Sequence
atgc intronic sequence ATGC exonic sequencegttcgtgatccccgcgtcagtggtccttttatgtaattcttgacatgacctgggaaatggtttcaaagatgctgagtcattgccgcctttcaagccatttatcagtgaaattcatcagtgaaatttatcagtgatcgccctgcacgtttatcttgtagctgagcatttgtaatgttaaccttcagGTTCAAATACAGCAAAAGATGAAGCAAGAATCTGAACAGTTTCGGTTGTGGAAAGCATCCAGAGAGAAAGAGGTTCTTCAG
Basic information
species | Physcomitrella patens |
transcript | PP1S42_71V6.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S42_71V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: GLYMA06G04520.1 (Glycine max), 3'ss of exon 15
gttcgtgatccccgcgtcagtggtccttttatgtaattcttgacatgacctgggaaatggtttcaaagatgctgagtcattgccgcctttcaagccatttatcagtgaaattcatcagtgaaatttatcagtgatcgccctgcacgtttatcttgtagctgagcatttgtaatgttaaccttcagGTTCAAATACAGCAAAAGATGAAGCAAGAATCTGAACAGTTTCGGTTGTGGAAAGCATCCAGAGAGAAAGAGGTTCTTCAG
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------------------------------------------------------------------------------------------------gttgactgctgtatttcttctaatccatggttgtaaaatcatttaatacactctctctgttat--aacttgaataaggttg-----cagGTTCAACTGCAGCAAAGGATAAAACAAGAAGCCGAACAGTTTCGGCAGTGGAAAGCGTCTAGAGAGAAAGAGCTGTTGCAA
upper sequence: PP1S42_71V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: GLYMA04G04380.1 (Glycine max), 3'ss of exon 15
gttcgtgatccccgcgtcagtggtccttttatgtaattcttgacatgacctgggaaatggtttcaaagatgctgagtcattgccgcctttcaagccatttatcagtgaaattcatcagtgaaatttatcagtgatcgccctgcacgtttatcttgtagctgagcatttgtaatgttaaccttcagGTTCAAATACAGCAAAAGATGAAGCAAGAATCTGAACAGTTTCGGTTGTGGAAAGCATCCAGAGAGAAAGAGGTTCTTCAG
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------------------------------------------------------------------------------------------------gtttaatgttgtatttcttctaatccatggttgtaaaatcacttaatacactctctccattatta--cctgaataatgttg-----cagGTTCAATTGCAGCAAAGGATAAAACAAGAAGCCGAACAGTTTCGGCAGTGGAAGGCTTCAAGAGAGAAAGAGCTGTTGCAA
upper sequence: PP1S42_71V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: Vv18s0001g07550.t01 (Vitis vinifera), 3'ss of exon 15
gttcgtgatccccgcgtcagtggtccttttatgtaattcttgacatgacctgggaaatggtttcaaagatgctgagtcattgccgcctttcaagccatttatcagtgaaattcatcagtgaaatttatcagtgatcgccctgcacgtttatcttgtagctgagcatttgtaatgttaaccttcagGTTCAAATACAGCAAAAGATGAAGCAAGAATCTGAACAGTTTCGGTTGTGGAAAGCATCCAGAGAGAAAGAGGTTCTTCAG
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------------------------------------------------------------------------------------------------gttctattttg----tcattgatgaaacttgtctacttgcaaaatgaaaatcaatttgct--ctaaccatcaatgctattt-tatctagGTTCAATTGCAACATAAGATCAAGCAAGAATCTGAGCAGTTTAGGTTATGGAAGGCATCGCGGGAAAAAGAAGTTCTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgatcgccctgcacgtttatcttgtagctgagcatttgtaatgttaaccttcagGTTCAAATACAGCAAAAGATGAAGCAAGAATCTGAACAGTTTCGGTTGTGGAAAGCATCCAGAGAGAAAGAGGTTCTTCAG
tgttaac putative branch site (score: 2)
ccttc CT-rich tract
atttgtaatgttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcgtgatccccgcgtcagtggtccttttatgtaattcttgacatgacctgggaaatggtttcaaagatgctgagtcattgccgcctttcaagccatttatcagtgaaattcatcagtgaaatttatcagtgatcgccctgcacgtttatcttgtagctgagcatttgtaatgttaaccttcagGTTCAAATACAGCAAAAGATGAAGCAAGAATCTGAACAGTTTCGGTTGTGGAAAGCATCCAGAGAGAAAGAGGTTCTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG