Sequence
atgc intronic sequence ATGC exonic sequencegtacttatctacttcttgaagagtttggtttcgacgcaaaagtcttttaaccaagaccttgtatgcgctttgatacgaagttttttgtatttgtttaatcttagtggttaaatcttgtttcgaaattgagaagaaattgattttaatttttgcagAAGCCAGATATCAATTTAATTATGACGGATTACTGCATGCCGGAGATGACTGGTTACGACCTTCTAAAACGAGTGAAG
Basic information
species | Physcomitrella patens |
transcript | PP1S172_31V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S172_31V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os02g58350.1 (Oryza sativa), 3'ss of exon 2
gtacttatctacttcttgaagagtttggtttcgacgcaaaagtcttttaaccaagaccttgtatgcgctttgatacgaagttttttgtatttgtttaatcttagtggttaaatcttgtttcgaaattgagaagaaattgattttaatttt--tgcagAAGCCAGATATCAATTTAATTATGACGGATTACTGCATGCCGGAGATGACTGGTTACGACCTTCTAAAACGAGTGAAG
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------------------------------------------------------------gtatgttctttgatccctatgcctgtggatgt---cagtc--agttttgaagaattgcta-gaaatgaatgtaaaattagtttgtgttatgatgcagGATCGGAATGTGCATATGATCATCACGGATTACTGCATGCCGGAGATGACAGGGTTCGATCTCCTCAAGAGGGTCAAG
upper sequence: PP1S172_31V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G096171_T01 (Zea mays), 3'ss of exon 2
gtacttatctacttcttgaagagtttggtttcgacgcaaaagtcttttaaccaagaccttgtatgcgctttgatacgaagttttttgtatttgtttaatcttagtggttaaatcttgtttcgaaattgagaagaaattgattttaatttttgcagAAGCCAGATATCAATTTAATTATGACGGATTACTGCATGCCGGAGATGACTGGTTACGACCTTCTAAAACGAGTGAAG
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-----------------------------------------------gaaaaaaaacatagaccgtgttctcatg----acgtgatgagatctttgactgcaagtg--caagtgcaag--cagaaatgaaactgagataagaatggtttttgcagCGGATAACCATTGACATCGTGCTCACGGACTACTGCATGCCGGAGATGACTGGCTACGACCTGCTCAAGGCCATCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagtggttaaatcttgtttcgaaattgagaagaaattgattttaatttttgcagAAGCCAGATATCAATTTAATTATGACGGATTACTGCATGCCGGAGATGACTGGTTACGACCTTCTAAAACGAGTGAAG
ttttaat putative branch site (score: 3)
tttttgc CT-rich tract
aaattgagaagaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttatctacttcttgaagagtttggtttcgacgcaaaagtcttttaaccaagaccttgtatgcgctttgatacgaagttttttgtatttgtttaatcttagtggttaaatcttgtttcgaaattgagaagaaattgattttaatttttgcagAAGCCAGATATCAATTTAATTATGACGGATTACTGCATGCCGGAGATGACTGGTTACGACCTTCTAAAACGAGTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG