Sequence
atgc intronic sequence ATGC exonic sequencegtaaggatccatctgaagcctgttcatcgttccagtctatgatcattggagatatggcattcctgcaattaccgatgtgttgggtttgaaacttatatgattcatttcagATCGGAGGAGCAAGCGAAGTTGAGGTGAGTGAAAAGAAAGATCGTGTTACTGATGCACTGAATGCTACTAAAGCTGCTGTCGAGGAGGGGATTGTACCTG
Basic information
species | Physcomitrella patens |
transcript | PP1S52_245V6.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 13
-gtaaggatccatctgaagcctgttcatcgttccagtctatgatcattggagatatg-gcattcctgcaattaccgatgtgttgggtttgaaacttatatgattcatttcagATCGGAGGAGCAAGCGAAGTTGAGGTGAGTGAAAAGAAAGATCGTGTTACTGATGCACTGAATGCTACTAAAGCTGCTGTCGAGGAGGGGATTGTACCTG
|| | ||| | || || | ||| ||| || | ||| | || |||| | ||| | || ||| || || ||| ||| |||| || ||||| || |||| ||||| |||| ||||| ||| | || ||||||||||| |||||||| ||||||||||| |||||||| |||||||| |
agtggcggaacattctattactattactgattctagtgactgtcct---gagttgtgagcatgggtattattttt----ttttaaa----aaaattggatctttccttt-agATTGGTGGAGCTAGTGAAGCGGAGGTTGGTGAGAAGAAGGATAGAGTGACTGATGCACTAAATGCTACCAAAGCTGCTGTAGAGGAGGGTATTGTACCAG
upper sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 13
gtaaggatccatctgaagcctgttcatcgttccagtctatgatcattgg-agatatggcattcctgcaattaccgatgtgttgggtttgaaacttatatgattcatttcagATCGGAGGAGCAAGCGAAGTTGAGGTGAGTGAAAAGAAAGATCGTGTTACTGATGCACTGAATGCTACTAAAGCTGCTGTCGAGGAGGGGATTGTACCTG
|| | | |||| | | ||| | || || || ||| |||| | ||| | || || | | || || | |||||||||||||| || |||| ||| || |||| ||||| ||| | || || |||||| ||||||| |||||||||||||| || ||||| |||||||| |
--------acacacaatga-tgttgagaatggaagttgaattgcactgctaggagtggtgc-cctgaagttat-attttgacctgtatatgcatcatgacctttcctacagATCGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCATTGAATGCCACTAAAGCTGCTGTGGAAGAGGGTATTGTACCAG
upper sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 12
-------------------gtaaggatccatctgaagcctgttcatcgttccagtctatgatcat--tggagatatggcattcctgcaatta-ccgatgtgt--tgggtttgaaact-tatatgattcatttc--agATCGGAGGAGCAAGCGAAGTTGAGGTGAGTGAAAAGAAAGATCGTGTTACTGATGCACTGAATGCTACTAAAGCTGCTGTCGAGGAGGGGATTGTACCTG
||| | || | | || |||| || | ||| | | | ||| | |||| | | ||| | | || |||| || | | || || |||| |||| |||||||| ||||||| || || |||| ||||| ||| | || || ||||||||||||||||||||||||||||| || ||||| |||||||| |
gtgaggttattgacctactgtatgtatttacgaatggtagattacatgttcttgttttatatcgtaattgtaataactgttacctgtggctctctgatatttcctgattttgtgcctatgtgtgcatcctttcctagATTGGAGGAGCCAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGCATTGTACCAG
upper sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GRMZM2G111477_T02 (Zea mays), 3'ss of exon 1
----------------gtaaggatccatctgaagcctgttcatcgttccag----tctatgatcattggagatatggcattcctg-caattaccgatgtgttgggtttgaaacttatatgattcatttcagATCGGAGGAGCAAGCGAAGTTGAGGTGAGTGAAAAGAAAGATCGTGTTACTGATGCACTGAATGCTACTAAAGCTGCTGTCGAGGAGGGGATTGTACCTG
| | | || ||| ||| || | | | ||| | || | || | | | || || || |||| | | | | |||| || ||||| ||||||| || || |||| ||||| ||| | || || ||||||||||||||||||||||||||||| || ||||| |||||||| |
gtgagattactgacctttgtatgtttactaatggcagattccatgtttcaaacattttttttctgttgtaatactgttacctgtgtctgtcctccatttgctgattttgtg-cctgtgcctcctttcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG
upper sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 13
----------------------gtaaggatccatctgaagcctgttcatcgttccagtctatgatc-attgga--gata-tggcattcctgca-attaccgatgtgttgggtttgaaacttata------tgattcattt--cagATCGGAGGAGCAAGCGAAGTTGAGGTGAGTGAAAAGAAAGATCGTGTTACTGATGCACTGAATGCTACTAAAGCTGCTGTCGAGGAGGGGATTGTACCTG
|| | | | || |||| | | | | || | | || | | || | |||| || | | | | | | ||| | | || ||| || ||||| |||||||| || |||| ||| || ||||| ||||||||| | ||||| ||||| || ||||||||||| || ||||| || || || |||||||| |
gtctgtatcaatttacaaatccccaacattactgtctaggcttgttgaggctctaaactcaggagctactgtactggtactcagattcatggggaatgttatctagatatatataaaaatggtggaaaattgcttccctttgcagATAGGAGGAGCTAGTGAAGCTGAAGTTAGTGAGAAGAAAGATAGGGTTACAGATGCTCTAAATGCTACTAAGGCAGCTGTAGAAGAAGGAATTGTACCAG
upper sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: EFJ32351 (Selaginella moellendorffii), 3'ss of exon 11
gtaaggatccatctgaagcctgttcatcgttccagtctatgatcattggagatatggcattcctgcaattaccgatgtgttgggtttgaaact--tatatgattcatttcagATCGGAGGAGCAAGCGAAGTTGAGGTGAGTGAAAAGAAAGATCGTGTTACTGATGCACTGAATGCTACTAAAGCTGCTGTCGAGGAGGGGATTGTACCTG
|||| | || | | | | | ||| | | | | | |||| ||||||| || |||| || || |||||||||| ||||| || || ||||| ||||||||||| || ||||| || |||||||| || || || |
---------------------------------------------------gtatg-tacaccaaagacttttgtggcagcgtttttattattgtttcgcgcgcgagcgtagATTGGAGGAGGTAGTGAAGCGGAAGTCGGTGAAAAGAAGGATCGGGTGACCGATGCGCTGAATGCTACAAAGGCTGCAGTGGAGGAGGGAATCGTGCCAG
upper sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: EFJ20894 (Selaginella moellendorffii), 3'ss of exon 11
gtaaggatccatctgaagcctgttcatcgttccagtctatgatcattggagatatggcattcctgcaattaccgatgtgttgggtttgaaact--tatatgattcatttcagATCGGAGGAGCAAGCGAAGTTGAGGTGAGTGAAAAGAAAGATCGTGTTACTGATGCACTGAATGCTACTAAAGCTGCTGTCGAGGAGGGGATTGTACCTG
|| | | || | | | | | ||| | | | | | | |||| ||||||| || |||| || || ||||||||||| ||||| || || ||||| ||||||||||| || ||||| || |||||||| || || || |
---------------------------------------------------gtacg-tacgccaaagacttttgtggcagcgtttttattattgtttcgcgcgcgagtgtagATTGGAGGAGGTAGTGAAGCGGAAGTCAGTGAAAAGAAGGATCGGGTGACGGATGCGCTGAATGCTACAAAGGCTGCAGTGGAGGAGGGAATCGTGCCAGMapped 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|162164865|gb|FC340535.1|FC340535EST: AGTTGCAAGAGAGGTTGGCTAAATTATCAGGGGGTGTTGCTGTGCTCAAG ATCGGAGGAGCAAGCGAAGTTGAGGTGAGTGAAAAGAAAGATCGTGTTACT
genomic: AGTTGCAAGAGAGGTTGGCTAAATTATCAGGGGGTGTTGCTGTGCTCAAGgtaaggatcc ... ttcatttcagATCGGAGGAGCAAGCGAAGTTGAGGTGAGTGAAAAGAAAGATCGTGTTACT
EST:
gi|37835503|gb|BJ593515.1|BJ593515EST: GTTGCAAGAGAGGTTGGCTAAATTATCAGGGGGTGTTGCTGTGCTCAAG ATCGGAGGGAGCAAGCGAAGTTGAGGTGAGTGAAAAGAAAGATCGTGTTAC
genomic: GTTGCAAGAGAGGTTGGCTAAATTATCAGGGGGTGTTGCTGTGCTCAAGgtaaggatcc ... ttcatttcagATCGGA-GGAGCAAGCGAAGTTGAGGTGAGTGAAAAGAAAGATCGTGTTAC
EST:
gi|37827871|gb|BJ585883.1|BJ585883EST: AGTTGCAAGAGAGGTTGGCTAAATTATCAGGGGGTGTTGCTGTGCTCAAG ATCGGAGGAGCAAGCGAAGTTGAGGTGAGTGAAAAGAAAGATCGTGTTACT
genomic: AGTTGCAAGAGAGGTTGGCTAAATTATCAGGGGGTGTTGCTGTGCTCAAGgtaaggatcc ... ttcatttcagATCGGAGGAGCAAGCGAAGTTGAGGTGAGTGAAAAGAAAGATCGTGTTACT
EST:
gi|162277341|gb|FC453147.1|FC453147EST: GGGGGTGTTGCTGTGCTCAAG ATCGGAGGAGCAAGCGAAGTTGAGGTGAGTGAAAAGAAAGATCGTGTTACT
genomic: GGGGGTGTTGCTGTGCTCAAGgtaaggatcc ... ttcatttcagATCGGAGGAGCAAGCGAAGTTGAGGTGAGTGAAAAGAAAGATCGTGTTACT
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:
31 (upstream exon),
28 (downstream exon)
Score:
6ATCCGAGAGGCTATCAACAGCGCAACTTCTGATTACGACAAGGAAAAGTTGCAAGAGAGGTTGGCTAAATTATCAGGGGGTGTTGCTGTGCTCAAGgtaaggatcc ... ttcatttcagATCGGAGGAGCAAGCGAAGTTGAGGTGAGTGAAAAGAAAGATCGTGTTACTGATGCACTGAATGCTACTAAAGCTGCTGTCGAGGAGGGGATTGTACCTG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggcattcctgcaattaccgatgtgttgggtttgaaacttatatgattcatttcagATCGGAGGAGCAAGCGAAGTTGAGGTGAGTGAAAAGAAAGATCGTGTTACTGATGCACTGAATGCTACTAAAGCTGCTGTCGAGGAGGGGATTGTACCTG
ttcatttc CT-rich tract
ttatatgattcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggatccatctgaagcctgttcatcgttccagtctatgatcattggagatatggcattcctgcaattaccgatgtgttgggtttgaaacttatatgattcatttcagATCGGAGGAGCAAGCGAAGTTGAGGTGAGTGAAAAGAAAGATCGTGTTACTGATGCACTGAATGCTACTAAAGCTGCTGTCGAGGAGGGGATTGTACCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG