Sequence
atgc intronic sequence ATGC exonic sequence...agaactgctgcgggttccatgtcgtctacgatgtattgcgctgtgcagcgttaagtttggtacgtcctgttctgaccgccgtcgccgtggcatgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
Basic information
| species | Physcomitrella patens |
| transcript | PP1S58_249V6.1 |
| intron # | 5 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S58_249V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 3
agaactgctgcgggttccatgtcgtctacgatgtattgcgctgtgcagcgttaagtttggtacgtcctgttctgaccgccgtcgccgtg-gcatgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
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---------gtaagcactaag-caccagcaacg-gcaacgccatcc-gtttcaacgacg--acgatgtgcttacgttttggttcgtgtgcgtgtg-tgcagGGCATGATGAACAACTGCTGGTTCAGGGTGAAGACGAAGACGTGCAGGCCGCACAAGGGGGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
upper sequence: PP1S58_249V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os08g36480.1 (Oryza sativa), 3'ss of exon 3
agaactgctgcgggttccatgtcgtctacgatgtattgcgctgtgcagcgttaagtttggtacgtcctgttctgaccgccgtcgccgtggcatgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
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-------gtaggtgcttcattccgtctccggc-caaggcgacg-gcgatgtagacgacgat--ggcaaattcattcgatcggt----tgggtttttgcagGGGATGATGAACAACTGCTGGTTCAAGGTGAAGGTGAACGTGTGCCGGCCGCACAAGGGTGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCCGGGA
upper sequence: PP1S58_249V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G428027_T01 (Zea mays), 3'ss of exon 3
-----------------------agaactgctgcgggttccatgtcgtc---tacgatg--tattgcgctgtgcagcgttaagtttggtacgt-cctgttctgaccgccgtcgccgtggcatgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
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gtgagttaccgcttcatcgtgcttcctttccggtggcttcgccgtcggtccgtccgatgcttgtcttccacggctgtgttagattaaatgcacgtgtggcttgtccgttcctgc----gcgcgc-gcagGGCATGATGAACAACTGCTGGTTCCGGGTGAAGGTCAACGCGTGCCGGCCGCACAAGGGCGAGATCGGCCTGGTGTTCGAGCACCCGACGCAGCCGGGCA
upper sequence: PP1S58_249V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM5G878558_T01 (Zea mays), 3'ss of exon 3
---------agaactgctgcgggttccatgtcgt----ctacg-atgtattgcgctgtgca---gcgttaagtttggtacgtcctgttctgaccgccgtcgccgtggcatgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
| | | | | || | ||| | | | |||| | | || | | |||| || ||| | | | | | | | | |||||| |||||||||||||||||||||||||||||| || | | | | | ||| ||| | ||| |||||||||||| | | ||||||||
gtgagttgccgctccatcgtgtttcccttcccgtggaaccatgcatgtcctcctctccacgactgtgttagcttaaatacacgcacgtgcgtctgtt-cctctacg------cgcagGGCATGATGAACAACTGCTGGTTCCGGGTGAAGATCAACGCGTGCCGGCCGCACAAGGGCGAGATCGGCATGGTGTTCGAGCACCCGGCGCAGCCGGGCA
upper sequence: PP1S58_249V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G568636_T01 (Zea mays), 3'ss of exon 3
agaactgctgcgggttccatgtcgtctacgatgtattgcgctgtgcagcgttaagtttggtacgtcctgttctgaccgc-cgtcgccgtggc-atgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
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------------gtacatatatatactagcacataatat-taatactgaat-aagtttc-tgtttctgctcctgatgatatataaatctgatgatggcacagGGGATGATGAACAACTGCTGGTTCAAGGTGAAGGTGAACGTGTGCCGTCCGCACAAGGGCGAGATCGGGCTGGTGTTCGAGCACCCGACGCAGCCCGGCA
upper sequence: PP1S58_249V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA14G33480.1 (Glycine max), 3'ss of exon 3
agaactgctgcgggttccatgtcgtctac--gatgtattgcgct-gtgcagcgttaagtttggtacgtcctgttctgaccgccgtcgccgtggcatgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
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---atttcaagggaccaaaaagtattttcccgctttttttcacaagtaaagcaattctaatgaatccttttgtgttatgttttgggaatgcaataatgtgtagGGTATGATGAACAACTGCTGGTTCAGGGTGAAAACAAATGTAGCCAAGCCCCACAAGGGTGAGATTGGCATAGTGTTTGAACACCCTACCCAACCAGCAA
upper sequence: PP1S58_249V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv18s0001g03910.t01 (Vitis vinifera), 3'ss of exon 3
--agaactgc---tgcgggttccatgtcgtctacgatgtattgcgctgtgcagcgttaagtttggtacgtcctgttctgaccgccgtcgccgtggcatgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
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tcatagttgcaaacatgagaggcgtg-cgtttatgacgtgattttcc-tataatttccattttgtcgtttctgattagg---gaaataataatggaattatgcagGGAATGATGAACAACTGCTGGTTCAGAGTAAAAACAAATGTGTGCAAGCGTCACAGGGGAGAGATTGGAATCGTATTCGAGCATCCAACTCTTCCAGGAA
upper sequence: PP1S58_249V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ14822 (Selaginella moellendorffii), 3'ss of exon 4
agaactgctgcgggttccatgtcgtctacgatgtattgcgctgtgcagcgttaagtttggtacgtcctgttctgaccgccgtcgccgtggcatgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
|| || ||| || || | | | || ||| | || || | || | | || ||| |||||| ||||||||||||||||||||||||||||||||| | | |||| || | | ||| | ||||| |||||||||||||| ||||||| ||
--------------------gtgagtggaagtgaatt---ctttggattgatcggt--ggttc-tcatggttcgatctctcgggctatggtg----gcagGGGATGATGAACAACTGCTGGTTCCGGGTGAAGGTCCGTCCCTGCAAGGGGAAGCTCGGGGGCGTGGCGCTGGCGTTCGAGCACCCGACGCGGCCGGCCA
upper sequence: PP1S58_249V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ26567 (Selaginella moellendorffii), 3'ss of exon 5
agaactgctgcgggttccatgtcgtctacgatgtattgcgctgtgcagcgttaagtttggtacgtcctgttctgaccgcc--gtcgccgtggc-atgctg-cagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
||| || ||| | | || | ||| | || ||||||| | || | ||| ||| || ||||| ||||||||||||||||||||||||||||||||| | |||| || | ||| | ||||| |||||||||||||| ||||||||||
--------------------------------gtaagtggcagtggatctttgggattgatcggta--gttctgatggttcgatctctcgggctatggtggcagGGGATGATGAACAACTGCTGGTTCCGGGTGAAGGTCCATCCCTGCAAGGGGAAGCTGGGGGGCGTGGCGCTGGCGTTCGAGCACCCGACGCGGCCGGGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagcgttaagtttggtacgtcctgttctgaccgccgtcgccgtggcatgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
ttctgac putative branch site (score: 2)
ttaagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaactgctgcgggttccatgtcgtctacgatgtattgcgctgtgcagcgttaagtttggtacgtcctgttctgaccgccgtcgccgtggcatgctgcagGGAATGATGAACAACTGCTGGTTCCGGGTGAAGGTCGGGATATCCAAGTTCGAGGACAGCGGCATCCACCTGGCATTCGAGCACCCGACTCGGCCGGGCA
- - -tgctgcg
