Sequence
atgc intronic sequence ATGC exonic sequencegtaatttcaaatcatattttgttttcaagtttcactcgcttagcgatcagaatgtggtgtaagaatcactttgcaacgtgttctgccccaggcagtacaagttcaagtgaaggtagccagtcatcaaccagccacttcactgagttgaattttatgcatttttacagGATGTATTTGACCTACCTTTTCATATGGCAAGAGATCAAATTGAACAAAGTTTGCGTGCCAAGATGTCCACTATTAAG
Basic information
species | Physcomitrella patens |
transcript | PP1S47_178V6.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S47_178V6.2 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA17G07040.1 (Glycine max), 3'ss of exon 11
gtaatttcaaatcatattttgttttcaagtttcactcgcttagcgatcagaatgtggtgtaagaatcactttgcaacgtgttctgccccaggcagtacaagttcaagtgaaggtagccagtcatcaaccagccacttcactgagttgaattttatgcatttttacagGATGTATTTGACCTACCTTTTCATATGGCAAGAGATCAAATTGAACAAAGTTTGCGTGCCAAGATGTCCACTATTAAG
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----------------------------------------------------------------------------------gtatggaaggtttttaaattttcat--actttattccgt-gtcaaactgccttctgaaattattgagtttgttac----ttgcagGATGTATTTGACCTTCCTTTTCACATGGCCAGAGATCAAATAGAAGAAAGTCTTCGCAACAAAATGGCTTCTATAAAG
upper sequence: PP1S47_178V6.2 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA13G00980.1 (Glycine max), 3'ss of exon 11
gtaatttcaaatcatattttgttttcaagtttcactcgcttagcgatcagaatgtggtgtaagaatcactttgcaacgtgttctgccccaggcagtacaagttcaagtgaaggtagccagtcatcaaccagccacttcactgagttgaattttatgcatttttacagGATGTATTTGACCTACCTTTTCATATGGCAAGAGATCAAATTGAACAAAGTTTGCGTGCCAAGATGTCCACTATTAAG
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----------------------------------------------------------------------------------gtatggaagattattaaattttcatactttattccctat-gtcaaactgccttctgaaattaatgagtttggtac----ttgcagGACGTATTTGACCTTCCTTTTCACATGGCCAGAGATCAAATAGAAGAAAGTCTTCGTAACAAAATGGCTTCTATAAAG
upper sequence: PP1S47_178V6.2 (Physcomitrella patens), 3'ss of exon 11
lower sequence: AT2G18876.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaatttcaaatcatattttgttttcaagtttcactcgcttagcgatcagaatgtggtgtaagaatcactttgcaacgtgttctgccccaggcagtacaagttcaagtgaaggtagccagtcatca-accagc-cacttcactgagt-tgaattttatgcatttttacagGATGTATTTGACCTACCTTTTCATATGGCAAGAGATCAAATTGAACAAAGTTTGCGTGCCAAGATGTCCACTATTAAG
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--------------------------------------------------------gtacataaatctcattataagctaattcaatttt--caat-cgattcctgttgtatatacacagccaaaacaccagtacatatcaacaagaatgaatatcg---gtattgacagGACGTTTTTGACCTACCTTTTCGTATGGCACGAGGTCAAATAGAAGATAGTTTACGCTCTAAGATGGTTTCCATCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtagccagtcatcaaccagccacttcactgagttgaattttatgcatttttacagGATGTATTTGACCTACCTTTTCATATGGCAAGAGATCAAATTGAACAAAGTTTGCGTGCCAAGATGTCCACTATTAAG
cattttt CT-rich tract
aattttatgcattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttcaaatcatattttgttttcaagtttcactcgcttagcgatcagaatgtggtgtaagaatcactttgcaacgtgttctgccccaggcagtacaagttcaagtgaaggtagccagtcatcaaccagccacttcactgagttgaattttatgcatttttacagGATGTATTTGACCTACCTTTTCATATGGCAAGAGATCAAATTGAACAAAGTTTGCGTGCCAAGATGTCCACTATTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG