Sequence
atgc intronic sequence ATGC exonic sequenceGTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTGgtgaatcattctactgtgttcctcgaattgaagcatttacattagatccttgccattgttggttattgagtgtcgtactcggcactgttccttatgtcgataaatttgcgttaccttttcatgaacag
Basic information
species | Physcomitrella patens |
transcript | PP1S112_186V6.1 |
intron # | 10 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GRMZM2G145595_T01 (Zea mays), 5'ss of exon 10
GTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTGgtgaatcattctactgtgttcctcgaattgaagcatttacattagatccttgccattgttggttattgagtgtcgtactcggcactgttccttatgtcgataaatttgcgttaccttttcatgaacag
|| || |||| || || ||||| ||||| ||||| ||| | ||||||||||||||||| ||||| ||||| || || ||| ||| |||| || | || || | | ||| || || | | ||| || | | || || || | |
GTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAGgtaaat------gttgtgctcacctgtttcttttatccatgctcgatgctgatcactat-agttcttatacg----agcaaatgttggtctgaatatag-----------------------------
upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA15G15310.1 (Glycine max), 5'ss of exon 10
GTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTGgtgaatcattc-tactgtgttcctcgaattgaagcatttacattagatccttgccattgttggttattgagtgtcgtactcggcactgttccttatgtcgataaatttgcgttaccttttcatgaacag
|| || |||||||| || || ||||||||||||||||||||||||||||||||||| || ||||| ||||| ||||| ||| | || ||| | | | | | ||| | | | ||| ||||| | ||| ||| | | | |
GTTCCTCATTTGTATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGCGCACAAGGAATTTCAGgtaagaagcaggtaatgtaattttgctactaa--tttttgagtcatttgctt-ccatt--tacttaatgaaaagattgttggatag-------------------------------------------
upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA07G37050.1 (Glycine max), 5'ss of exon 10
GTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTGgtgaatcatt-ctactgtgttcctcgaattgaagcatttacattagatccttgccattgttggttattgagtgtcgtactcggcactgttccttatgtcgataaatttgcgttaccttttcatgaacag
|| || ||||| ||||| || ||||||||||||||||||||||||||||||||||| || || || ||||| ||||| ||| | | | || ||| | || || |||| || | ||| || | || ||| | ||
GTGCCTCATTTATACTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagtggtaactcatgtaattttc---ccaaaaattttagttt---ttgctgcaat-atcatttgatgaaaaaattgtctaacag-------------------------------------------
upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA09G04270.1 (Glycine max), 5'ss of exon 5
GTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTGgtgaatcattc-tactgtgttcctcgaattgaagcatttacattagatccttgccattgttggttattgagtgtcgtactcggcactgttccttatgtcgataaatttgcgttaccttttcatgaacag
|| || |||||||| ||||| |||||| |||||||||||||||||||||||||||| || || || ||||| ||||| ||| | || ||| | | | | | |||| | | | ||| | | | | | | | || | || |
GTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagaagcaagtaatgtaattttgctactaa--tatttgagtcatttgcttccattcacttaatga-aaatattgttgttggaaag------------------------------------------
upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA17G03560.1 (Glycine max), 5'ss of exon 10
GTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTGgtgaatcatt-ctactgtg--ttcctcgaattgaagcatttacattagatccttgccattgttggttattgagtgtcgtactcggcactgttccttatgtcgataaatttgcgttaccttttcatgaacag
|| || ||||| || || || ||||||||||||||||||||||||||||||||||| || || || ||||| ||||| ||| | | | || ||| || | || | || | | || | | |||| || | | | | || |
GTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAGgtaagtggtaactgatgtaacttttccaaaatttagtttatgcagcaa-----tatcatt--tgatgaaaaaattgtctaacag-----------------------------------------------
upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 5'ss of exon 10
GTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTGgtgaatcattctactgtgttcctcgaattgaa-gcatttacattagatccttgccattgttggttattgagtgtcgtactcggcactgttccttatgtcgataaatttgcgttaccttttcatgaacag
|| || || |||||||||||||||||||| ||||| || ||||||||||||||||||| || || ||||| ||||||||| ||| || || | || || |||| | || | || | || | | ||| | || | || || | | || || || | | || || | |
GTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTGgtaaatggttttatca-atatttcactccaaatgcatctttcttttgtttttccttttcta---cactgaatacgttagattg-acctttattaaactctatgcatctac-ttgtgttggctag-----
upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: AT3G16950.2 (Arabidopsis thaliana), 5'ss of exon 10
GTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTGgtgaatcattc--tactgtgttcctcgaattgaagcatttacattagatccttgccattgttggttattgagtgtcgtactcggcactgttccttatgtcgataaatttgcgttaccttttcatgaacag
|| ||| | ||||||||||| |||||||| ||||| || |||||||||| |||||||| || |||||||| ||||||||| ||| | | | | || | | ||| | | ||| | || || ||| ||| | | |||| | || || || ||| | ||
GTTCCGAACTTGTACTGCATTGGTGATGCCAATGGTAAATTGATGCTTGCACATGCAGCCAGTGCCCAAGGAATTTCTGgtaaatggcttatcagtaggaggctactaacaatgcaataatattttcccttttttcttcttgagccttg--tattaaactctgagctcttactc-tgtggctag-------------------------
upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 5'ss of exon 10
GTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTGgtgaatcattctactgtgttcctcgaattgaagcatttacattagatccttgccattgttggttattgagtgtcgtactcggcactgttccttatgtcgataaatttgcgttaccttttcatgaacag
|| || || ||||| ||||| |||||||||||||| || ||||||||||||||||| ||||| |||||||| || |||||| ||| | | | |||| | | | | ||||| | | ||| |||| ||| | | | | ||| ||| || |||||| | |
GTTCCTCACTTGTATTGCATTGGTGATGCAAATGGAAAAATGATGCTTGCTCATGCTGCAAGTGCCCAAGGAATCTCTGgt-aattaccttgtt-tgttgc-cactctctctctactacat--ggtttttgtcattcagttttaatatctacttgaaacctgacttttcttt-tgtcgacatag-----------------------
upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 5'ss of exon 10
GTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTGgtgaatcatt-ctactgtgttcctcgaattgaagcatttacattagatcctt--gccattgttggttattgagtgtcgtactcggcactgttccttatgtcgataaatttgcgttaccttttcatgaacag
|| || || ||||| ||||| |||||||||||||| || ||||||||||||||||||||||| || ||||| ||||| ||| | | | |||| | | | | | |||| | | | ||| |||| | || ||| || | | | |
GTTCCTCACTTGTATTGCATAGGTGATGCAAATGGTAAAATGATGCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAGgttagtggtaactacctcatattttgctgttttacctttaaaaatgctacttaaaccatcttcattttttgcttggctcttgtgatgcag-----------------------------------------
upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: EFJ06739 (Selaginella moellendorffii), 5'ss of exon 10
GTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTGgtgaatc--attctactgtgttcctcgaattgaagcatttacattagatccttgccattgttggttattgagtgtcgtactcggcactgttccttatgtcgataaatttgcgttaccttttcatgaacag
||||| ||||||||||||||||| |||||||||||||| ||||||||||||| || || || || || |||||||| ||| | | |||| | || | | | | || || ||
GTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAGgtaatctcgagagagacatgttttgtgtgatgtgaccgtgatcgtgtctcttttgcag------------------------------------------------------------------------
upper sequence: PP1S112_186V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: EFJ16882 (Selaginella moellendorffii), 5'ss of exon 10
GTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTGgtgaatcattctactgtgttcctcgaattgaagcatttacattagatccttgccattgttggttattgagtgtcgtactcggcactgttccttatgtcgataaatttgcgttaccttttcatgaacag
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GTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAGgtaatctcgagagaaacatgttttgtatgatgtgaccgtgatcgtgtctcttttgcag----------------------------------------------------------------------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|208366234|gb|DC943808.1|DC943808EST: AAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTG TGATTGAGCAGATCGCTGGGCGGGACAACATTTTGAACCATAATAGCGTAC
genomic: AAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTGgtgaatcatt ... tcatgaacagTGATTGAGCAGATCGCTGGGCGGGACAACATTTTGAACCATAATAGCGTAC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTGgtgaatcattctactgtgttcctcgaattgaagcatttacattagatccttgccattgttggttattgagtgtcgtactcggcactgttccttatgtcgataaatttgcgttaccttttcatgaacag
- - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG