Sequence
atgc intronic sequence ATGC exonic sequencegtctgtccctcattttgatgacgttaagttgaagttaccaccccttgaattatttttttgtgtatgttggtctgtttgaagttcacttctagttaatgtgcggtgaatggccagggatttgacttcaaattttttttacagAGCATTATGGAATATGAGGAGCATGAAAAGAGGGCCTGGAGTGTGGATTTTTCACGAACTGATCCGACCATGCTAGTCTCGGGAAGTGATGATGGCAAG
Basic information
species | Physcomitrella patens |
transcript | PP1S135_17V6.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os02g53140.1 (Oryza sativa), 3'ss of exon 8
gtctgtccctcattttgatgacgttaagttgaagttaccaccccttgaattatttttttgtgtatgttggtctgtttgaagttcacttctagttaatgtgcggtgaatggccagggatttgacttcaaattttttttacagAGCATTATGGAATATGAGGAGCATGAAAAGAGGGCCTGGAGTGTGGATTTTTCACGAACTGATCCGACCATGCTAGTCTCGGGAAGTGATGATGGCAAG
| ||| || | | | || |||| | | || || || | || | | | || ||||| || ||| |||| | ||||| ||||| || ||||||||||| || |||||||| |||||||| ||||| || || | |||||||| || || ||||||||| |||||
----------------------------------------------gtatttcttgctctgttccacagttcattttgcacacttgtgttattttctgaacttggattcatgatatttatgtattcaatcttcttt---agAGTGTGATGGAGTATGAAGAACATGAAAAGAGAGCATGGAGTGTTGATTTTTCTCGAACAGAACCCTCGATGCTAGTATCTGGGAGTGATGATTGCAAG
upper sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 7
gtctgtccctcattttgatgacgttaagttgaagttaccaccccttgaattatttttttgtgtatgttggtctgtttgaagttcacttctagttaatgtgcggtgaatggccagggatttgacttcaaattttttttacagAGCATTATGGAATATGAGGAGCATGAAAAGAGGGCCTGGAGTGTGGATTTTTCACGAACTGATCCGACCATGCTAGTCTCGGGAAGTGATGATGGCAAG
| | | | | | || || | || |||| ||| ||| | ||| | | | | |||| | ||||||||||| |||||||| ||||| || |||||||| |||||||| || || || | | |||||||| || || ||||||||| |||||
------------------------------------------------gtatccactctctattcgacagttcattctgcaatggctgtattgtaattcaaactga--ggcatatggtttctgtgtattgtgccatgctagAGTGTGATGGAATATGAAGAGCATGAGAAGAGAGCATGGAGTGTTGATTTTTCTCGCACAGACTCTTCAATGCTAGTATCTGGGAGTGATGATTGCAAG
upper sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G126795_T01 (Zea mays), 3'ss of exon 9
gtctgtccctcattttgatgacgttaagttgaagttaccaccccttgaattatttttttgtgtatgttggtctgtttgaagttcacttcta-gttaatgtgcggtgaatggccagggatttgacttcaaattttttttacagAGCATTATGGAATATGAGGAGCATGAAAAGAGGGCCTGGAGTGTGGATTTTTCACGAACTGATCCGACCATGCTAGTCTCGGGAAGTGATGATGGCAAG
| | | | || | | | |||| | | || | || ||| | | ||| | | ||| | | | | |||| | ||||||||||| |||||||| || || || |||||||| |||||||| ||||| || || | |||||||| || || ||||| ||| |||||
---------------------------------------------gtatccactctattttacagttcattctgc--aatggccattgctgtattataattcaaactgaggcatgtggtttttgtgtattgtgacatgctagAGTGTGATGGAATATGAAGAGCATGAGAAAAGAGCATGGAGTGTTGATTTTTCTCGAACAGAGCCTTCAATGCTAGTATCTGGGAGTGACGATTGCAAG
upper sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA14G05430.1 (Glycine max), 3'ss of exon 8
gtctgtccctcattttgatgacgttaagttgaagt--taccaccccttgaattatttt--tttgtgtatgttggtct---gtttgaagttcacttctagttaatgtgcggtgaatggccagggatttgacttcaaattttttttacagAGCATTATGGAATATGAGGAGCATGAAAAGAGGGCCTGGAGTGTGGATTTTTCACGAACTGATCCGACCATGCTAGTCTCGGGAAGTGATGATGGCAAG
|| | ||| ||| || | ||| | || || | ||| ||| || || | || || | | || | | ||| | || | | | || || | | | || || |||| ||||| | ||||||||||| |||||||||||| | || |||||||| ||||||||| |||| || || | ||||| || || || || ||||| | |||
gtaaatgttgaattcaaatg--gtcagtttgttcttgtatcagctctttgggtatcttaattcattaatatttttttaatgtcatgtgcttgcttaaattttctacagattatttactcatggctatcattt----ttccttttgcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTTGATTTTTCAAGAACAGACCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG
upper sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 8
gtctgtccctcattttgatga-cgttaagttgaagttaccaccccttgaat-tatttttttgtgtatgttggtctgtttgaagttcacttctagttaatgtgcggtgaatggccagggatttgacttcaaattt-tttttacagAGCATTATGGAATATGAGGAGCATGAAAAGAGGGCCTGGAGTGTGGATTTTTCACGAACTGATCCGACCATGCTAGTCTCGGGAAGTGATGATGGCAAG
|| | ||| ||| | | ||| || | | ||| | | || || | || ||| | || ||| | ||| | | | | | || | | | ||| || ||| ||||| | ||||||||||| |||||||||||| | || |||||||| || |||||| |||| ||||| | ||||| || || || || ||||| | |||
gtaaatgttgaattcaaatggtcagtttgttcttgtatcagatctttgggtatcttcattcattaatattgttttgattgtcatgtgcttgct-taagttttctacagattatttacgcatggctatcattttaactttggcagAGTTTAATGGAATATGAAGAGCATGAAAAGCGTGCATGGAGTGTAGACTTTTCAAGAACAGATCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG
upper sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv10s0523g00030.t01 (Vitis vinifera), 3'ss of exon 8
gtctgtccctcattttgatgacgttaagttgaagttaccaccccttgaattatttttttgtgtatgttggtctgtttgaagttcacttctagttaatgtgcggtgaatggccagggatttgacttcaaat--tttttttacagAGCATTATGGAATATGAGGAGCATGAAAAGAGGGCCTGGAGTGTGGATTTTTCACGAACTGATCCGACCATGCTAGTCTCGGGAAGTGATGATGGCAAG
| | | | | | |||| | || || || | | |||||| |||| ||||| | ||| | | || | || || ||| | | |||| || |||| | |||||||| ||||||||||||||| | || |||||||| ||||||||||| ||||| || | ||||| || || || |||||||| |||||
--------gtagaaattgtatctcttctcttctgttaatctcaattacatcatatatgcacaaatgttgatctgc-----attcacaattttctaacctcccaatgatttcgagtttgttcactaagattctttttcttctagAGTGTGATGGAATACGAGGAGCATGAAAAGCGAGCATGGAGTGTTGATTTTTCACGCACTGAACCTTCAATGCTCGTATCCGGCAGTGATGACTGCAAG
upper sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv12s0059g01420.t01 (Vitis vinifera), 3'ss of exon 8
gtctgtccctcattttgatgacgttaagttgaagttaccaccccttgaattattt-ttttgtgtatgttggtctgtttgaagttcacttctagttaatgtgcggtgaatggccagggatttgacttcaaatttttttta-cagAGCATTATGGAATATGAGGAGCATGAAAAGAGGGCCTGGAGTGTGGATTTTTCACGAACTGATCCGACCATGCTAGTCTCGGGAAGTGATGATGGCAAG
|| |||||| | || || | | ||| | || | | || || || | | || | || || |||| ||||||| ||||| | ||||||||||| ||||||||||| |||| |||||||| ||||||||||| || || || | | ||| || || || ||||||||| | |||
--------------------------------------ggtcctttgaatgaaaaattctgggctcgcca--ctgactatagatttgtccttgtatatata---tatatatatatatatatgctaataaatgttttttatcagAGTGTGATGGAATATGAAGAGCATGAAAAACGGGCATGGAGTGTTGATTTTTCACGCACAGAACCCTCAAGGCTTGTATCTGGCAGTGATGATTGTAAGMapped 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|100393347|gb|BY989832.1|BY989832EST: GCAGTGATTATGAGGGGATTATTACTGTCTGGGATGTTAATACGCATCAG AGCATTATGGAATATGAGGAGCATGAAAAGAGGGCCTGGAGTGTGGATTTT
genomic: GCAGTGATTATGAGGGGATTATTACTGTCTGGGATGTTAATACGCATCAGgtctgtccct ... ttttttacagAGCATTATGGAATATGAGGAGCATGAAAAGAGGGCCTGGAGTGTGGATTTT
EST:
gi|100353725|gb|BY983279.1|BY983279EST: GCAGTGATTATGAGGGGATTATTACTGTCTGGGATGTTAATACGCATCAG AGCATTATGGAATATGAGGAGCATGAAAAGAGGGCCTGGAGTGTGGATTTT
genomic: GCAGTGATTATGAGGGGATTATTACTGTCTGGGATGTTAATACGCATCAGgtctgtccct ... ttttttacagAGCATTATGGAATATGAGGAGCATGAAAAGAGGGCCTGGAGTGTGGATTTT
EST:
gi|162157156|gb|FC333726.1|FC333726EST: GGGGATTATTACTGTCTGGGATGTTAATACGCATCAG AGCATTATGGAATATGAGGAGCATGAAAAGAGGGCCTGGAGTGTGGATTTT
genomic: GGGGATTATTACTGTCTGGGATGTTAATACGCATCAGgtctgtccct ... ttttttacagAGCATTATGGAATATGAGGAGCATGAAAAGAGGGCCTGGAGTGTGGATTTT
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:
32 (upstream exon),
20 (downstream exon)
Score:
2AAAATTAAGCTGCCTTAGTTGGAACAAATACATCAATTCACATATCGCTAGCAGTGATTATGAGGGGATTATTACTGTCTGGGATGTTAATACGCATCAGgtctgtccct ... ttttttacagAGCATTATGGAATATGAGGAGCATGAAAAGAGGGCCTGGAGTGTGGATTTTTCACGAACTGATCCGACCATGCTAGTCTCGGGAAGTGATGATGGCAAG
<
<
<
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctagttaatgtgcggtgaatggccagggatttgacttcaaattttttttacagAGCATTATGGAATATGAGGAGCATGAAAAGAGGGCCTGGAGTGTGGATTTTTCACGAACTGATCCGACCATGCTAGTCTCGGGAAGTGATGATGGCAAG
atttgac putative branch site (score: 2)
ttttttttac putative PPT
atttgacttcaaattt TA-rich tract