Sequence
atgc intronic sequence ATGC exonic sequence...agtgagaaatgtttgctacttttcttacgtctgaatagtgtttgtgtgtctttaagtttgcattaccttagcctgatttgatatgtatccatttctgcagAGTGTGCTTGGTATAATTCTAGGTGGCGGAGCAGGGACACGTTTGTATCCTTTGACCAAAAAGCGTGCCAAGCCAGCTGTGCCGATAGGTGCCAATTACC
Basic information
species | Physcomitrella patens |
transcript | PP1S2_337V6.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S2_337V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 1
agtgagaaatgtttgctact-tttcttacgtctgaatagtgttt-gtgtgtctttaagtttgcattaccttagcctgatttgatatgtatccatttctgcagAGTGTGCTTGGTATAATTCTAGGTGGCGGAGCAGGGACACGTTTGTATCCTTTGACCAAAAAGCGTGCCAAGCCAGCTGTGCCGATAGGTGCCAATTACC
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--ttcaaattgcacaataatcttttttaagacaagattttgccccactcatcgtttttgttggataattatctctactgatgctcttcttttgttggtgcagAGTGTGCTTGGAATCATTCTTGGAGGTGGTGCAGGGACTAGATTGTATCCCCTCACCAAGAAGCGTGCCAAGCCTGCCGTGCCTCTGGGTGCCAACTACA
upper sequence: PP1S2_337V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EDP04344 (Chlamydomonas reinhardtii), 3'ss of exon 3
agtgagaaatgtttgctacttttcttacgtctgaatagtgtttgtgtgtctttaagtttgcattaccttagcctgatttgatatgtatccatttctgcagAGTGTGCTTGGTATAATTCTAGGTGGCGGAGCAGGGACACGTTTGTATCCTTTGACCAAAAAGCGTGCCAAGCCAGCTGTGCCGATAGGTGCCAATTACC
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------------------gtatgctcgcgctggccca---tttg-atgcttccggactcg--tcgatgtgacc-gtcccgccatctcgttgccgatgcagACGGTGCTGGGTATTATTCTGGGTGGTGGTGCCGGCACCCGTCTGTATCCTCTGACCAAGAAGCGTGCCAAGCCGGCGGTGCCCCTGGGCGCCAACTATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtctttaagtttgcattaccttagcctgatttgatatgtatccatttctgcagAGTGTGCTTGGTATAATTCTAGGTGGCGGAGCAGGGACACGTTTGTATCCTTTGACCAAAAAGCGTGCCAAGCCAGCTGTGCCGATAGGTGCCAATTACC
tccatttct CT-rich tract
tttaagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtgagaaatgtttgctacttttcttacgtctgaatagtgtttgtgtgtctttaagtttgcattaccttagcctgatttgatatgtatccatttctgcagAGTGTGCTTGGTATAATTCTAGGTGGCGGAGCAGGGACACGTTTGTATCCTTTGACCAAAAAGCGTGCCAAGCCAGCTGTGCCGATAGGTGCCAATTACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG