCGAGAGTCGTACAGCAAGCAGAAGGTGAAAGGTCATATCACGTTTTTTATCAACTGTGTGCTGGAGCT--GATGAATCTTTACGAG
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------------------------------------------------------------------------------------------gtaacttgtgatgctctttttgaacaaaagtgtgaaac-tgaaatatttattattcttcacttctgaa-atcatcttgtctcctgtgttcagTCTAGAGTTGTTCAACTTGCATTGGGTGAGAGGTCATATCACATATTTTATCAACTTTGTGCTGGATCTTCATCTGATCTTAAAG--
upper sequence: PP1S104_215V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 10
gtaagcactttcttacagtacttctatggttggtccaaaattgaattctatgattttgtgggcaatttttttgtgtgtatttttggagatagggggtgggatgttgacatcaaacgaaaccgtttatcatttcttatcttttatccatgattgctaagtggtgcaacttctttcgtttgtagTCGAGAGTCGTACAGCAAGCAGAAGGTGAAAGGTCATATCACGTTTTTTATCAACTGTGTGCTGGAGCTGATGAATCTTTACGAG
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-------------------------------------------------------------gtagcttctttggatg-atttt-------atttgcttgatttctttcctttttaaacatgattcattaacattgacattttttctttgtatgttga------------ctcattttaacagTCTAGAGTGGTCCAATGTGCTGAAGGGGAAAGGTCATATCATATTTTTTATCAACTTTGTGCTGGGGCTTCACCTGCACTTAGAG
upper sequence: PP1S104_215V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 8
gtaagcactttcttacagtacttctatggttggtccaaaattgaattctatgattttgtgggcaatttttttgtgtgtatttttggagatagggggtgggatgttgacatcaaacgaaaccgtttatcatttcttatcttttatccatgattgctaagtggtgcaacttctttcgtttgtagTCGAGAGTCGTACAGCAAGCAGAAGGTGAAAGGTCATATCACGTTTTTTATCAACTGTGTGCTGGAGCTGATGAATCTTTACGAG
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-------------------------------------------------------------------------------------------------gtaattctttctttatctgtatctattgtttggtctgtttgattttctcataatgggttgttaattgtgtctcttttatgaacagTCTAGAGTGGTCCAATGTGCAGAAGGAGAGAGGTCATATCATATATTTTATCAACTCTGTGCTGGAGCTCCACCAGCTCTTAGAG
upper sequence: PP1S104_215V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ20281 (Selaginella moellendorffii), 3'ss of exon 7
gtaagcactttcttacagtacttctatggttggtccaaaattgaattctatgattttgtgggcaatttttttgtgtgtatttttggagatagggggtgggatgttgacatcaaacgaaaccgtttatcatttcttatcttttatccatgattgctaagtggtgcaacttctttcgtttgtagTCGAGAGTCGTACAGCAAGCAGAAGGTGAAAGGTCATATCACGTTTTTTATCAACTGTGTGCTGGAGCTGATGAATCTTTACGAG
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---------------------------------------------------------------------------------------------------------------------------gtaacaaacttcctctattcaaaacagttgctaatcttaataa----tttgctctaaagTCTAGAGTCGTACATCAAGCACCAGGTGAAAGGTCATACCATGTGTTTTACCAGCTGTGTGCTGGGGCAGACGCTGGCATGCGAG
upper sequence: PP1S104_215V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ23280 (Selaginella moellendorffii), 3'ss of exon 7
gtaagcactttcttacagtacttctatggttggtccaaaattgaattctatgattttgtgggcaatttttttgtgtgtatttttggagatagggggtgggatgttgacatcaaacgaaaccgtttatcatttcttatcttttatccatgattgctaagtggtgcaacttctttcgtttgtagTCGAGAGTCGTACAGCAAGCAGAAGGTGAAAGGTCATATCACGTTTTTTATCAACTGTGTGCTGGAGCTGATGAATCTTTACGAG
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---------------------------------------------------------------------------------------------------------------------------gtaacaaacttcctctattcaaaacagttgctaatcttaataa----tttgctctaaagTCTAGAGTCGTACATCAAGCACCAGGTGAAAGGTCATACCATGTGTTTTACCAGCTATGTGCTGGGGCAGATGCTGGCATGCGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catttcttatcttttatccatgattgctaagtggtgcaacttctttcgtttgtagTCGAGAGTCGTACAGCAAGCAGAAGGTGAAAGGTCATATCACGTTTTTTATCAACTGTGTGCTGGAGCTGATGAATCTTTACGAG
cttctttcgtttgt CT-rich tract
ttatcttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcactttcttacagtacttctatggttggtccaaaattgaattctatgattttgtgggcaatttttttgtgtgtatttttggagatagggggtgggatgttgacatcaaacgaaaccgtttatcatttcttatcttttatccatgattgctaagtggtgcaacttctttcgtttgtagTCGAGAGTCGTACAGCAAGCAGAAGGTGAAAGGTCATATCACGTTTTTTATCAACTGTGTGCTGGAGCTGATGAATCTTTACGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT