Sequence
atgc intronic sequence ATGC exonic sequencegtacgtcagcatttttttttactttcttagttatgttgtgttttgttttgttttactttattttatttcttggacaaaaattccggaattttttcgtagttgatgctttgaccttaaattaatatcgtggattgcctctgctgtgaagagtgtggtagtggcgttcgcttgatgatgcagGGCCAGATTAAGACTGGAGCTCCTTGCCGCTCTGAGAGATTGTCCAAGTACAACCAG
Basic information
species | Physcomitrella patens |
transcript | PP1S133_85V6.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S133_85V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os03g14450.2 (Oryza sativa), 3'ss of exon 12
gtacgtcagcatttttttttactttcttagttatgttgtgttttgttttgttttactttattttatttcttggacaaaaatt--ccggaattttttcgtagttgatgctttgaccttaaattaatatcgtggattgcctctgctgtgaagagtgtggtagtggcgttcgcttgatgatgcagGGCCAGATTAAGACTGGAGCTCCTTGCCGCTCTGAGAGATTGTCCAAGTACAACCAG
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-------------------------------------gtatat-actttgcgtgccttctttagtgtgcttcaacaaatataggccgcttatcttttgaaagagcttgtgagatccgctcttaatggtgatgataactt--------ggaaatgcatcaatg----ttttgtcatgaaacagGGCCAGATCAAGACTGGAGCTCCTTGCAGATCTGAGCGCCTTGCCAAGTACAACCAG
upper sequence: PP1S133_85V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 15
---gtacgtcagcatttttttttactttcttagttatgttgtgttttgttttgttttactttattttatttcttggacaaaaatt--ccggaatttt--ttcgtagttgatgctttgaccttaaattaatatcgtggattgcctctgctgtgaagagtgtggtagtggcgttcgcttgatgatgcagGGCCAGATTAAGACTGGAGCTCCTTGCCGCTCTGAGAGATTGTCCAAGTACAACCAG
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gtaagttgtcaaaatcagaagctcttttcctaatcgtatcatgttctttttcattcttccc-gtggtgtcttatgggccaaattttgtctaaattttgaataacgattcttttttttaccttaagctgatataat---ttgatcatgttatgtca----------------ttatttaa-----cagGGCCAGATCAAGACTGGAGCTCCCTGCCGATCTGAAAGGCTTGCCAAGTACAACCAG
upper sequence: PP1S133_85V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv16s0022g01770.t01 (Vitis vinifera), 3'ss of exon 15
gtacgtcagcatttttttttactttcttagttatgttgtgttttgttttgttttactttattttatttcttggacaaaaattccggaattttttcgtagttgat-gctttgaccttaaattaatatcgtggattgcctctgctgtgaagagtgtggtagtggcgttcgcttgatg---atgcagGGCCAGATTAAGACTGGAGCTCCTTGCCGCTCTGAGAGATTGTCCAAGTACAACCAG
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---------------------------------------------------------------------------aataaaattgtagtagtatcatatttaagagatttgac--------agttttctggacagcatctcaagttgata-tgacctgatgatgtgtgccttatatgcaaacagGGCCAGATCAAGACTGGAGCTCCTTGCAGGTCTGAACGCCTTGCCAAATATAACCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgtggattgcctctgctgtgaagagtgtggtagtggcgttcgcttgatgatgcagGGCCAGATTAAGACTGGAGCTCCTTGCCGCTCTGAGAGATTGTCCAAGTACAACCAG
gcttgat putative branch site (score: 5)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtcagcatttttttttactttcttagttatgttgtgttttgttttgttttactttattttatttcttggacaaaaattccggaattttttcgtagttgatgctttgaccttaaattaatatcgtggattgcctctgctgtgaagagtgtggtagtggcgttcgcttgatgatgcagGGCCAGATTAAGACTGGAGCTCCTTGCCGCTCTGAGAGATTGTCCAAGTACAACCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT