Sequence
atgc intronic sequence ATGC exonic sequence...tttttttttttgtttgaaatctgcaactttgttttgcatattataaactggttaattttgggaggatggtgtgctcagagctaactatcgttgttcacagGGCTTCAACGGAGCTGATCTTCGCAACGTGTGCACTGAAGCGGGCATGTTTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAGG
Basic information
species | Physcomitrella patens |
transcript | PP1S47_46V6.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os02g10640.1 (Oryza sativa), 3'ss of exon 8
tttttttttttgtttgaaatctgcaactttgttttgcatattataaactggttaattttgggaggatggtgtgctcagagctaactatcgttgttcacagGGCTTCAACGGAGCTGATCTTCGCAACGTGTGCACTGAAGCGGGCATGTTTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAGG
| | ||||| || || | || | || || || | | || || ||| | || ||| |||||||||| || ||||||||||||||||| |||||||||||||| ||| ||| || || ||||| |||||||| ||||| || || ||||| ||||||
----------------------gtgagtttgtcttatttaacttc--cttatcaacttgggcaacct-------tc----ctgactctggtggttt-tagGGCTTCAATGGGGCTGATCTTCGCAACGTCTGCACTGAAGCGGGTATGGCTGCAATTCGTGCTGAACGGGACTACGTTGTCCATGAGGACTTCATGAAG-
upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G074037_T01 (Zea mays), 3'ss of exon 8
tttttttttttgtttgaaatctgcaactttgttttgcatattataaactggttaattttgggaggatggtgtgctcagagctaactatcgttgt----tcacagGGCTTCAACGGAGCTGATCTTCGCAACGTGTGCACTGAAGCGGGCATGTTTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAGG
| || | | || || | | | || | ||| | | |||||| | | | || | |||||||| | | | |||||||||||| ||||| ||| | |||||| ||||||| ||||| |||||| ||||||||| || || || |||||||| | || || ||||| ||||||
---gtgagccagtctttagtc---aatctagctatgtaaattccttaaca--tgattttgag----ctatctcctgaaccctaactattgcaataatattacagGGCTTCAATGGAGCCGATATGCGCAACTTGTGCACAGAAGCCGGCATGGCTGCTATCCGAGCGGAGCGTGACTATGTCATTCACGAGGACTTCATGAAG-
upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G165817_T01 (Zea mays), 3'ss of exon 8
tttttttttttgtttgaaatctgcaactttgttttgcatattataaactggttaattttgggaggatggtgtgctcagagctaactatcgttgttcacagGGCTTCAACGGAGCTGATCTTCGCAACGTGTGCACTGAAGCGGGCATGTTTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAGG
| | || ||| || |||| | | | | | || | | | | || ||| || | ||| ||||| ||||| || ||||||||||| ||||||||||| ||||| |||||| ||| || || || || | || || || || || |||||||| ||||||
----------------------gtgagttagttgtg----ttattcatatctaacctctaatcccatcctatagtttcaccttactctcctggttt-cagGGTTTCAATGGGGCTGATCTTCGGAACGTGTGCACCGAAGCTGGCATGGCTGCAATTCGTGCAGAGAGAGATTACGTAGTCCACGAAGACTTCATGAAG-
upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G171604_T01 (Zea mays), 3'ss of exon 8
tttttttttttgtttgaaatctgcaactttgttttgcatattataaactggttaattttgggaggatggtgtgctcagagctaactatcgttgttcacagGGCTTCAACGGAGCTGATCTTCGCAACGTGTGCACTGAAGCGGGCATGTTTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAGG
| | || ||| | ||| ||| | | | | || || | | | || ||| || | ||| |||| ||||| || ||||||||||| ||||||||||||||||| || ||| ||| || || || || | || ||||| || || |||||||| ||||||
----------------------gtgagttagttgtat-tatcatatc----taacctctaatcccattgtatagtttcaccttactctcctggttt-tagGGTTTCAATGGTGCTGATCTTCGGAACGTGTGCACTGAAGCTGGTATGGCTGCAATTCGTGCAGAGAGAGATTATGTAGTCCACGAAGACTTCATGAAG-
upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EDP04786 (Chlamydomonas reinhardtii), 3'ss of exon 10
tttttttttttgtttgaaatctg-caacttt--gttttgcatattataaactggttaattttgggaggatggtgtgctcagagcta---actatcgttgttcacagGGCTTCAACGGAGCTGATCTTCGCAACGTGTGCACTGAAGCGGGCATGTTTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAGG
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------gttgtgcgagagaccaggctgcctcacgtgctgctcatcacccactcctcccataaacctcaaccacacacgcatacccacacacgttcacccgccgcagGGCTTCAACGGAGCCGACCTGCGCAACATCTGCACGGAGGCGGGCATGTTCGCCATCCGGGACGAGCGCGATTACGTGGTGCAGGAGGACTTCATGAAG-Mapped 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|18338881|gb|BJ170907.1|BJ170907EST: TTACTAAGCATGGAGAGATTGATTATGAGGCTATTGTTAAACTTGCTGAG GGCTTCAACGGAGCTGATCTTCGCAACGTGTGCACTGAAGCGGGCATGTTT
genomic: TTACTAAGCATGGAGAGATTGATTATGAGGCTATTGTTAAACTTGCTGAGgtacagtgtc ... ttgttcacagGGCTTCAACGGAGCTGATCTTCGCAACGTGTGCACTGAAGCGGGCATGTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactggttaattttgggaggatggtgtgctcagagctaactatcgttgttcacagGGCTTCAACGGAGCTGATCTTCGCAACGTGTGCACTGAAGCGGGCATGTTTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAGG
agctaac putative branch site (score: 2)
ttaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttttttttgtttgaaatctgcaactttgttttgcatattataaactggttaattttgggaggatggtgtgctcagagctaactatcgttgttcacagGGCTTCAACGGAGCTGATCTTCGCAACGTGTGCACTGAAGCGGGCATGTTTGCTATCCGGGCTGATCGGGACTATGTTGTACAAGAAGACTTTATGAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG