Sequence
atgc intronic sequence ATGC exonic sequencegtatggagtctatcaagatctattcttttctgatagaggcctatggcctcagatattctatgttttgttttaaagcgacgctcgttaagtatgctgctgaaatgacttggtatatatgatcgagttttccatggatctgtcatagcaaacacctatttcaactttatctttcttgcagGAGCCAGAGAAACACGTTTTTCACATTGTTACCGACAAGCTAAATTTTGGTGCCATGATGATGTGGTTTTTAGCAAATCCTCCCGGGGCTGCTGTCATAC
Basic information
species | Physcomitrella patens |
transcript | PP1S128_25V6.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S128_25V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G076276_T03 (Zea mays), 3'ss of exon 7
gtatggagtctatcaagatctattcttttctgatagaggcctatggcctcagatattctatgttttgttttaaagcgacgctcgttaagtatgctgctgaaatgacttggtatatatgatcgagttttccatggatctgtcatagcaaacacct-atttcaactttatctttcttgcagGAGCCAGAGAAACACGTTTTTCACATTGTTACCGACAAGCTAAATTTTGGTGCCATGATGATGTGGTTTTTAGCAAATCCTCCCGGGGCTGCTGTCATAC
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--------------------------------------------------------------------gttagtgtaatccccatcttgaa-actggaagtgtaatctcttcattatg-tctaccattgaatg-acccattatatagcacttttgattttctttctataaatttt-cagGAGCCTGAAAAACATGTGTTTCACCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATGC
upper sequence: PP1S128_25V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G147145_T02 (Zea mays), 3'ss of exon 4
gtatggagtctatcaagatctattcttttctgatagaggcctatggcctcagatattctatgttttgttttaaagcgacgctcgttaagtatgctgctgaaatgacttggtatatatgatcgagttttccatggatctgtcatagcaaacacctatttcaactttatctttcttgcagGAGCCAGAGAAACACGTTTTTCACATTGTTACCGACAAGCTAAATTTTGGTGCCATGATGATGTGGTTTTTAGCAAATCCTCCCGGGGCTGCTGTCATAC
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---------------------------------------------------------------gttagtttaatgca----tcttcaag----ctggaaatatgatctctt-cat-tgtttgtaccattgactggtcaattatattacactcttatttttcttgctataaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC
upper sequence: PP1S128_25V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA07G08910.1 (Glycine max), 3'ss of exon 5
gtatggagtctatcaagatctattcttttctgatagaggcctatggcctcagatattctatgttttgttttaaagcgacgctcgttaagtatgctgctgaaatgacttggtatatatgatcgagttttccatggatctg---tcatagcaaacacctatttcaactttatctttcttgcagGAGCCAGAGAAACACGTTTTTCACATTGTTACCGACAAGCTAAATTTTGGTGCCATGATGATGTGGTTTTTAGCAAATCCTCCCGGGGCTGCTGTCATAC
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---------------------------------------------------------------------------------gcaccaaaaatatcgtgcatgtgaaagtgtatctatgatttagtaaattatacttttaaaaccaggcctcataactttgttattgtcttcaacgttgcagGATCCTTCAAAGCATGTTTTTCACCTTGTTACCGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTCTTTTAAACCCTCCTGAAAAAGCTACAATCC
upper sequence: PP1S128_25V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA03G02250.1 (Glycine max), 3'ss of exon 13
-----gtatggagtctatcaagatctattcttttctg-atagaggcctatggcctcagatattctatgttttgttttaaagcgacg----ctcgttaagtatgctgctgaaatgacttggtatatatgatcgagttttccatggatctgtcatagcaaacacc-tatttcaactt-tatctt---tcttgcagGAGCCAGAGAAACACGTTTTTCACATTGTTACCGACAAGCTAAATTTTGGTGCCATGATGATGTGGTTTTTAGCAAATCCTCCCGGGGCTGCTGTCATAC
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gtgacttgggctgtctttttaaccataccagtatttgtgtgcaagttcattgtttcc--ttttatagattgcaaataagggtgccttgaccatggtcaacatatcgtgcatgtgaaagtgtatctatgatttagtaaattat--attattaaaaccaggcctcataacttagtttctgtcttcaatgttgcagGATCCATCGAAGAATGTTTTTCACCTTGTTACTGATAAACTAAATTTTGGAGCCATGAGCATGTGGTTTCTTTTAAACCCTCCTGGAAAAGCTACAATCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttttccatggatctgtcatagcaaacacctatttcaactttatctttcttgcagGAGCCAGAGAAACACGTTTTTCACATTGTTACCGACAAGCTAAATTTTGGTGCCATGATGATGTGGTTTTTAGCAAATCCTCCCGGGGCTGCTGTCATAC
ctttatctttcttgc CT-rich tract
tatttcaactttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggagtctatcaagatctattcttttctgatagaggcctatggcctcagatattctatgttttgttttaaagcgacgctcgttaagtatgctgctgaaatgacttggtatatatgatcgagttttccatggatctgtcatagcaaacacctatttcaactttatctttcttgcagGAGCCAGAGAAACACGTTTTTCACATTGTTACCGACAAGCTAAATTTTGGTGCCATGATGATGTGGTTTTTAGCAAATCCTCCCGGGGCTGCTGTCATAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT