Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgaattcaagcaaattccagtactttgaatctactcttttgagaaattgcgagtccaagttaattctctactcgtgtcacagatcacatatctggattttttacaattttgcagCGGAGTTCTTCACGGATCGAACAGATGTGCAATGCTTGCACAGATGGCAAAAGGTTCTCAACCCAGATCTGGTCAAGGGTGCATGGACCAAAGAGGAAGA
Basic information
species | Physcomitrella patens |
transcript | PP1S36_43V6.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S36_43V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os12g13570.1 (Oryza sativa), 3'ss of exon 3
gtgagtgaattcaagcaaattccagtact-ttgaatctactcttttgagaaattgcgagtccaa-gttaattctctactcgtgtcacagatcacatatctggattttttacaattttgcagCGGAGTTCTTCACGGATCGAACAGATGTGCAATGCTTGCACAGATGGCAAAAGGTTCTCAACCCAGATCTGGTCAAGGGTGCATGGACCAAAGAGGAAGA
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-------aagtcatgctc-ttctggcattgtttttcctactttgttgatgagattcttgtatatcgttaaaaatccaagctt-tgacaga-----------gatccttc-taattttccagCGGAATGTTTTCCGGATAGAACCGATGTACAATGCTTGCACAGGTGGCAAAAGGTTCTAAACCCTGAATTGGTCAAAGGGCCATGGTCCAAAGAA-----
upper sequence: PP1S36_43V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os01g12860.1 (Oryza sativa), 3'ss of exon 3
gtgagtgaattcaagcaaattccagtactttgaatctactcttttga-gaaattgcgagtccaa-gttaattctctactcgtgtcacagatcacatatctggattttttacaattttgcagCGGAGTTCTTCACGGATCGAACAGATGTGCAATGCTTGCACAGATGGCAAAAGGTTCTCAACCCAGATCTGGTCAAGGGTGCATGGACCAAAGAGGAAGA
| ||| | || | | || || | ||| || |||| || ||| | ||| | ||||| || | | | ||||| |||| | |||||| ||||||| | ||| ||||| |||| ||||| |||||||||||||| |||||||||||||| ||||| || | ||||| || ||||| |||||||
----tttcattaactcacaccctag-acat---gcttaccctgttgatgagatttccagtatattgttaaaaatccaagttt-tgacagagaacat------------tctaattttccagCGGAATGCTTTCCGGATAGAACCGATGTACAATGCTTGCACAGGTGGCAAAAGGTTCTAAACCCTGAATTAGTCAAAGGGCCATGGTCCAAAGAA-----
upper sequence: PP1S36_43V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G470307_T01 (Zea mays), 3'ss of exon 1
gtgagtgaattcaagcaaattccagtactttgaatctactcttttgagaaattgcgagtccaagttaattctctactcgtgtcacagatcacatatctggattttttacaattttgcagCGGAGTTCTTCACGGATCGAACAGATGTGCAATGCTTGCACAGATGGCAAAAGGTTCTCAACCCAGATCTGGTCAAGGGTGCATGGACCAAAGAGGAAGA
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-------------------------------------------------------------aagctctgcctcttgccttaagtccaaac-cttgacaaaatgcgttctactttttcagcggaaagttttccagacagaaccgatgtacaatgtttgcacagGTGGCAAAAGGTTCTAAACCCTGAATTGGTCAAAGGGCCATGGTCCAAAGAA-----
upper sequence: PP1S36_43V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv04s0008g03780.t01 (Vitis vinifera), 3'ss of exon 3
gtgagtgaattcaagcaaattccagtactttgaatctactcttttgagaaattgc---gagtccaagttaattctctactcgtgtcacagatcacatatctggattttttacaattttgcagCGGAGTTCTTCACGGATCGAACAGATGTGCAATGCTTGCACAGATGGCAAAAGGTTCTCAACCCAGATCTGGTCAAGGGTGCATGGACCAAAGAGGAAGA
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----------------aatccacaacattttaagcttctcctattattgtattgcctaaaatttgaaatgtatctctgttgacgg-atatttctaatagtaaaacttgtt-----tttttagCGGAATGTTTCAAGGATCGGACAGATGTGCAATGCTTGCACAGGTGGCAGAAGGTCTTGAATCCAGAACTTGTCAAAGGTCCATGGTCAAAAGAG----- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaattctctactcgtgtcacagatcacatatctggattttttacaattttgcagCGGAGTTCTTCACGGATCGAACAGATGTGCAATGCTTGCACAGATGGCAAAAGGTTCTCAACCCAGATCTGGTCAAGGGTGCATGGACCAAAGAGGAAGA
agttaat putative branch site (score: 4)
attttttacaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgaattcaagcaaattccagtactttgaatctactcttttgagaaattgcgagtccaagttaattctctactcgtgtcacagatcacatatctggattttttacaattttgcagCGGAGTTCTTCACGGATCGAACAGATGTGCAATGCTTGCACAGATGGCAAAAGGTTCTCAACCCAGATCTGGTCAAGGGTGCATGGACCAAAGAGGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA