Sequence
atgc intronic sequence ATGC exonic sequence...tgtggcatcgcgtgtgccgatgaggtctcttatgcgagcaaagaatccagcaataagtaaatgttgtttttgagataacgttggtgctgttacactgcagTTTGTGGCTCTAACTCAACCAATCAACTCATTAGCATTTGTCTTTGATGGCATTCATTATGGAGCGTCAGACTTTCCTTATGCTGCTTACTCAATG
Basic information
species | Physcomitrella patens |
transcript | PP1S88_225V6.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S88_225V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: LOC_Os10g13940.1 (Oryza sativa), 3'ss of exon 9
-----------------------------------------------------------------------------tgtggcatcgcgtgtgccgatgaggtctcttatgc-gagcaaagaa---------tccagcaataagtaaatgttgtttttgagataacgttggtgctgttacactgcagTTTGTGGCTCTAACTCAACCAATCAACTCATTAGCATTTGTCTTTGATGGCATTCATTATGGAGCGTCAGACTTTCCTTATGCTGCTTACTCAATG
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gtaaactttctttatactgatgccaaaataattacaattttaagtcatattgtagttaggattcctcagttgtgtgcgggagcctgatgttcctttatgatatctttcctactgtgcattgggatgcctgcctactgtcagagttacctggaatttttttaactaaagagttatttttcctgttcagTTTGTCTCTCTGACTCAACCAATCAATGCGTTAGCTTTTGTTTTTGATGGTATCAATTATGGAGCATCAGATTTTGGATATGCTGCTTATTCAATG
upper sequence: PP1S88_225V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA13G27300.1 (Glycine max), 3'ss of exon 11
tgtggcatcgcgtgtgccgatgaggtctcttatg----cgagcaaagaatccagcaataagtaaatg-ttgtttttgagataacgttggtgctgttacactgcagTTTGTGGCTCTAACTCAACCAATCAACTCATTAGCATTTGTCTTTGATGGCATTCATTATGGAGCGTCAGACTTTCCTTATGCTGCTTACTCAATG----
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----gtaatccctataacaataaattcaacaatggaattgaccataaaatttatgtgtgaattgttaattgataattatctaatttcaaaaatataatccaccagTTTGTGGCTGCTACTCAACCAATCAATTCATTAGCCTTTGTATTTGATGGAGTGAACTATGGAGCTTCTGATTTTGCATATTCAGCATACTCTCTGGCAA
upper sequence: PP1S88_225V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA12G36620.1 (Glycine max), 3'ss of exon 12
tgtggcatcgcgtgtgccgatgaggtctcttatgcgagcaaagaatc-cagcaataagtaaatgttgtttttgagataacgttggtgctgttacactgcagTTTGTGGCTCTAACTCAACCAATCAACTCATTAGCATTTGTCTTTGATGGCATTCATTATGGAGCGTCAGACTTTCCTTATGCTGCTTACTCAATG----
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----gtaacccatataacaacaaattcaacaatatttggaaaccatgatatttatatttgaat--tgttaattatctaatttcatttatataatccactagTTTGTGGCTGCTACTCAACCAATCAATTCATTAGCCTTTGTATTTGATGGAGTGAACTATGGTGCTTCTGATTTTGCATATTCAGCATACTCTCTGGCAA
upper sequence: PP1S88_225V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA09G15550.1 (Glycine max), 3'ss of exon 10
-tgtggcatcgcgtgtgccgatgaggtctcttatgcgagcaaagaatccagcaataagta-aatgttgtttttgagataacgttggtgctgttacactgcagTTTGTGGCTCTAACTCAACCAATCAACTCATTAGCATTTGTCTTTGATGGCATTCATTATGGAGCGTCAGACTTTCCTTATGCTGCTTACTCAATG
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tttttacattgtcagtgtataatccctttatctcatatatcacttgcacaaaaatgaatttgatattattttctatttcatttt--taattttactcgccagTTTGTTGCTGCCACACAACCAATCAATTCATTAGCCTTTGTCTTTGATGGTGTGAACTATGGGGCATCTGATTTTGCATATTCTGCATACTCCTTG
upper sequence: PP1S88_225V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA12G36610.1 (Glycine max), 3'ss of exon 9
tgtggcatcgcgtgtgccgatgaggtctcttatgcgagcaaagaatccagcaataagtaaatgttgtttttgagataacgtt----ggtgctgtta--cactgcagTTTGTGGCTCTAACTCAACCAATCAACTCATTAGCATTTGTCTTTGATGGCATTCATTATGGAGCGTCAGACTTTCCTTATGCTGCTTACTCAATG----
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-----tatgaatttcaccaataagataaagcgcgaaag-aaagagtgtattgatagtatttctctatacatgttttattgttttctgatatcatttatttcaccagTTTGTTGCAGCTACTCAACCAATCAATTCATTGGCCTTTGTCTTTGATGGTGTCAACTATGGGGCATCCGATTTTGCATATTCTGCCTATTCTTTGGCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccagcaataagtaaatgttgtttttgagataacgttggtgctgttacactgcagTTTGTGGCTCTAACTCAACCAATCAACTCATTAGCATTTGTCTTTGATGGCATTCATTATGGAGCGTCAGACTTTCCTTATGCTGCTTACTCAATG
agataac putative branch site (score: 3)
aataagtaaatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtggcatcgcgtgtgccgatgaggtctcttatgcgagcaaagaatccagcaataagtaaatgttgtttttgagataacgttggtgctgttacactgcagTTTGTGGCTCTAACTCAACCAATCAACTCATTAGCATTTGTCTTTGATGGCATTCATTATGGAGCGTCAGACTTTCCTTATGCTGCTTACTCAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT