Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgatattgcttcgtgctgttgatcaattcaacggttagtaacatgtaatgttcatggtgtggaagacattttggtgctactagagtgcacagggtggtgtattgaatattggagccctgattcgtatcggcgtttggtcttcagGTGGAAACTTTTGGTGCCATGGCAAAAACTGAGAAGATTGCTTTCATTCTTGAACAA
Basic information
species | Physcomitrella patens |
transcript | PP1S257_89V6.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S257_89V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G013750_T04 (Zea mays), 3'ss of exon 4
gtatgtgatattgcttcgtgctgttgatcaattcaacggttagtaacatgtaatgttcatggtgtggaagacattttggtgctactagagtgcacagggtggtgtattgaatattggagccctgattcgtatcggcgtttggtcttcagGTGGAAACTTTTGGTGCCATGGCAAAAACTGAGAAGATTGCTTTCATTCTTGAACAA
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------------------------tgaacc-ctaaatactacggtattcataaattccatagttt------tatcttgaaactccaaaaatac------tgagctaccaaaac---aggccctaacaagc---------tatttatcagGTCGAAACATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG
upper sequence: PP1S257_89V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G014116_T02 (Zea mays), 3'ss of exon 4
gtatgtgatattgcttcgtgctgttgatcaattcaacggttagtaacatgtaatgttcatggtgtg-gaagacattttggtgctactagagtgcacagggtggtgtattgaatattggagccctgattcgtatcggcgtttggtcttcagGTGGAAACTTTTGGTGCCATGGCAAAAACTGAGAAGATTGCTTTCATTCTTGAACAA
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-----------------gtaagtttgccccgcactataattgaggacatgtaat-tccatattctgtgacaatgtttttgtcattctttagtac-cgttcctcaattctcactatccatgactataatggactaacaagctgtttatcagGTTGAAACATTTGGCTCTATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG
upper sequence: PP1S257_89V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA04G39520.1 (Glycine max), 3'ss of exon 4
gtatgtgatattgcttcgtgctgttgatcaattcaacggttagtaacatgtaatgttcatggtgtggaagacattttggtgctactagagtgcacagggtggtgta-ttgaatattggagccctgattcgtatcggcg-tttggtcttcagGTGGAAACTTTTGGTGCCATGGCAAAAACTGAGAAGATTGCTTTCATTCTTGAACAA
||| | | ||| ||| ||| ||| || | | || |||||| | || ||| | | ||| | || | || | ||| | || | ||| | |||||||||||||||||||||||||| ||||||||||| || || |||||||||||||||
--------------------------gtcagtgtgaatttta--aacgtgtgatgg--attttattatgcac-ctttggtttttgtatgt--cactagttagtgaaattagctgtttg----ttgacttacatgattgatttccttaacagGTGGAAACTTTTGGTGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA
upper sequence: PP1S257_89V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA06G15330.1 (Glycine max), 3'ss of exon 4
gtatgtgatattgcttcgtgctgttgatcaattcaacggttagtaacatgtaatgttcatggtgtggaagacattttggtgctactagagtgcacagggtggtgtattgaatattggagccctgattcgtatcggcg-tttggtcttcagGTGGAAACTTTTGGTGCCATGGCAAAAACTGAGAAGATTGCTTTCATTCTTGAACAA
|| | | ||| || ||| ||| || | | || ||| | | | | | | || ||| ||| | ||| | || | ||| | ||||||||||||||||| |||||||| ||||||||||| || || |||||||||||||||
--------------------------gtccgtgtgaatttta--aatgtgtgatgg--attttattatgtacctttggtttttgtatgtctctagtaattgaa--attagctatcag----ttgacttacatgattggtttccttaacagGTGGAAACTTTTGGCGCCATGGCTAAAACTGAGAAAATCGCATTCATTCTTGAACAA
upper sequence: PP1S257_89V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA05G32030.2 (Glycine max), 3'ss of exon 4
gtatgtgatattgcttcgtgctgttgatcaattcaacggttagtaacatgtaatgttcatggtgtggaagacattttggtgctactagagtgcacagggtggtgtattgaatattggagccctgattcgtatcggcgtttggtcttcagGTGGAAACTTTTGGTGCCATGGCAAAAACTGAGAAGATTGCTTTCATTCTTGAACAA
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----------------------------------gtcagtgtg-aacgtgt----ctcatgttttgttggc--ttcta----tactttgttttttggacttaactgataagtattcagtttacttatggaatgggtaatc--ttaacagGTGGAAACTTTTGGTGCCATGGCCAAGACTGAGAAAATTGCATTCATTCTCGAACAA
upper sequence: PP1S257_89V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA08G15340.1 (Glycine max), 3'ss of exon 4
gtatgtgatattgcttcgtgctgttgatcaattcaacggttagtaacatgtaatgttcatggtgtggaagacattttggtgctactagagtgcacagggtggtgtattgaatattggagccctgattcgtatcggcgtttggtcttcagGTGGAAACTTTTGGTGCCATGGCAAAAACTGAGAAGATTGCTTTCATTCTTGAACAA
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--------------------------gtcagtgtgaatgt--gtcacatgttttgtt---ggcttgta---tactttgttttt--tggatgtaactaattagtattcagtttacttatggaatgggtaatctgaac-----------agGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTTGAACAA
upper sequence: PP1S257_89V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT5G64760.2 (Arabidopsis thaliana), 3'ss of exon 4
gtatgtgatattgcttcgtgctgttgatcaattcaacggttagtaacatgtaatgttcatggtgtggaagacattttggtgctactagagtgcacagggtggtgtattgaatattggagccctgattcgtatcggcgtttggtcttcagGTGGAAACTTTTGGTGCCATGGCAAAAACTGAGAAGATTGCTTTCATTCTTGAACAA
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--------------------------gtaagcttttcttcctctactttccaactttc-----gtggaaatcgttttttatttatttta----------tagtttatc-aatgt----gcattgattgtgatta-----tgaattatagGTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCTTTCATTCTTGAACAA
upper sequence: PP1S257_89V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT5G09900.2 (Arabidopsis thaliana), 3'ss of exon 4
gtatgtgatattgcttcgtgctgttgatcaattcaacggttagtaacatgtaatgttcatggtgtggaagacattttggtgctactagagtgcacagggtggtgtattgaatattggagccctgattcgtatcggcgtttggtcttcagGTGGAAACTTTTGGTGCCATGGCAAAAACTGAGAAGATTGCTTTCATTCTTGAACAA
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----------------------------------------------------------gtaagattttgtgcatttggctatta----aatctcctggaaattttcttcccttgttaacccctg---caatttgataaataattaacagGTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCATTTATCCTTGAACAA
upper sequence: PP1S257_89V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 4
gtatgtgatattgcttcgtgctgttgatcaattcaacggttagta-acatgtaatgttcatggtgtggaagacattttggtgctactagagtgcacagggtggtgtattgaatattggagccctgattcgtatcggcgtttggtcttcagGTGGAAACTTTTGGTGCCATGGCAAAAACTGAGAAGATTGCTTTCATTCTTGAACAA
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----------------------gtcagttaaaaatagagttaccatgggctttttatttttggtattagaaa-acactaaccccgttg-------tttgtttttatatt--acacgagcactttggttgatgtta---cttaatca-cagGTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTTGAACAAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|162160423|gb|FC337424.1|FC337424EST: CAAGAAGTCGCG GTGGAAACTTTTGGTGCCATGGCAAAAACTGAGAAGATTGCTTTCATTCTT
genomic: CAAGAAGTCGCGgtatgtgata ... tggtcttcagGTGGAAACTTTTGGTGCCATGGCAAAAACTGAGAAGATTGCTTTCATTCTT
EST:
gi|100403833|gb|BY955124.1|BY955124EST: AAGAACAAGGAAACATCGCCGAAGCTGCGGATTGCATGCAAGAAGTCGCG GTGGAAACTTTTGGTGCCATGGCAAAAACTGAGAAGATTGCTTTCATTCTT
genomic: AAGAACAAGGAAACATCGCCGAAGCTGCGGATTGCATGCAAGAAGTCGCGgtatgtgata ... tggtcttcagGTGGAAACTTTTGGTGCCATGGCAAAAACTGAGAAGATTGCTTTCATTCTT
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
33 (upstream exon),
32 (downstream exon)
Score:
14CGTTGAGATAGAAAGAGCTCGCTTAATCAAGAAGCTAGCGAAGATCAAGGAAGAACAAGGAAACATCGCCGAAGCTGCGGATTGCATGCAAGAAGTCGCGgtatgtgata ... tggtcttcagGTGGAAACTTTTGGTGCCATGGCAAAAACTGAGAAGATTGCTTTCATTCTTGAACAA
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagggtggtgtattgaatattggagccctgattcgtatcggcgtttggtcttcagGTGGAAACTTTTGGTGCCATGGCAAAAACTGAGAAGATTGCTTTCATTCTTGAACAA
ccctgat putative branch site (score: 14)
tcttc putative PPT
tattgaatatt TA-rich tract