Sequence
atgc intronic sequence ATGC exonic sequence...ggctattggatgatttttattcgtttatttattttgacgattatgatgcgtattaatattattattattttgaatgcacatctcttctctgtttgtgcagCCATGCAGAGGCCTTTTGCTATTTGGACCACCAGGTACAGGGAAGACTATGTTAGCTAAGGCTGTTGCAACTGAAGCAGGGGCTAACTTCATAAACATTT
Basic information
species | Physcomitrella patens |
transcript | PP1S3_184V6.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S3_184V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 21
ggctattggatgatttttattcgtttatttattttgacgattatgatgcgtattaatattattattattttgaa---tgcacatctcttctctgtt-tgtgcagCCATGCAGAGGCCTTTTGCTATTTGGACCACCAGGTACAGGGAAGACTATGTTAGCTAAGGCTGTTGCAACTGAAGCAGGGGCTAACTTCATAAACATTT
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--ctatattttgggacggatggagtattatatgttggctacc-taattt-tctctatttaagtcctatcttaaaaattgcctctggtaaatctgttacttgcagCCTTGCAAGGGAATATTGCTGTTTGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATAT
upper sequence: PP1S3_184V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
ggctattggatgatttttattcgtttat-ttattttgacgattatgatgcgtattaatattattattattttga---atgcacatctcttctctgtt-tgtgc-agCCATGCAGAGGCCTTTTGCTATTTGGACCACCAGGTACAGGGAAGACTATGTTAGCTAAGGCTGTTGCAACTGAAGCAGGGGCTAACTTCATAAACATTT
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----atagcaatattcttattttttgatgctaagctagcaatgg-aacacaccttttagctgacagaaagctaacttatgt-tgtttatattctattctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT
upper sequence: PP1S3_184V6.1 (Physcomitrella patens), 3'ss of exon 17
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 21
--ggctattggatgatttttattcgtttatttattttgacgattatgatgcgtattaatattattattattttgaatgcacatctcttctctgtttgtgcagCCATGCAGAGGCCTTTTGCTATTTGGACCACCAGGTACAGGGAAGACTATGTTAGCTAAGGCTGTTGCAACTGAAGCAGGGGCTAACTTCATAAACATTT
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cagttcatcaggctgaacagagcacttcaaatactat--cagctattgatctttgcaattgtgttctaaggaacaatcttagtgtaattgttccatgtgcagCCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|162227223|gb|FC403867.1|FC403867EST: TGCTTCCGTTGCAGCGCCCGGAGCTTTTTGTCAAAGGCCAGTTGACGAAG CCATGCAGAGGCCTTTTGCTATTTGGAC-ACCAGGTACA
genomic: TGCTTCCGTTGCAGCGCCCGGAGCTTTTTGTCAAAGGCCAGTTGACGAAGgtaagattct ... gtttgtgcagCCATGCAGAGGCCTTTTGCTATTTGGACCACCAGGTACA
EST:
gi|100366753|gb|BY985261.1|BY985261EST: TGCTTCCGTTGCAGCGCCCGGAGCTTTTTGTCAAAGGCCAGTTGACGAAG CCATGCAGAGGCCTTTTGCTATTTGGACCACCAGGTACAGGGAAGACTATG
genomic: TGCTTCCGTTGCAGCGCCCGGAGCTTTTTGTCAAAGGCCAGTTGACGAAGgtaagattct ... gtttgtgcagCCATGCAGAGGCCTTTTGCTATTTGGACCACCAGGTACAGGGAAGACTATG
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
8 (upstream exon),
28 (downstream exon)
Score:
1TCATATTGGTGCCCTGGACAATGTGAAAGAAACCTTGCGTGAGTTGGTAATGCTTCCGTTGCAGCGCCCGGAGCTTTTTGTCAAAGGCCAGTTGACGAAGgtaagattct ... gtttgtgcagCCATGCAGAGGCCTTTTGCTATTTGGACCACCAGGTACAGGGAAGACTATGTTAGCTAAGGCTGTTGCAACTGAAGCAGGGGCTAACTTCATAAACATTT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgcgtattaatattattattattttgaatgcacatctcttctctgtttgtgcagCCATGCAGAGGCCTTTTGCTATTTGGACCACCAGGTACAGGGAAGACTATGTTAGCTAAGGCTGTTGCAACTGAAGCAGGGGCTAACTTCATAAACATTT
tattaat putative branch site (score: 1)
catctcttctctgttt putative PPT
tattaatattattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggctattggatgatttttattcgtttatttattttgacgattatgatgcgtattaatattattattattttgaatgcacatctcttctctgtttgtgcagCCATGCAGAGGCCTTTTGCTATTTGGACCACCAGGTACAGGGAAGACTATGTTAGCTAAGGCTGTTGCAACTGAAGCAGGGGCTAACTTCATAAACATTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC