Sequence
atgc intronic sequence ATGC exonic sequenceGAGAATAGCATCCACAGACCATGGGCAGGCCGCAGAAATACCGAGGAGTGCGACAACGGCACTGGGGATCATGGGTCTCCGAGATCCGCCACCCTCAATTgtaagcatcagtcatcttatcactccgtaccttgttcgccctcctcaatgcaccgtgtccagatgtgtgttatgtattgggataatgtggggggctagct...
Basic information
species | Physcomitrella patens |
transcript | PP1S21_214V6.1 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S21_214V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os06g08340.1 (Oryza sativa), 5'ss of exon 1
GAGAATAGCATCCACAGACCATGGGCAGGCCGCAGAAATACCGAGGAGTGCGACAACGGCACTGGGGATCATGGGTCTCCGAGATCCGCCACCCTCAATTgtaagcatcagtcatcttatcactccgtaccttgttcgccctcctcaatgcaccgtgtccagatgtgtgttatg----tattgggataatgtggggggctagct-----
| | | || |||| || || || ||||| || || |||||||| |||||||||||||||||||||||||||| ||||| ||| | | |||| | ||| | | | | || | |||| || | || | || | || | || |||
-----------------ATGGCGCGGCCGCAGCAGCGGTATCGCGGCGTGCGGCAGCGCCACTGGGGCTCATGGGTCTCCGAGATCCGCCACCCTCTCCTgtaattcatcgtcgccatcctcctcctga--ttgattgattctttgtttcttcctcgcgtagattggtttcttggccatggcggtttgatttcttggttgggcttgcag
upper sequence: PP1S21_214V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os02g55380.1 (Oryza sativa), 5'ss of exon 1
GAGAATAGCATCCACAGACCATGGGCAGGCCGCAGAAA---TACCGAGGAGTGCGACAACGGCACTGGGGATCATGGGTCTCCGAGATCCGCCACCCTCAATTgta----agcatcagtcatcttatcactccgtaccttgttcgccctcctcaatgcac----cgtgtccagatgtgtgtt-atgtattgggataatgtggggggctagct-----
|| ||| | || || |||| ||||||||| || ||||| || ||||| || || |||||||| || ||||||||||||||||||||||||| |||| || | || | | || ||| |||||| || || | | | || | | | ||| || | | | | |||| | |
--GACAAGCCTACA-AGCTGATGGCGAGGCCGCAGCAACGATACCGCGGCGTGCGGCAGCGCCACTGGGGCTCCTGGGTCTCCGAGATCCGCCACCCTCTCCTgtacgtgcgcgcgcgacaccgtcgtcttcttcttcttcttcgccgtcgtcgccgtgcgtttcttggttggttaggggttcgctcatggtggtgcaccgtggggtgattttgcag
upper sequence: PP1S21_214V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G135452_T01 (Zea mays), 5'ss of exon 1
GAGAATAGCATCCACAGACCATGGGCAGGCCGCAGAAA---TACCGAGGAGTGCGACAACGGCACTGGGGATCATGGGTCTCCGAGATCCGCCACCCTCAATTgtaagca-----tcagtcatcttatcactccgtaccttgttcgccctcctcaatgcaccgtg-tccagatgtgt-gttatgtattgggataatgtggggggctagct------------------
| || || | |||| |||| ||| || ||||| || ||||| ||||| |||||||| || ||||||||||||||||||||||||| ||| | | ||| || || | | | | || | ||| || | || | | || | | | | | | | ||| |
--GGGCGCCA-CCGTCTCCAATGGCTCGGCCACAGCAACGGTACCGCGGCGTGCGGCAACGCCACTGGGGCTCCTGGGTCTCCGAGATCCGCCACCCTCTCCTgtgcgtaaccctgcagccacgttcttcttgcctggactgggctatatccccatcgatcctcggcctaggcggctagctggccacggcggcggcgtgattattggattctctgtgagtgcgtgcag
upper sequence: PP1S21_214V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G111415_T01 (Zea mays), 5'ss of exon 1
GAGAATAGCATCCACAGACCATGGGCAGGCCGCAGAAA---TACCGAGGAGTGCGACAACGGCACTGGGGATCATGGGTCTCCGAGATCCGCCACCCTCAATTgtaagca--tcagtcatcttatcactccgtaccttgttc----gccctcctcaatgcaccgtgtccag-atgtgtgttatgtat-tgggataatgtgg-----ggggctagct--------------------------------
| | ||| |||| |||||||||| || ||||| || ||||| || || |||||||| || ||||||||||||||||||||||||| |||| | | | | | | | || || | | ||| | | | | | | | |||| | | | || | | || ||| |
---GACGACCGAAGGCGACGATGGCCAGGCCGCAGCAACGGTACCGCGGCGTGCGGCAGCGCCACTGGGGCTCCTGGGTCTCCGAGATCCGCCACCCTCTCCTgtacgtagctagcttagcccagcagcgtatagtataggccacggccacctacgctacgctacgcgcgccgcccctgttcctcacctcgcatcgtcccgttcccggagctgaccgcgcccggctggggctgttgatttgcatgcag
upper sequence: PP1S21_214V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G156006_T01 (Zea mays), 5'ss of exon 1
GAGAATAGCATCCACAGACCATGGGCAGGCCGCAGAAA---TACCGAGGAGTGCGACAACGGCACTGGGGATCATGGGTCTCCGAGATCCGCCACCCTCAATTgtaagcatcagtcatcttatcactccgtaccttgttcgccctcctca-atgcaccgtgtccagatgtgtgttatgtattgggataatgtggggggctagct----------------------
|| ||| | |||| |||| ||| || ||||| || ||||| ||||| |||||||| || |||||||| |||||||||||||| | ||| | | | | | | |||| || | || || | | | || || || | ||| | | || | || | || ||| | |
--CCATC-TGTCCGTCTCCAATGGCGCGGCCACAGCAACGGTACCGCGGCGTGCGGCAACGCCACTGGGGCTCCTGGGTCTCGGAGATCCGCCACCCCCTCCTgtgcgtaacg--taacacgt-gctcctcgactggaccggacttattatactcatcgattcttggcgtgagcggcgggctg--acaacggcggcggcgtgttctctgtgcgtgggtgcgtgcag
upper sequence: PP1S21_214V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA14G13470.1 (Glycine max), 5'ss of exon 1
GAGAATAGCATCCACAGACCATGGGCAGGCC---GCAGAAATACCGAGGAGTGCGACAACGGCACTGGGGATCATGGGTCTCCGAGATCCGCCACCCTCAATTgtaagcatcagtcatcttatcactccgtaccttgttcgccctcctcaatgcaccgtgtccagatgtgtgttatgtattgggataatgtggg---gggctagct---
|||| ||| || ||| |||||||| || |||||| |||| ||||| || ||||||||||| || ||||||||| |||||||| | | | | | | || | |||| |||| | || | | | | | || ||| | || | |
--------------------ATGGCCAGACCTCAACAGCGTTACCGAGGTGTCCGACAAAGGCATTGGGGTTCTTGGGTCTCCGAAATTCGCCACCCTATATTgtaagttt------ttccactcccatgcaagttttcacacctcttcaaaaaattaaccacattcatttccaaaaaaaaatgttagtgtatgtccttgcaaattgtaMapped 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|67574317|gb|BJ947141.1|BJ947141EST: CGACAACGGCACTGGGGATCATGGGTCTCCGAGATCCGCCACCCTCAATT GAAGACCAGGGTGTGGTTGGGTACATTCGAGACTGCTGAAGATGCTGCGCA
genomic: CGACAACGGCACTGGGGATCATGGGTCTCCGAGATCCGCCACCCTCAATTgtaagcatca ... cgtcgtgcagGAAGACCAGGGTGTGGTTGGGTACATTCGAGACTGCTGAAGATGCTGCGCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GAGAATAGCATCCACAGACCATGGGCAGGCCGCAGAAATACCGAGGAGTGCGACAACGGCACTGGGGATCATGGGTCTCCGAGATCCGCCACCCTCAATTgtaagcatcagtcatcttatcactccgtaccttgttcgccctcctcaatgcaccgtgtccagatgtgtgttatgtattgggataatgtggggggctagct
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