Sequence
atgc intronic sequence ATGC exonic sequenceGACGTCAGAAGATCATGTTTGCCCTGACCTCCATTAAGGGGGTTGGGCGTCGTTTTGCCAACTTGGTTTGCAAGAAGGCCGATGTCGACATGAGCAAGAGgtatgtgatcttgtttgatttttgtattttataccggtatttttatttttatttttatttttatatttttttcttgccttcgtctctgcccacacgtccc...
Basic information
species | Physcomitrella patens |
transcript | PP1S72_222V6.2 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S72_222V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G178341_T01 (Zea mays), 5'ss of exon 2
GACGTCAGAAGATCATGTTTGCCCTGACCTCCATTAAGGGGGTTGGGCGTCGTTTTGCCAACTTGGTTTGCAAGAAGGCCGATGTCGACATGAGCAAGAGgtatgtgatct-tgtttgatttttgtattttataccggtatttttatttttatttttatttttatatttttttcttgccttcgtctctgcccacacgtccc
| |||||||||||||| ||| |||||||||| ||||| |||||||| || || ||||| | || |||||||||||||| ||||||||| ||||||| | | | | | | || | | | | | |||| | ||| | | | | || | | | |||| || | |||
GGAAGCAGAAGATCATGTTCGCCATGACCTCCATAAAGGGTGTTGGGCGCCGCTTCTCCAACATCGTCTGCAAGAAGGCCGACATCGACATGAACAAGAGgcaagcgctgtgttttcgctctgaggaccttat-caggtctctctggtgacg-----------atgtgcctgacatgccggcgagtgtgcag---------
upper sequence: PP1S72_222V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G130544_T01 (Zea mays), 5'ss of exon 1
GACGTCAGAAGATCATGTTTGCCCTGACCTCCATTAAGGGGGTTGGGCGTCGTTTTGCCAACTTGGTTTGCAAGAAGGCCGATGTCGACATGAGCAAGAGgtatgtgatcttgtttgatttttgtattttataccggtatttttatttttatttttatttttatatttttttcttgccttcgtctctgcccacacgtccc
| |||||||||||||| ||| ||||||| || ||||| || ||||| || || ||||| | || |||||||||||||| ||||||||| ||||||| | | | || | || | | | || | | || | | | | | | | |||| || | | | | || || ||
GGAAGCAGAAGATCATGTTCGCCATGACCTCAATCAAGGGTGTCGGGCGCCGCTTCTCCAACATCGTCTGCAAGAAGGCCGACATCGACATGAACAAGAGgcaagcg-tcgcgctttagctccaaggatattatcag-atctctctggtgacgatgtggctgatatgttgtgat-gtttcggtgagtgtgcag-------
upper sequence: PP1S72_222V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G062911_T01 (Zea mays), 5'ss of exon 2
GACGTCAGAAGATCATGTTTGCCCTGACCTCCATTAAGGGGGTTGGGCGTCGTTTTGCCAACTTGGTTTGCAAGAAGGCCGATGTCGACATGAGCAAGAGgtatgtgatcttgtttgatttttgtattttata-ccggtatttttatttttatttttatttttatatttttttcttgccttcgt-ctctgcccacacgtccc-
| |||||||||||||||||||| |||||||| ||||| || || | | ||| ||||| | || ||||| |||||| | ||||||||| |||| || || || || ||||| | || || ||| | || | || ||| | | | | | || | || | | |
GCAAGCAGAAGATCATGTTTGCCCTCACCTCCATCAAGGGTGTCGGCCACCATTTCTCCAACATCGTCTGCAAAAAGGCCAACATCGACATGAACAAGCAgtgagttat---agatggcttttgcaattgctagttggttcatgtagtggaatgagtatgagaggttcatgtagtggaacaagtacgagatgcaaggggcgct
upper sequence: PP1S72_222V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT1G34030.1 (Arabidopsis thaliana), 5'ss of exon 2
GACGTCAGAAGATCATGTTTGCCCTGACCTCCATTAAGGGGGTTGGGCGTCGTTTTGCCAACTTGGTTTGCAAGAAGGCCGATGTCGACATGAGCAAGAGgtatgtgatcttgtttgatttttgtattttataccggtatttttatttttatttttatttttatatttttttcttgcctt-cgtctctgcccacacgtccc-
| || ||||| ||||||||||| ||||| || || || |||| | | || |||||| | || |||||||| |||||||||||||||| |||||||||| |||| | | | || ||| | | || || ||| | | | | | ||| ||| || || | || | |||
GTAAGCAAAAGATTATGTTTGCCCTTACCTCTATCAAAGGTATTGGAAGGAGATTGGCCAACATTGTCTGCAAGAAAGCCGATGTCGACATGAACAAGAGgtat-tgatttcaatcaaacttcaacctttggaaagttagaattgaaattagcagtctctgtttgcatttgatttgatttgtgtatgtgttttga-gtcttg
upper sequence: PP1S72_222V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv05s0020g03450.t01 (Vitis vinifera), 5'ss of exon 2
GACGTCAGAAGATCATGTTTGCCCTGACCTCCATTAAGGGGGTTGGGCGTCGTTTTGCCAACTTGGTTTGCAAGAAGGCCGATGTCGACATGAGCAAGAGgt-atgtgatcttgtttgat----ttttgtattttataccggtatttttatttttatttttatttttatatttttttcttgccttcgtctctgcccacacgtccc
| |||||||||||||||||||| || ||||| ||||| |||| || ||||| ||||| | || |||||||| |||||||||||||||| ||| |||| || | | | | | |||| | || ||| | | | | | |||| | || | ||| | | | || | || || |
GGAAGCAGAAGATCATGTTTGCCCTCACTTCCATCAAGGGTATTGGTCGCCGTTTCGCCAATATCGTCTGCAAGAAAGCCGATGTCGACATGAACAAAAGgtcattttttttcatctctccacgttttaaacttcatatgg--aactcggatctaggatttagctgaatcagatattcatacatacga-tatgaacatattag--
upper sequence: PP1S72_222V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv18s0072g00060.t01 (Vitis vinifera), 5'ss of exon 3
GACGTCAGAAGATCATGTTTGCCCTGACCTCCATTAAGGGGGTTGGGCGTCGTTTTGCCAACTTGGTTTGCAAGAAGGCCGATGTCGACATGAGCAAGAGgtatgtga-tcttgtttgatttttgtattttataccggtatttttatttttatttttatttttatatttttttcttgccttcgtctctgcccacacgtccc
| |||||||| ||||||||||| || || || ||||| ||||| | || || || || | |||||||||||||||||||| ||||||| ||| |||| | || | || ||| ||| | | | | | ||| | |||| || || | | | |
GGAAACAGAAGATAATGTTTGCCCTCACGTCAATCAAGGGTATTGGGAGGCGATTCGCTAATATTGTTTGCAAGAAGGCCGATGTTGACATGAACAAAAGgtctctgccttttcttttattctaagccctctgtttgatttcacggaaaatatgggaaaggaaggatttggaattttagttaatgcacttcttaatgcta-
upper sequence: PP1S72_222V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ25542 (Selaginella moellendorffii), 5'ss of exon 2
GACGTCAGAAGATCATGTTTGCCCTGACCTCCATTAAGGGGGTTGGGCGTCGTTTTGCCAACTTGGTTTGCAAGAAGGCCGATGTCGACATGAGCAAGAGgtatgtgatcttgtttgatttttgtattttataccggtatttttatttttatttttatttttatatttttttcttgccttcgtctctgcccacacgtccc
| || |||||||| ||||| || ||||| ||||| ||||| ||||||| || || |||||| | || ||||||||||| ||||| ||||||| |||||||||| | ||| ||| | | | | ||| | | | || || | | ||||| || | | | | || | |
GGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGGGAATTGGGCGCCGATTCGCCAACATCGTCTGCAAGAAGGCGGATGTGGACATGAACAAGAGgtattgtttgccctttcttttcctcttgctctgctggtgagctgaaagatcttgttttctcgtcattttcttgatctttcgggttgggcttctatggatg
upper sequence: PP1S72_222V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ22352 (Selaginella moellendorffii), 5'ss of exon 2
GACGTCAGAAGATCATGTTTGCCCTGACCTCCATTAAGGGGGTTGGGCGTCGTTTTGCCAACTTGGTTTGCAAGAAGGCCGATGTCGACATGAGCAAGAGgtatgtgatcttgtttgatttttgtattttataccggtatttttatttttatttttatttttatatttttttct-tgccttcgtctctgcccacacgtccc----------------------------------------------------------------------------------------
| || |||||||| ||||| || ||||| ||||| ||||| ||||||| || || |||||| | || ||||||||||| ||||| ||||||| |||||||||||| | || || | | | | | | ||| | | | || || | | ||||| |||| || | | ||| || | | |
GGCGGCAGAAGATTATGTTCGCGCTGACTTCCATCAAGGGAATTGGGCGCCGATTCGCCAACATCGTCTGCAAGAAGGCGGATGTGGACATGAACAAGAGgtatgtttgccctttcttttcctct-tgctctgctggtgagctgaaagatcttgttttctcgtcattttcttctatggatgactatcttccttgatctttcggattgattgattgagcttcttcattgatttgaaaaaaaaaatctgtgcttatcatttttctttgtttctttctcttccatcgaacagMapped 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|162279285|gb|FC455208.1|FC455208EST: CGTTTTGCCAACTTGGTTTGCAAGAAGGCCGATGTCGACATGAGCAAGAG GGCTGGCGAGCTCTCCGCAGCTGAGCTCGAGAACCTGATGGTCATCGTTGC
genomic: CGTTTTGCCAACTTGGTTTGCAAGAAGGCCGATGTCGACATGAGCAAGAGgtatgtgatc ... ttgaatatagGGCTGGCGAGCTCTCCGCAGCTGAGCTCGAGAACCTGATGGTCATCGTTGC
EST:
gi|67578021|gb|BJ950188.1|BJ950188EST: CGTTTTGCCAACTTGGTTTGCAAGAAGGCCGATGTCGACATGAGCAAGAG GGCTGGCGAGCTCTCCGCAGCTGAGCTCGAGAACCTGATGGTCATCGTTGC
genomic: CGTTTTGCCAACTTGGTTTGCAAGAAGGCCGATGTCGACATGAGCAAGAGgtatgtgatc ... ttgaatatagGGCTGGCGAGCTCTCCGCAGCTGAGCTCGAGAACCTGATGGTCATCGTTGC
EST:
gi|162279286|gb|FC455209.1|FC455209EST: CGTTTTGCCAACTTGGTTTGCAAGAAGGCCGATGTCGACATGAGCAAGAG GGCTGGCGAGCTCTCCGCAGCTGAGCTCGAGAACCTGATGGTCATCGTTGC
genomic: CGTTTTGCCAACTTGGTTTGCAAGAAGGCCGATGTCGACATGAGCAAGAGgtatgtgatc ... ttgaatatagGGCTGGCGAGCTCTCCGCAGCTGAGCTCGAGAACCTGATGGTCATCGTTGC
EST:
gi|100412675|gb|BY974852.1|BY974852EST: CGTTTTGCCAACTTGGTTTGCAAGAAGGCCGATGTCGACATGAGCAAGAG GGCTGGCGAGCTCTCCGCAGCTGAGCTCGAGAACCTGATGGTCATCGTTGC
genomic: CGTTTTGCCAACTTGGTTTGCAAGAAGGCCGATGTCGACATGAGCAAGAGgtatgtgatc ... ttgaatatagGGCTGGCGAGCTCTCCGCAGCTGAGCTCGAGAACCTGATGGTCATCGTTGC
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:
34 (upstream exon),
35 (downstream exon)
Score:
14GACGTCAGAAGATCATGTTTGCCCTGACCTCCATTAAGGGGGTTGGGCGTCGTTTTGCCAACTTGGTTTGCAAGAAGGCCGATGTCGACATGAGCAAGAGgtatgtgatc ... ttgaatatagGGCTGGCGAGCTCTCCGCAGCTGAGCTCGAGAACCTGATGGTCATCGTTGCTAACCCTCGTCAATTCAAGATCCCAGACTGGTTCTTGAACAGGAAGAAA
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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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GACGTCAGAAGATCATGTTTGCCCTGACCTCCATTAAGGGGGTTGGGCGTCGTTTTGCCAACTTGGTTTGCAAGAAGGCCGATGTCGACATGAGCAAGAGgtatgtgatcttgtttgatttttgtattttataccggtatttttatttttatttttatttttatatttttttcttgccttcgtctctgcccacacgtccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA