Sequence
atgc intronic sequence ATGC exonic sequencegtatgaatccggcatattcgtacacaatttgatcctgtataaaattctggtgggaggtattctttgtggttgcttggccggtcatttgtgggcaggtgctccaagtgctaaaacagcaattgtggttttaacagTCTTTGCGGAAGCTGAATCATCCTAACATCGTGAAGCTGAAGGAGGTTATCCGTGAAAACGATGAACTGTTTTTCGTTTTTGAGTATATG
Basic information
| species | Physcomitrella patens |
| transcript | PP1S173_136V6.1 |
| intron # | 3 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S173_136V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os02g47220.3 (Oryza sativa), 3'ss of exon 1
gtatgaatccggcatattcgtacacaatttgatcctgtataaaattctggtgggaggtattctttgtggttgcttggccggtcatttgtgggcaggtgctccaagtgctaaaacagcaattgtggttttaacagTCTTTGCGGAAGCTGAATCATCCTAACATCGTGAAGCTGAAGGAGGTTATCCGTGAAAACGATGAACTGTTTTTCGTTTTTGAGTATATG
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--------------------------------------------------------gtattttaactgaaagatgtaccc-tctttcctgctatgaaccttcaactgatatttctcctatattga-------agTCTTTGCGGCGCATGAATCACCCTAACATCGTGAAGCTCAAGGAGGTTATAAGGGAAAATGACATATTATACTTCATAATGGAATACATG
upper sequence: PP1S173_136V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 6
gtatgaatccggcatattcgtacacaatttgatcctgtataaaattctggtgggaggtattcttt-gtggttgcttggccggtcatttgtgggcaggtgctccaagtgctaaaacagcaattgtggttttaacagTCTTTGCGGAAGCTGAATCATCCTAACATCGTGAAGCTGAAGGAGGTTATCCGTGAAAACGATGAACTGTTTTTCGTTTTTGAGTATATG
| || | | | | || ||| | || | || || ||| | | | | || ||| | | || | ||||||||||| |||||||||||||||| |||||||| || ||||||||||| ||||| ||| | | | ||| | | || || |||
----------------------------------------gtattttagaccagcgatgtttttttatcattccctgttatgttctttc--aactgacatttcttgtt-----------attattttgttga-agTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATG
upper sequence: PP1S173_136V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 7
gtatgaatccggcatattcgtacacaatttgatcctgtataaaattctggtgggaggtattctttgtggttgcttggccggtcatttgtgggcaggtgctccaagtgctaaaacagcaattgtggtttta--acagTCTTTGCGGAAGCTGAATCATCCTAACATCGTGAAGCTGAAGGAGGTTATCCGTGAAAACGATGAACTGTTTTTCGTTTTTGAGTATATG
| || | | ||| |||||| | | | | ||||| | | || || || | ||||| ||||| ||||||||||| |||||||||||||||| |||||||| || ||||||||| | ||||| ||| | | | ||| | | || || |||
----------------------------------------gtattttagaccagtggtgttcttttta-----tcattctctgttttgt-------tctttcagctgatatttcttttattgttattttattgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCAGGGAAAATGATATATTATACTTCATAATGGAATACATG
upper sequence: PP1S173_136V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT5G45430.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatgaatccggcatattcgtacacaatttgatcctgtataaaattctggtgggaggtattctttgtggttgcttggccggtcatttgtgggcaggtgctccaagtgctaaaacagcaattgtggttttaacagTCTTTGCGGAAGCTGAATCATCCTAACATCGTGAAGCTGAAGGAGGTTATCCGTGAAAACGATGAACTGTTTTTCGTTTTTGAGTATATG
| |||||| ||| | || |||| || ||| | || || | ||| || | | | | ||| | || ||| || ||| |||||||||| ||||| |||||||||||||| || ||||| ||||| ||| || | || || |||||||| |||
-------------------------------gtactgtatctcatta-gctgaaaggttttgttttttttttttt---ttactgtatgttcgctgatttttttcttttc-------tcattatagTCA-------CTTAGCAGAA--TGAATCATCCAAACATTGTGAAGCTGAAGGAAGTCATCCGGGAAAATGATATCCTATACTTTGTGTTTGAGTACATG
upper sequence: PP1S173_136V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ22662 (Selaginella moellendorffii), 3'ss of exon 2
gtatgaatccggcatattcgtacacaatttgatcctgtataaaattctggtgggaggtattctttgtggttgcttggccggtcatttgtgggca-ggtgctccaagtgctaaaacagcaattgtggttttaacagTCTTTGCGGAAGCTGAATCATCCTAACATCGTGAAGCTGAAGGAGGTTATCCGTGAAAACGATGAACTGTTTTTCGTTTTTGAGTATATG
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-----------------------------------------------------------------------------------gtttgtgtccttgaaatttttcttgctggccttatcttttctcttcttacagTCGCTGCGGAAGTTGAACCATCCGAATATAGTCAAGCTGAAGGAGGTTATCCGGGAAAATAACGAGCTATTCTTCGTTTTTGAGTATATGMapped 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|162190105|gb|FC365847.1|FC365847EST: AGAGGAAATTTTACTCATGGGATGAATGCATGAATCTAAGAGAAGTGAAG TCTTTGCGGAAGCTGAATCATCCTAACATCGTGAAGCTGAAGGAGGTTATC
genomic: AGAGGAAATTTTACTCATGGGATGAATGCATGAATCTAAGAGAAGTGAAGgtatgaatcc ... gttttaacagTCTTTGCGGAAGCTGAATCATCCTAACATCGTGAAGCTGAAGGAGGTTATC
EST:
gi|162164083|gb|FC340372.1|FC340372EST: AGAGGAAATTTTACTCATGGGATGAATGCATGAATCTAAGAGAAGTGAAG TCTTTGCGGAAGCTGAATCATCCTAACATCGTGAAGCTGAAGGAGGTTATC
genomic: AGAGGAAATTTTACTCATGGGATGAATGCATGAATCTAAGAGAAGTGAAGgtatgaatcc ... gttttaacagTCTTTGCGGAAGCTGAATCATCCTAACATCGTGAAGCTGAAGGAGGTTATC
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:
35 (upstream exon),
35 (downstream exon)
Score:
32GAAAGCAGTTAATAATGCCACTAACGAGGTCGTGGCGATCAAGAAGATGAAGAGGAAATTTTACTCATGGGATGAATGCATGAATCTAAGAGAAGTGAAGgtatgaatcc ... gttttaacagTCTTTGCGGAAGCTGAATCATCCTAACATCGTGAAGCTGAAGGAGGTTATCCGTGAAAACGATGAACTGTTTTTCGTTTTTGAGTATATG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtcatttgtgggcaggtgctccaagtgctaaaacagcaattgtggttttaacagTCTTTGCGGAAGCTGAATCATCCTAACATCGTGAAGCTGAAGGAGGTTATCCGTGAAAACGATGAACTGTTTTTCGTTTTTGAGTATATG
tgctaaa putative branch site (score: 32)
ttttaaca TA-rich tract
