Sequence
atgc intronic sequence ATGC exonic sequencegtacatttctggagcatggaagagtcttttgaacagttgattcttgtggttttgtagaagtttgtgtgcgcttacagcatgagcactgtagttcaaaactatcgccggaactggagattcgtttcaagtcgtatggttaaactaatattgtgacattgttgcagAAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTTTTGATGGCTATTTTCTCCATCTACACTGGTTTCATATACAATGAGTTCT
Basic information
species | Physcomitrella patens |
transcript | PP1S6_159V6.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S6_159V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA12G04330.1 (Glycine max), 3'ss of exon 11
gtacatttctggagcatggaagagtcttttgaacagttgattcttgtggttttgtag---aagtttgtgtgcgcttacagcatgagcactgtagttcaaaactatcgccggaactggag-attcgtttcaagtcgtatggttaaactaatattgtgacattgttg-cagAAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTTTTGATGGCTATTTTCTCCATCTACACTGGTTTCATATACAATGAGTTCT
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----------gtatccttttagtttgccttgaaaaaatatcctttaagagtataaaaggcaagcttttatattttaatgggagaaattaagtagattttctccaccttagtagaaagtgtgtgtgttttcaaccagttttctaacatagaatcttcgtgtaaaaaacagAAGCTTGATGACATCACGGAGATGACTTTTGGAGGTCGTTATGTTATTTTGTTGATGGCTATATTCTCAATCTACACTGGCTTTATCTATAATGAGTTCT
upper sequence: PP1S6_159V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA11G12120.1 (Glycine max), 3'ss of exon 11
gtacatttctggagcatggaagagtcttttgaacagttgattcttgtggttttgtagaagtttgtgtgcgcttacagcatgagcactgtagttcaaaactatcgccggaactggagattcgtttcaagtcgtatggttaaactaatattgtgacattgttgcagAAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTTTTGATGGCTATTTTCTCCATCTACACTGGTTTCATATACAATGAGTTCT
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---------------------------------------------------tagttagggtctctttcccctga-----tgaaccagagagttaaagacaaaaa---aaagtgtatgttttttactagtcttctaac---atgaaatctgtgtgaaaa--acagAAGCTTGATGACATCACGGAGATGACTTTTGGAGGTCGTTATGTTATTTTGTTGATGGCAATATTCTCAATCTACACTGGCTTTATCTATAATGAGTTCT
upper sequence: PP1S6_159V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 11
---------------gtacatttctggagcatggaagagtcttttgaacagttgattcttgtggttttgtagaagtt-tgtgtgcgcttacagcatgagcactgtagttcaaaa-ctatcgccggaactgg------agattcgttt------caagtcgtatg-gttaaactaata----ttgtgacattgttgcagAAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTTTTGATGGCTATTTTCTCCATCTACACTGGTTTCATATACAATGAGTTCT
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gtaatacccctaattgacagcatctattttccgactgagcacagtataagattggtttctgt--ttcagaaaaagttgtgtgcaaatttcaaattcaagaaaattattttgagagttgttactttgattggtcatcaatgtttgtctttcttgcaagttctagatgctaaaccatcaatccttgcttcgtgacaacagAAACTTGGGGATATTATGGAAATGGCTTTTGGTGGCCGTTACGTTATTTTTATGATGTCACTATTCTCAATATACACTGGTTTAATCTACAACGAGTTCTMapped 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|162192954|gb|FC371456.1|FC371456EST: TTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGGAAAACAG AAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTT
genomic: TTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGGAAAACAGgtacatttct ... attgttgcagAAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTT
EST:
gi|162174814|gb|FC352230.1|FC352230EST: TTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGGAAAACAG AAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTT
genomic: TTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGGAAAACAGgtacatttct ... attgttgcagAAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTT
EST:
gi|162156043|gb|FC332210.1|FC332210EST: TTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGGAAAACAG AAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTT
genomic: TTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGGAAAACAGgtacatttct ... attgttgcagAAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTT
EST:
gi|162156985|gb|FC333347.1|FC333347EST: TTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGGAAAACAG AAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTT
genomic: TTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGGAAAACAGgtacatttct ... attgttgcagAAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTT
EST:
gi|162173250|gb|FC350032.1|FC350032EST: TTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGNAAAACAG AAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTT
genomic: TTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGGAAAACAGgtacatttct ... attgttgcagAAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTT
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:
29 (upstream exon),
35 (downstream exon)
Score:
16CTTCCTGTTCGCTGTTATGTTTGGTGATTGGGGGCACGGTATTTGCCTACTTTTGGGGGCGCTTTATTTAGTGTTGAATGAGAAAAAACTTGGAAAACAGgtacatttct ... attgttgcagAAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTTTTGATGGCTATTTTCTCCATCTACACTGGTTTCATATACAATGAGTTCT
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actggagattcgtttcaagtcgtatggttaaactaatattgtgacattgttgcagAAACTCGGTGATATTATGGAGATGGCTTATGGAGGTCGTTATGTAATTCTTTTGATGGCTATTTTCTCCATCTACACTGGTTTCATATACAATGAGTTCT
aactaat putative branch site (score: 16)
ttaaactaatattgt TA-rich tract