Sequence
atgc intronic sequence ATGC exonic sequencegtacacactatctagagctcttgcatctgaaacttgcgaattagttaaagaaccagcatgtgcatcctattttcatttaaatcttggtatgcctaatatttaatgctgaacttgaattttaatccgttgcttccagTGGAGGAAGTAAGATCAAAGGGCATATACCGTATAGAGACTCAAAGCTGACGAGGATTCTACAGCATTCGTTGGGAGGAAATGCAAGAACTGCTATTATT
Basic information
species | Physcomitrella patens |
transcript | PP1S343_28V6.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S343_28V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os02g43050.1 (Oryza sativa), 3'ss of exon 5
gtacacactatctagagctcttgcatctgaaacttgcgaattagttaaagaaccagcatgtgcatcctatt-ttcatttaaatcttggtatgcctaatatttaatgctgaacttgaattttaatccgttgcttccagTGGAGGAAGTAAGATCAAAGGGCATATACCGTATAGAGACTCAAAGCTGACGAGGATTCTACAGCATTCGTTGGGAGGAAATGCAAGAACTGCTATTATT------
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-------------------------ttgggattttatatagtgtacaataaagtgggatgtttacagtaatgtttgcttggaatttcgcccaagtgatatc---------agttatatctt--ttcattaatgc-agCATGGGAAGTAATGC------ACACATACCGTATAGAGATTCAAAGCTTACACGCATACTACAGCCATCTTTGGGAGGTAATGCAAGAACTGCAATTATTTGTACA
upper sequence: PP1S343_28V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os08g43400.4 (Oryza sativa), 3'ss of exon 8
gtacacactatctagagctcttgcatctgaaacttgcgaattagttaaagaaccagcatgtgcatcctattttcatttaaatcttggtatgcctaatatttaatgctgaacttgaattttaatccgttgcttccagTGGAGGAAGTAAGATCAAAGGGCATATACCGTATAGAGACTCAAAGCTGACGAGGATTCTACAGCATTCGTTGGGAGGAAATGCAAGAACTGCTATTATT------
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--------------------------------tggatgaactaattttgaattccttttgcgcgtcgca-----attcaactctttgattgcattat---taccatccaatttag--tctaagctatatgttcatgttgcagTAAGGGAAGAAATGGCCATATCCCCTACAGAGATTCAAAGCTGACTCGTATATTACAGTCTTCCTTGGGAGGCAATGCAAGAACTGCTATTATCTGCACA
upper sequence: PP1S343_28V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G136838_T02 (Zea mays), 3'ss of exon 9
gtacacactatctagagctcttgcatctgaaacttgcgaattagttaaagaaccagcatgtgcatcctattttcatttaaatcttggtatgcctaatatttaatgct----gaacttgaattttaatccgttgcttccagTGGAGG--AAGTAAGATCAAAGGGCATATACCGTATAGAGACTCAAAGCTGACGAGGATTCTACAGCATTCGTTGGGAGGAAATGCAAGAACTGCTATTATT---
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--------------------------------------------tagaaagacatgcat-tgtttctaggttgtaatagaaaattcaagcaacaaatatccatcgttatttgtaactgaaacttaactgtaaacttcaattgcagTTCGGGGAAAAGAAGTGGACACATTCCCTACCGGGACTCAAAGCTGACACGCATTCTACAGCTTTCTTTGGGTGGAAATGCAAGAACAGCAATCATCTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttggtatgcctaatatttaatgctgaacttgaattttaatccgttgcttccagTGGAGGAAGTAAGATCAAAGGGCATATACCGTATAGAGACTCAAAGCTGACGAGGATTCTACAGCATTCGTTGGGAGGAAATGCAAGAACTGCTATTATT
ttttaat putative branch site (score: 3)
ttgcttcc putative PPT
aacttgaattttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacacactatctagagctcttgcatctgaaacttgcgaattagttaaagaaccagcatgtgcatcctattttcatttaaatcttggtatgcctaatatttaatgctgaacttgaattttaatccgttgcttccagTGGAGGAAGTAAGATCAAAGGGCATATACCGTATAGAGACTCAAAGCTGACGAGGATTCTACAGCATTCGTTGGGAGGAAATGCAAGAACTGCTATTATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC