Sequence
atgc intronic sequence ATGC exonic sequenceTGAGGTGGCCAAAAAGTATCCCGCCATCAAGTATAACGAGGTCATTGTGGATAATTGCTGTATGCAGCTTGTGTCGAAGCCTCAACAATTTGATGTCATGgtaagttctcgtatgtcaggctcaattttctccgacttttagttattggcagtgtttatgctaatgacttgatgttactgtgacatcagctggaactctgattcaagttgtttgccttggtgctattgtgtgtatttttcccccag
Basic information
species | Physcomitrella patens |
transcript | PP1S152_81V6.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S152_81V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os04g40310.2 (Oryza sativa), 5'ss of exon 2
TGAGGTGGCCAAAAAGTATCCCGCCATCAAGTATAACGAGGTCATTGTGGATAATTGCTGTATGCAGCTTGTGTCGAAGCCTCAACAATTTGATGTCATGgtaagttctcgtatgtcaggctcaattttctccgacttttagttattggcagtgtttatgctaatgacttgatgttactgtgacatcagctggaactctgattcaagttgtttgccttggtgctattgtgtgtatttttcccccag
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TGAGGTTGCCTCAAAGTATCCTGGTATTCAGTATAATGAGATCATTGTCGACAACTGCTGTATGCAACTTGTTGCAAAGCCTGAGCAATTTGATGTCATGgtatgctctt-tacttcatac---attctatctgg---------agcatcactgtctgttc-agtactttggagctgccttg-------tttgaactgc-actgagtttctttgcgt--gtgct----------------------
upper sequence: PP1S152_81V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os02g38200.1 (Oryza sativa), 5'ss of exon 2
TGAGGTGGCCAAAAAGTATCCCGCCATCAAGTATAACGAGGTCATTGTGGATAATTGCTGTATGCAGCTTGTGTCGAAGCCTCAACAATTTGATGTCATGgtaagttctcgtatgtcaggctcaat-tttctccgacttttagttattggcagtgtttatgctaatgacttgatgttactgtgacatcagctggaactctgattcaagttgtttgccttggtgctattgtgtgtatttttcccccag
|||||| || | ||||||||| | || | ||||| || |||| ||||| || || |||||||||||||| | |||||| ||||||||||||| ||||||||| |||| || | || || | | ||| | || || || || | | || | | || | | ||| || ||||| | | | ||| |
TGAGGTTGCAACAAAGTATCCTGGAATTCAATATAATGAAATCATCGTGGACAACTGTTGTATGCAGCTTGTTGCTAAGCCTGAACAATTTGATGTTATGgtaagt------atgttagttctatcattactatgcatcttaacaaatg-ca----ttctgtttgtaacgtcaccatattctatactcaccta-----ctgatctatgct-tttatc------------------------------
upper sequence: PP1S152_81V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G006672_T02 (Zea mays), 5'ss of exon 2
TGAGGTGGCCAAAAAGTATCCCGCCATCAAGTATAACGAGGTCATTGTGGATAATTGCTGTATGCAGCTTGTGTCGAAGCCTCAACAATTTGATGTCATGgtaagttctcgtatgtcaggctcaattttctccgacttttagttattggcagtgtttatgctaatgacttgatgttactgtgacatcagctggaactctgattcaagttgtttgccttggtgctattgtgtgtatttttcccccag
|||||| || || ||||| || | || || ||||| || |||||||||| || || |||||||||||||| | |||||| ||||||||||||| |||||| ||||| | ||| | || | |||| | | | ||| | || || | || | | | ||| | ||| || |
TGAGGTTGCAAAGAAGTACCCTGGAATTAAATATAATGAAATCATTGTGGACAACTGTTGTATGCAGCTTGTTGCAAAGCCTGAACAATTTGATGTTATGgta------cgtatattca-ctcttatcacttatatacgcagtttctcacctaggagatgttg--gatgtggttttcttactctacaaaggagaaggacaa--caactttt-----------------------------------
upper sequence: PP1S152_81V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G025366_T02 (Zea mays), 5'ss of exon 2
TGAGGTGGCCAAAAAGTATCCCGCCATCAAGTATAACGAGGTCATTGTGGATAATTGCTGTATGCAGCTTGTGTCGAAGCCTCAACAATTTGATGTCATGgtaagttctcgtatgtcaggctcaattttctccgacttttagttattggcagtgtttatgctaatgacttgatgttactgtgacatcagctggaactctgattcaagttgtttgccttggtgctattgtgtgtatttttcccccag
||| || || ||| ||||| | || |||| || || | ||||| || || |||| |||||| ||||| || |||||| |||||||||||||||||||| || || || || || |||||| | | || ||| | | |||| | || ||| ||| | || |||| | || | || |
TGAAGTTGCTTCAAAATATCCTGGTATTCAGTACAATGAAATGATTGTTGACAACTGCTCTATGCAACTTGTTTCAAAGCCTGAACAATTTGATGTCATGgtatgtatctaaatttctggg-catttttctgtgtatactatttaat--------------ttggaactttacttttttgt----tcaaacaaaccttggattacatttctctgttcta---------------------------
upper sequence: PP1S152_81V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA02G04780.1 (Glycine max), 5'ss of exon 2
TGAGGTGGCCAAAAAGTATCCCGCCATCAAGTATAACGAGGTCATTGTGGATAATTGCTGTATGCAGCTTGTGTCGAAGCCTCAACAATTTGATGTCATGgtaagttctcgtatgtcaggctcaattttctccgacttttagttattggcagtgtttatgctaatgacttgatgttactgtgacatcagctggaactctgattcaagttgtttgccttggtgctattgtgtgtatttttcccccag
||||| || | |||||| || | |||||||||||||| | ||||||||||| ||||||||||||||||| || |||||| |||| ||||||||||||||| || |||| | ||||| | | ||| || |||| | ||||| | | | |||| |||| | | | | | | | |
AGAGGTTGCTACAAAGTACCCTGGAATCAAGTATAACGAAATTATTGTGGATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgt----gtatttacatttcaatcct----ggcttgcagctatttat-gcacttatgtaatttgtctaatgtatttgtgcagtaaccc----ccccgccccccgcccccc---------------------------------
upper sequence: PP1S152_81V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA16G22640.1 (Glycine max), 5'ss of exon 2
TGAGGTGGCCAAAAAGTATCCCGCCATCAAGTATAACGAGGTCATTGTGGATAATTGCTGTATGCAGCTTGTGTCGAAGCCTCAACAATTTGATGTCATGgtaagttctcgtatgtcaggctcaattttctccgacttttagttattggcagtgtttatgctaatgacttgatgttactgtgacatcagctggaactctgattcaagttgtttgccttggtgctattgtgtgtatttttcccccag
||||| || | |||||| || | || ||||||||||| | ||||||||||| ||||||||||||||||| || |||||| |||| ||||||||||||||| || || | || ||| | | |||| | | ||| |||||| || ||| ||| | | ||| | ||
AGAGGTTGCTACAAAGTACCCTGGAATAAAGTATAACGAAATTATTGTGGATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtatttacattctattctggtttg-ctgctgtttatgcacttatgtaattttgtctaatgtatttatgcagtaagcacacacac-----ccttgagttaa----------------------------------------
upper sequence: PP1S152_81V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT4G35650.1 (Arabidopsis thaliana), 5'ss of exon 2
TGAGGTGGCCAAAAAGTATCCCGCCATCAAGTATAACGAGGTCATTGTGGATAATTGCTGTATGCAGCTTGTGTCGAAGCCTCAACAATTTGATGTCATGgtaa-gttctcgtatgtcaggct-caattttctccgact--tttagttat-tggcagtgtttatgctaatgacttgatgttactgtgacatcagctggaactctgattcaagttgtttgccttggtgctattgtgtgtatttttcccccag
||||| || ||| | ||| | | || | || || || | || || || |||||||||||||||||||| | |||||| | ||||||||||||||||||| | ||| | | | | | ||| | || | ||| | || || ||| | || | |||||||| | ||| || | | || | ||||| | |
AGAGGTTGCTAAACATTATTCGGGGATTACTTACAATGAAATAATCGTAGACAATTGCTGTATGCAGCTTGTCGCCAAGCCTGAGCAATTTGATGTCATGgtaatgctcttcttttcctagttacaaatcaaaatgagtcattttgaaatgtgacagacgatgaaaccatca-ttgatgttgttttgatgtctctcatggatattttttgt-tggtttgtttcag--------------------------
upper sequence: PP1S152_81V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv04s0210g00180.t01 (Vitis vinifera), 5'ss of exon 2
TGAGGTGGCCAAAAAGTATCCCGCCATCAAGTATAACGAGGTCATTGTGGATAATTGCTGTATGCAGCTTGTGTCGAAGCCTCAACAATTTGATGTCATGgtaagttctcgtatgtcaggctcaattttctccgacttttagttattggcagtgtttatgctaatgacttgatgttactgtgacatcagctggaactctgattcaagttgtttgccttggtgctattgtgtgtatttttcccccag
||||| || | ||| ||||| | |||||||| | || | |||||||| |||||||| ||||||||||| || |||||| | || ||||||||||||||| || || | ||| | | ||||| | | | |||| ||| |||| | | || ||| ||| || | | || | || || | |
AGAGGTTGCAACAAAATATCCTGGAATCAAGTACAGTGAAATTATTGTGGACAATTGCTGCATGCAGCTTGTTTCAAAGCCTGAGCAGTTTGATGTCATGgtatgtgaatata---------ctattgtatagcactttaattgag-----------atgcaaattgcttggtcaatgtttgtcatgttctgtaattattcttaagatttcctga--tagca------------------------
upper sequence: PP1S152_81V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ29002 (Selaginella moellendorffii), 5'ss of exon 2
TGAGGTGGCCAAAAAGTATCCCGCCATCAAGTATAACGAGGTCATTGTGGATAATTGCTGTATGCAGCTTGTGTCGAAGCCTCAACAATTTGATGTCATGgtaagttctcgtatgtcaggctcaattttctccgacttttagttattggcagtgtttatgctaatgacttgatgttactgtgacatcagctggaactctgattcaagttgtttgccttggtgctattgtgtgtatttttcccccag
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CGAGGTGGCCAAGAAGTATCCCGGGATCAAGTACAACGAGATCATCGTCGACAACTGCTGTATGCAGCTCGTGTCTCGCCCCGAGCAATTCGATGTCATGgtaaccagttgctcctt----ccatttcattgcagtgttttatcatccac-gaacctgtgcag-----------------------------------------------------------------------------------
upper sequence: PP1S152_81V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ13705 (Selaginella moellendorffii), 5'ss of exon 2
TGAGGTGGCCAAAAAGTATCCCGCCATCAAGTATAACGAGGTCATTGTGGATAATTGCTGTATGCAGCTTGTGTCGAAGCCTCAACAATTTGATGTCATGgtaagttctcgtatgtcaggctcaattttctccgacttttagttattggcagtgtttatgctaatgacttgatgttactgtgacatcagctggaactctgattcaagttgtttgccttggtgctattgtgtgtatttttcccccag
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CGAGGTGGCCAAGAAGTACCCCGGGATCAAGTACAACGAGATCATCGTCGACAACTGCTGTATGCAGCTCGTGTCTCGCCCCGAGCAATTCGACGTCATGgtaaccagttgctcctt----ccatttcattgcagtgttttatcatccac-gaacctgtgcag-----------------------------------------------------------------------------------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|162191774|gb|FC367507.1|FC367507EST: ATAATTGCTGTATGCAGCTTGTGTCGAAGCCTCAACAATTTGATGTCATG GTAACACCAAATTTGTATGGAACACTGGTGGCCAATACTGCAGCTGGTATT
genomic: ATAATTGCTGTATGCAGCTTGTGTCGAAGCCTCAACAATTTGATGTCATGgtaagttctc ... tttcccccagGTAACACCAAATTTGTATGGAACACTGGTGGCCAATACTGCAGCTGGTATT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGAGGTGGCCAAAAAGTATCCCGCCATCAAGTATAACGAGGTCATTGTGGATAATTGCTGTATGCAGCTTGTGTCGAAGCCTCAACAATTTGATGTCATGgtaagttctcgtatgtcaggctcaattttctccgacttttagttattggcagtgtttatgctaatgacttgatgttactgtgacatcagctggaactctgattcaagttgtttgccttggtgctattgtgtgtatttttcccccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT