Sequence
atgc intronic sequence ATGC exonic sequencegtaaggctcttcacttttgtattcttcatgtgtggtactaaaacaatatttgagcagttgcaagctgatatcgcttcgcgcacggacttctacaccccatcatattgagtctaagtgagggattatttttctgttccacacaatatgctagaaagggatgaaagactttatcttacatgtacttcattatgttgcagATGAGTATGTTATGTGCAATGGTTGCAAGAGTCCAGACACTATCCTTTCCAAGGAGAATCGGCTGTTCTTTCTTCGTTGTGAACAG
Basic information
species | Physcomitrella patens |
transcript | PP1S81_161V6.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S81_161V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os03g21550.2 (Oryza sativa), 3'ss of exon 8
gtaaggctcttcacttttgtattcttcatgtgtggtactaaaacaatatttgagcagttgcaagctgatatcgcttcgcgcacggacttctacaccccatcatattgagtctaagtgagggattatttttctgttccacacaatatgctagaaagggatgaaagactttatcttacatgtacttcattatgttgcagATGAGTATGTTATGTGCAATGGTTGCAAGAGTCCAGACACTATCCTTTCCAAGGAGAATCGGCTGTTCTTTCTTCGTTGTGAACAG
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-------------------------------------------------------------------------------gtttattctcttgttcctt-ttatga-ggtcctatgtgtgggattgtcattaaagtct---tgttgtgctaaac------------ttacatccttttttaatttcactccttt-cagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTAAGGAGAATAGGTTGTTCTTCCTTCGTTGCGAACAG
upper sequence: PP1S81_161V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os07g48300.1 (Oryza sativa), 3'ss of exon 8
gtaaggctcttcacttttgtattcttcatgtgtggtactaaaacaatatttgagcagttgcaagctgatatcgcttcgcgcacggacttctacaccccatcatattgagtctaagtgagggattatttttctgttccacacaatatgctagaaagggatgaaagactttatcttacatgt-acttcatt--atgttgcagATGAGTATGTTATGTGCAATGGTTGCAAGAGTCCAGACACTATCCTTTCCAAGGAGAATCGGCTGTTCTTTCTTCGTTGTGAACAG
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---------------------------gtaagttatcctacttcattcccttggttga-acagatgagcttcccctttttcatg---tgtggtaaactatcataagttgtacgtttgttgt-ttactgttttgttagtgttagttgactt--aagatttcaagggttatatgcaacttattgcgtctttaaacctttcagATGAGTACGTCATTTGCAATGGTTGCAAAAGCCCTGATACCATTCTATCCAAGGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG
upper sequence: PP1S81_161V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G030646_T02 (Zea mays), 3'ss of exon 6
gtaaggctcttcacttttgtattcttcatgtgtggtactaaaacaatatttgagcagttgcaagctgatatcgcttcgcgcacggactt-ctacaccccatcat-attgagtctaagtgagggattatttttctgttccacacaatatgctagaaagggatgaaagactttatcttacatgtacttcattatgttgcagATGAGTATGTTATGTGCAATGGTTGCAAGAGTCCAGACACTATCCTTTCCAAGGAGAATCGGCTGTTCTTTCTTCGTTGTGAACAG
||||| || | || ||| | || || | || || || | | |||| | || |||| | || || | |||| || | || || ||||| | | ||| | || ||| | || | | | | | ||| | |||| | || | |||| ||||||||||||| || |||||||| |||||||| || || ||||| | ||||| || ||||| |||||||| ||||| || ||||||
gtaag-ctatccattttgattgcgttgatatttg-tagtatgcc--tttttggatatatg-gtgctgctttccttttataagcatacttgctgtttgctattatgattgaataaatatgattg--tagtttaccttttttctctctcccc------gcgatctgaaacttgac------tgaatttca--------cagATGAGTATGTCATCTGCAATGGATGCAAGAGCCCTGATACTATTTTGTCCAAAGAAAATCGTCTGTTCTTCCTTCGCTGCGAACAG
upper sequence: PP1S81_161V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA14G38600.1 (Glycine max), 3'ss of exon 8
gtaaggctcttcacttttgtattcttcatgtgtggtactaaaacaatatttgagcagttgcaagctgatatcgcttcgcgcacggacttctacaccccatcat-attgagtctaagtgagggattatttttctgttccacacaatatgctagaaagggatgaaagactttatcttacatgtacttcattatgttgcagATGAGTATGTTATGTGCAATGGTTGCAAGAGTCCAGACACTATCCTTTCCAAGGAGAATCGGCTGTTCTTTCTTCGTTGTGAACAG
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---------------------------------------------------------------------------------------tagcagacatgaactttaataactctaccttggctattgctttgctgtctactatctcgggccatca---gttgaag--------ttgatatacctttttgtttatctcagATGAATATGTTATTTGCCTTGGGTGCAAGAGTCCGGATACTATACTTTCAAAGGAGAATCGTCTCTTCTTTCTCCGGTGTGAGAAG
upper sequence: PP1S81_161V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv06s0004g08180.t01 (Vitis vinifera), 3'ss of exon 8
gtaaggctcttcacttttgtattcttcatgtgtggtactaaaacaatatttgagcagttgcaagctgatatcgcttcgcgcacggacttctacaccccatcatattgagtctaagtgagggattatttttctgttccacacaatatgctagaaagggatgaaagactttatcttacatgtacttcattatgttgcagATGAGTATGTTATGTGCAATGGTTGCAAGAGTCCAGACACTATCCTTTCCAAGGAGAATCGGCTGTTCTTTCTTCGTTGTGAACAG
||| ||| || || | | ||| ||| | | |||| | | | | || ||| | | | | || || | ||| ||||||||||||| || ||| ||| ||||| ||||| ||||| || ||||| ||||||||||| || |||||||| | || || |||
--------------------------------------------------------------------------------------tgcctaagatccaaaatttttgctgcca-tgatggac-acatggatgtttcttgtagcctat------gacattcttaactct-tttgatggctatttggt-gtgtc-cagATGAGTATGTAATATGCCTTGGGTGCAAAAGTCCGGACACAATTCTTTCAAAGGAGAATCGTCTCTTCTTTCTCAGATGCGAGCAG
upper sequence: PP1S81_161V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ28838 (Selaginella moellendorffii), 3'ss of exon 7
gtaaggctcttcacttttgtattcttcatgtgtggtactaaaacaatatttgagcagttgcaagctgatatcgcttcgcgcacggacttctacaccccatcatattgagtctaagtgagggattatttttctgttccacacaatatgctagaaagggatgaaagactttatcttacatgtacttcattatgttgcagATGAGTATGTTATGTGCAATGGTTGCAAGAGTCCAGACACTATCCTTTCCAAGGAGAATCGGCTGTTCTTTCTTCGTTGTGAACAG
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--------------------------------------------------------------------------------------------------------------gtaagttctcaatc-tcttttcatttccttcgtttcgtttgtctaggagaaatcattt-------------ctttatcg-atcgcagATGAATACGTTATGTGCAATGGCTGCAAGAGCCCCGACACTATTCTTTCGAAAGAAAACAGGCTCTTTTTTCTACGATGCGAGCAA
upper sequence: PP1S81_161V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ17507 (Selaginella moellendorffii), 3'ss of exon 3
gtaaggctcttcacttttgtattcttcatgtgtggtactaaaacaatatttgagcagttgcaagctgatatcgcttcgcgcacggacttctacaccccatcatattgagtctaagtgagggattatttttctgttccacacaatatgctagaaagggatgaaagactttatcttacatgtacttcattatgttgcagATGAGTATGTTATGTGCAATGGTTGCAAGAGTCCAGACACTATCCTTTCCAAGGAGAATCGGCTGTTCTTTCTTCGTTGTGAACAG
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--------------------------------------------------------------------------------------------------------------gtaagttctcaatc-tcttttcatttccttcgtttcgtttatctaggagaaatcattt-------------ctttatcg-atcgcagATGAATACGTTATGTGCAATGGCTGCAAGAGCCCCGACACTATTCTTTCGAAAGAAAACCGGCTCTTTTTTCTACGATGCGAGCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatgctagaaagggatgaaagactttatcttacatgtacttcattatgttgcagATGAGTATGTTATGTGCAATGGTTGCAAGAGTCCAGACACTATCCTTTCCAAGGAGAATCGGCTGTTCTTTCTTCGTTGTGAACAG
atcttac putative branch site (score: 3)
cttcatt putative PPT
tttatctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggctcttcacttttgtattcttcatgtgtggtactaaaacaatatttgagcagttgcaagctgatatcgcttcgcgcacggacttctacaccccatcatattgagtctaagtgagggattatttttctgttccacacaatatgctagaaagggatgaaagactttatcttacatgtacttcattatgttgcagATGAGTATGTTATGTGCAATGGTTGCAAGAGTCCAGACACTATCCTTTCCAAGGAGAATCGGCTGTTCTTTCTTCGTTGTGAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT