Sequence
atgc intronic sequence ATGC exonic sequence...ataggcaacacaatcattggtacagtgtcacagccgattgacttcacacttcaagggcatgttcatttttgagttacgaatgctaatggtggttttgtagGAGTTGGTCACAGAAGTAGATCCGGATATTATCATTGGATACAACATTTGTAAATTTGACTTACCCTATCTTATCGAG
Basic information
species | Physcomitrella patens |
transcript | PP1S54_271V6.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S54_271V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os11g08330.1 (Oryza sativa), 3'ss of exon 7
ataggcaacacaatcattggtacagtgtcacagccgattgacttcacacttcaagggcatgttcatttttgagttacgaatgctaatggtggttttgt--agGAGTTGGTCACAGAAGTAGATCCGGATATTATCATTGGATACAACATTTGTAAATTTGACTTACCCTATCTTATCGAG
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-------------------gta-agtaatgctg--gttggagtttacaa--caggtacacagaacttactaaaaaccaa--gctgattctgattctttccagGATTTCATACGTGAAGTGGACCCTGATATTATTATTGGATACAATATCTGCAAATTTGACTTACCCTATCTTATTGAG
upper sequence: PP1S54_271V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AC196278.2_FGT004 (Zea mays), 3'ss of exon 3
ataggcaacacaatcattggtacagtgtcacagccgattgact-tcacacttcaagggcatgttc-atttttgagttacgaatgctaatggtggttttgtagGAGTTGGTCACAGAAGTAGATCCGGATATTATCATTGGATACAACATTTGTAAATTTGACTTACCCTATCTTATCGAG
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--aaacacacttattcctgaaaagaagttaaatacattttcttattgtagacaaaggacttggccgaaaattatctgattcttatttggaaataatttgcagGATTTCATACGTGAAGTGGATCCTGATATCATAATTGGATACAACATTTGCAAATTTGACATGCCCTATCTTATTGAG
upper sequence: PP1S54_271V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA04G38800.1 (Glycine max), 3'ss of exon 7
ataggcaacacaatcattggtacagtgtcacagccgattgacttcacacttcaagggcatgttcatttttgagttacgaatgctaatggtggtt--ttgtagGAGTTGGTCACAGAAGTAGATCCGGATATTATCATTGGATACAACATTTGTAAATTTGACTTACCCTATCTTATCGAG
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cttgaatacg-agtcaatttgataatgtaactgttgaatgaatt-acaatcctttctctattacgctcttatagtttgatggacgcggttttttaattgcagGATTTTATTCGTGAAGTGGACCCTGATATTATTATTGGATACAACATTTGCAAATTTGACTTGCCATATCTTATTGAG
upper sequence: PP1S54_271V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA06G16110.2 (Glycine max), 3'ss of exon 7
ataggcaacacaa-tcattggtacagtgtcacagccgattgacttcacacttcaagggcatgttcatttttgagttacgaatgctaatggtggttttgtagGAGTTGGTCACAGAAGTAGATCCGGATATTATCATTGGATACAACATTTGTAAATTTGACTTACCCTATCTTATCGAG
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ctgaatatcatgagtcaatttgataatgtaactgttgaatgaattataatcctttctctattatgcttatagtttgatggacg-tgatttttttattgcagGATTTAATTCGTGAAGTGGACCCGGATATTATTATTGGATACAACATCTGCAAATTTGACTTGCCATATCTTATTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acacttcaagggcatgttcatttttgagttacgaatgctaatggtggttttgtagGAGTTGGTCACAGAAGTAGATCCGGATATTATCATTGGATACAACATTTGTAAATTTGACTTACCCTATCTTATCGAG
tgctaat putative branch site (score: 2)
ttcattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataggcaacacaatcattggtacagtgtcacagccgattgacttcacacttcaagggcatgttcatttttgagttacgaatgctaatggtggttttgtagGAGTTGGTCACAGAAGTAGATCCGGATATTATCATTGGATACAACATTTGTAAATTTGACTTACCCTATCTTATCGAG
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