Sequence
atgc intronic sequence ATGC exonic sequenceTTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGGCAGACATGATAGGACCTGCGgtaatcttttggtttgaagctttgtattactccgatattctgaacaggctttctcacggtcgcactgaacaggtcttgcgtgaacttcatcgctgctttgtatgaagttcttgctgaaatttttcttctctggttgcag
Basic information
species | Physcomitrella patens |
transcript | PP1S147_62V6.1 |
intron # | 10 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S147_62V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 5'ss of exon 10
TTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGGCAGACATGATAGGACCTGCGgtaatcttttggtttgaagctttgtattactccga---tattctgaacag-gctttctcacggtcgcactgaacaggtcttgcgtgaacttcatcgctgctttgtatg-aagttctt--gctgaaattt-----ttcttctctggttgcag
||| |||||||||||| | || ||||||||||||||||| || || ||||| ||||||||||| || | || || ||| || ||||| ||||| | |||| | |||| ||| ||| | | | || |||||| | | ||| | ||| | | | || ||| || | |||| ||| ||||| || | || | |||
TTTCTATGAGGAGCAATTGCACCGGATGGAGTGCATGGCACAAGAACCTGTGCTTTTTGAGGACATATTATGCCAGATGATTGATATGATTGGACCAGAGgtagcatcttggacagaattattgatgcattttaggcctgtttggaacagtggaatgtcagcatgttgaggaattgcaccatttaatgcaaaattcctgtgttccaaacaagtccttaaactgaatttgataaatcttttcttttccacag
upper sequence: PP1S147_62V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: LOC_Os02g09840.1 (Oryza sativa), 5'ss of exon 9
TTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGGCAGACATGATAGGACCTGCGgtaatc---ttttggtttgaagctttgtattactccgatattctgaacaggctttctca-cggtcgcactgaacaggt-cttgcgtgaacttcatcgctgctttgtatgaagttcttgctgaaatttttcttctctggttgcag
|||| |||||||||||||||||| ||||| |||||||| ||||| ||||| || ||||| || ||| | |||||| | || ||||| ||||||| ||||| | || | || | | | | | | | | |||| ||||||| | | | | | | || || |||| | |
CTTTTTTGAGGAGCAACTTCATCGCATGGAATGCATGGCCCAGGAACCTGTACTGTTTGAAGACATCTTGTGTCAACTAATTGATATGATTGGACCTGAGgtaaccaaacatttttctgtatttctattctgttactaggttct---taggctttttaagctgatatatttaatttgttcttgtttcag-------------------------------------------------------
upper sequence: PP1S147_62V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GRMZM2G080083_T01 (Zea mays), 5'ss of exon 9
TTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGGCAGACATGATAGGACCTGCGgtaatcttttggtttgaagctttgtattactccgatattctgaacaggctttctcacggtcgcactgaacaggtcttgcgtgaacttcatcgctgctttgtatgaagttcttgctgaaatttttcttctctggttgcag
|| | |||||||||||||||||| |||||||||||||| ||||| |||||||| |||||||| ||| | ||||| | || ||||| ||||||| ||| |||| | | ||||| | | | || || | ||| | | | | ||||| | | ||| | || || | | |
CTTCTTTGAGGAGCAACTTCATCGCATGGAGTGCATGGCCCAGGAACCTGTTCTATTTGAGGACATCTTGTGTCAGCTCATTGATATGATTGGACCTGAGgttgcctttagtact-----tttgtgc-atttccatgttatagaca-----ttttatg------ctgaata--ttatgcattaattttgttccag--------------------------------------------
upper sequence: PP1S147_62V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GRMZM2G040094_T01 (Zea mays), 5'ss of exon 9
TTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGGCAGACATGATAGGACCTGCGgtaatcttttggtttgaagctttgtattactccgatattctgaacaggctttctcacggtcgcactgaacaggtcttgcgtgaacttcatcgctgctttgtatgaagttcttgctgaaatttttcttctctggttgcag
|||| ||||||||||||||||| |||||||||||||| || || |||||||| |||||||| ||| | ||||| | || ||||| ||||||| ||| |||| || | | || ||| | | || | |||| | | | | ||||| || ||| | || | | | |
CTTTTTCGAGGAGCAACTTCATCGCATGGAGTGCATGGCCCAAGAACCTGTTCTATTTGAGGACATCTTGTGTCAGCTCATCGATATGATTGGACCTGAGgttgccttta---ttaattttgtgcattgcc---aagttataaaca-----ttttatg------ctgaattagttatgcattaatcttgttccag--------------------------------------------
upper sequence: PP1S147_62V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA20G36530.1 (Glycine max), 5'ss of exon 10
TTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGGCAGACATGATAGGACCTGCGgtaatcttttggtttgaagctttgtattactccgatattctgaacaggctttc-tcacggtcgcactgaacaggtcttgcgtgaacttcatcgctgctttgtatgaagttcttgctgaaatttttcttctctggttgcag
|||||||||||| ||| | |||||||||||||||||||| || |||||||| ||||||||||| || | ||||| || |||||||| ||||| ||| || ||| | |||| | || | ||| | ||| | |||| | | | || | |||| || | | | | || |
TTTTTATGAGGAACAATTGCATCGGATGGAGTGCATGGCCCAAGAGCCTGTGCTTTTTGAGGACATATTGTGTCAGATAATTGACATGATTAAACCTGAGgt-----ttgcctttccatctttcttttgat--gattgtttgatctttttttcattgtgttgttgtgaaataacctttgcctggaaaagaaagtacaactctagtga---------------------------------
upper sequence: PP1S147_62V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA19G43790.1 (Glycine max), 5'ss of exon 10
TTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGGCAGACATGATAGGACCTGCGgtaatcttttggtttgaagctttgtattactccgatattctgaacaggctttctcacggtcgcactgaacaggtcttgcgtgaacttcatcgctgctttgtatgaagttcttgctgaaatttttcttctctggttgcag
|||||||||||||||| | ||||| |||||||||||||| || || ||||| |||||||||||||| | || || || |||||||| ||||||| ||| || ||| || ||| | ||| | || | || | | || | | | | ||| ||| | | || | || || |||
TTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAAGAACCTGTGCTTTTTGAGGATATACTGTGCCAGATTATTGACATGATTGGACCTGAGgt-----ttgtctttcaatgttttttttattt--attgtttgcccttgtattgtgttgatgagaagtcacattagttg-gaatatgatatgctaatctagtctgtagt-------------------------------
upper sequence: PP1S147_62V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA03G41180.1 (Glycine max), 5'ss of exon 10
TTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGGCAGACATGATAGGACCTGCGgtaatcttttggtttgaagctttgtattactccgatattct--gaacaggctttctcacggtcgcactgaacaggtcttgcgtgaacttcatcgctgctttgtatgaagttcttgctgaaatttttcttctctggttgcag
|||||||||||||||| | ||||| |||||||||||||| || || ||||| |||||||||||||| | || || || |||||||| ||||||| ||| ||| || ||| || | | | || | | | | ||| || | | ||| ||| || | |||
TTTTTATGAGGAGCAATTGCATCGAATGGAGTGCATGGCCCAAGAACCTGTGCTTTTTGAGGATATACTGTGCCAGATTATTGACATGATTGGACCTGAGgtttgtctttcaattttttttttctactgattgtttgcccttgtattatgttgatgagaagtcacattagctgga----atatgatattctaatctagtcagta-------------------------------------
upper sequence: PP1S147_62V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA10G30930.1 (Glycine max), 5'ss of exon 10
TTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGGCAGACATGATAGGACCTGCGgtaatcttttggtttgaagctttgtattactccgatattctgaacaggctttctcacggtcgcactgaacaggtcttgcgtgaacttcatcgctgctttgtatgaagttcttgctgaaatttttcttctctggttgcag
|||||||||||||||| | ||||||||||| |||||||| || |||||||| || |||||||| || | ||||| || |||||||| ||||| ||| || ||| | ||| | || | ||| | ||| | | | ||| || | || | | | ||| | | || | ||| | |
TTTTTATGAGGAGCAATTGCATCGGATGGAATGCATGGCCCAAGAGCCTGTGCTCTTTGAGGACATATTGTGTCAGATAATTGACATGATTAAACCTGAGgt-----ttgcctttccatatttcttttgat--gattgtttgatc---ttctatcattgtggtgttgtaaaattgttggacaagtgacctcaataatttaaggggggggg-----------------------------
upper sequence: PP1S147_62V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA10G32500.1 (Glycine max), 5'ss of exon 10
TTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGGCAGACATGATAGGACCTGCGgtaatcttttggtttgaagctttgtattactccgatattctgaacaggctttctcacggtcgcactgaacaggtcttgcgtgaacttcatcgctgctttgtatgaagttcttgctgaaatttttcttctctggttgcag
|||||||||||||| | |||||||||||||||||||| || |||||||| || ||||| ||||| | ||||| || | || ||||| ||||| | ||| | |||| | | ||| ||| | | | | ||| | || | | | | | |||| | |||| |
CTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAAGAGCCTGTGCTGTTTGAAGATATATTGTGTCAGATTGTGGATATGATTGGACCAGAGgtttttctttgttcttgttcttg----cgtcttgattcttttacttgtttttgttttactcctctgcagtatagcaagtggtaactgtcctacg--tttgcag------------------------------------
upper sequence: PP1S147_62V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA20G35090.1 (Glycine max), 5'ss of exon 10
TTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGGCAGACATGATAGGACCTGCGgtaatcttttggtttgaagctttgtattactccgatattctgaacaggctttctcacggtcgcactgaacaggtcttgcgtgaacttcatcgctgctttgtatgaagttcttgctgaaatttttcttctctggttgcag
|||||||||||||| | |||||||||||||||||||| || |||||||| || ||||| ||||| | ||||| || | || ||||| ||||| | ||| | |||| | | ||| ||| | | | | ||| | | || | | | | | |||| | |||| |
CTTTTATGAGGAGCAGTTGCATCGGATGGAGTGCATGGCCCAAGAGCCTGTGCTGTTTGAAGATATATTGTGTCAGATTGTGGATATGATTGGACCAGAGgtttttctttgttcttgttcttg----cgtcttgattcttttacttgtttttgtttcattcctctgcagtatagcaagtggtaactgtcctacg--tttgcag------------------------------------
upper sequence: PP1S147_62V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: AT5G28900.1 (Arabidopsis thaliana), 5'ss of exon 10
TTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGGCAGACATGATAGGACCTGCGgta-atcttttggtttgaagctttgtattactccgatattctgaacaggctttctcacggtcgcactgaacaggtct-tgcgtgaacttcatcgc--tgctttgtatgaagttcttgctgaaatttttcttctctggttgcag
|||||||| ||||| | ||| | |||||||||||||| || ||| |||||||||| ||||||||| | ||||| ||| || ||||| ||||||| ||| | | | | | | ||| | | | | ||||| | | || | || | ||| | | | ||| | | || ||||| | || || | | ||| |||| |
CTTTTATGAAGAGCAGTTGCATAGAATGGAGTGCATGGCGCAAGAGGCTGTTCTTTTCGAGGATATCTTATGTCAGATGATTGATATGATCGGACCTGAGgttcaacaatatatctcttgttttcttct--ttctatatttagtatagtcacagaagtagtttgtgttcccagttttctttctgagtcttgtgattttgttttgtgtttgattgtttttta---tttccttccacag------
upper sequence: PP1S147_62V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: AT5G28850.1 (Arabidopsis thaliana), 5'ss of exon 9
TTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGGCAGACATGATAGGACCTGCGgtaatcttttggtttgaagctttgtattactccgatattctgaacaggctttctcacggtcgcactgaacaggtct---tgcgtgaacttcatcgctgctttgtatgaagttct----tgctgaaatttttcttctctggttgcag--
|||||||| ||||| | ||| | |||||||||||||| || ||| |||||||||| ||||||||| | ||||| ||| || ||||| ||||||| ||| | || ||| | || ||| | | | | | | | || ||| || ||| || | | | || | ||| | | || || | || | | | ||| || | | || ||
CTTTTATGAAGAGCAGTTGCATAGAATGGAGTGCATGGCGCAAGAGGCTGTTCTTTTCGAGGATATCTTATGTCAGATGATTGATATGATCGGACCTGAGgt---tcaacaatatgtctcttgtttttttctttctatattaaggaagatatatgacagtcaca--gaagtagtttgggttcccagtttttctttctgactcttgcgattttgtcttgtgtttgattgttttttatttccttccacag
upper sequence: PP1S147_62V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: Vv07s0005g03730.t01 (Vitis vinifera), 5'ss of exon 11
TTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGGCAGACATGATAGGACCTGCGgtaatcttttggtttgaagctttgtattactccgatattctg--aacaggctttctcacggtcgcactgaacaggtcttgcgtgaacttcatcgctgctttgtatgaagttcttgctgaaatttttcttctctggttgcag
||||||||||||||| | ||||| ||||| |||||||| || |||||||| || |||||||||||| | ||||| || | |||||||| | ||| | ||| | || || | | | | | |||| | |||| | || | | | | || | | | |||| || |
CTTTTATGAGGAGCAATTGCATCGAATGGAATGCATGGCCCAAGAGCCTGTACTATTTGAGGATATCTTATGTCAGATAGTTGACATGATTGCACCAGAGgtcacggcttttttcgtacccagatcat-ctcccgtgttctagtagttagcaataactcattttcagggcatgatttttgcttgcag------------------------------------------------------
upper sequence: PP1S147_62V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: Vv14s0036g00750.t01 (Vitis vinifera), 5'ss of exon 7
TTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGGCAGACATGATAGGACCTGCGgtaatcttttggtttgaagctttgtattactccgatattctgaacaggctttctcacggtcgcactgaacaggtcttgcgtgaacttcatcgctgctttgtatgaagttcttgctgaaatttttcttctctggttgcag
|||||||||||||| | ||||| ||||| |||||||| || |||||||| || ||||||||||| | ||||| || | || ||||| || || | |||| | | ||| | || | ||| | ||| | | |||| | | | | | | || || || | | || | | || |||
CTTTTATGAGGAGCAGTTGCATCGAATGGAATGCATGGCCCAAGAGCCTGTGCTCTTTGAGGATATATTGTGTCAGATAGTTGATATGATTGGTCCAGAGgtagaccctc---ttgttgtttcat-ttattgtaatagattagtgacattttcccttact-gtattttat--gttgtgtttggaagcaa-----gccaagaaaaaacgactt---------------------------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|162193203|gb|FC369963.1|FC369963EST: TTCTTTTTGAGGATATCGTTTGTCAAATGGCAGACATGATAGGACCTGCG AAAGAGGGGCAACTGACACTTAANGATTTGAAGCGATGTAAATTGTCTGGG
genomic: TTCTTTTTGAGGATATCGTTTGTCAAATGGCAGACATGATAGGACCTGCGgtaatctttt ... ctggttgcagAAAGAGGGGCAACTGACACTTAAGGATTTGAAGCGATGTAAATTGTCTGGG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTTTTATGAGGAGCAACTTCATCGGATGGAGTGCATGGCTCAGGAGCCTGTTCTTTTTGAGGATATCGTTTGTCAAATGGCAGACATGATAGGACCTGCGgtaatcttttggtttgaagctttgtattactccgatattctgaacaggctttctcacggtcgcactgaacaggtcttgcgtgaacttcatcgctgctttgtatgaagttcttgctgaaatttttcttctctggttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT