Sequence
atgc intronic sequence ATGC exonic sequenceATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAGgtatgcgttgacacgaagccgctgttttttgcaacttatcgtctgatttacctcatttttatggtggtatggtttatattctaaatttaaacatggggcgatcatcctgaacaattatgtcgaaacggttcgatatttgttataaccatgctgcaaacactatag
Basic information
species | Physcomitrella patens |
transcript | PP1S124_47V6.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S124_47V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 2
ATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAGgtatgcgttgacacgaagccgctgttttttgcaacttatcgtctgatttacctcatttttatggtggtatggtttatattctaaatttaaacatggggcgatcatcctgaacaattatgtcgaaacggttcgatatttgttataaccatgctgcaaacactatag
|||| |||||||| ||||| ||||||||||| || ||||| || || |||||||| |||||||| || ||||| || || || || |||||||| || | | | | | || | | || || ||| | | || ||| || || | || || | | ||| |
ATGCGGACATGGAGGATTACGGGTTCGAGTACTCCGACGACGAGCCGGAGGAGCAGGATGTTGACATCGAGAACCAGTACTACAACTCCAAAGgttcgcttccaatctctttcattcttgtgtttc-ctcggcggtgcgttttctcggaccctgtgtatgtagtgtg-gtagtgtagtattcgaggagaggccac---------------------------------------------------------------
upper sequence: PP1S124_47V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G079196_T01 (Zea mays), 5'ss of exon 2
ATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAGgtatgcgttgacacgaagccgctgttttttgcaacttatcgtctgatttacctcatttttatggtggtatggtttatattctaaatttaaacatggggcgatcatcctgaacaattatgtcgaaacggttcgatatttgttataaccatgctgcaaacactatag
|||| |||||||| || || ||||||||||| || ||||| || || |||||||| ||||| || |||||||| || ||||| || |||||||| || | || | ||| | | ||| | | |||| | | || | || | || | || || || | || || || || | ||
ATGCGGACATGGAGGACTACGGGTTCGAGTACTCTGACGAAGAGCCGGAGGAGCAGGATGTCGACATTGAGAACCAGTATTACAACTCCAAAGgttggctctt-----------cttctctttcgagttgcgagtccggtg------atttctgaagagggaacgtat-----ctggtgctcaaaggggtacggtgctcatgtgca--cattttaaa-----------------------------------------
upper sequence: PP1S124_47V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G132804_T01 (Zea mays), 5'ss of exon 2
ATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAGgtatgcgttgacacgaagccgctgttttttgcaacttatcgtctgatttacctcatttttatggtggtatggtttatattctaaatttaaacatggggcgatcatcctgaacaattatgtcgaaacggttcgatatttgttataaccatgctgcaaacactatag
|||| || ||||| || || ||||||||||| || |||||||| || |||||||| ||||| ||||| ||||| || ||||| || | |||||| | | | | | | | |||| | | | || | | | | || | | | ||| |||| | | | ||
ATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAGgttcg------------gtcttgttctccttcgacttgcgagtcgggtgatttc----tcagaaagtcagaaactag---cgcgaccggactatgc--tagtcattttttatgctcttgct--------------------------------------------
upper sequence: PP1S124_47V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA19G30100.1 (Glycine max), 5'ss of exon 2
ATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAGgtatgcgttgacacgaagccgctgttttttgcaacttatcgtctgatttacctcatttttatggtg-gtatggtttatattctaaatttaaacatggggcgatcatcctgaacaattatgtcgaaacggttcgatatttgttataaccatgctgcaaacactatag
|||| || ||||| || ||||| || ||||| || || ||||| | ||||||||||||||||||||||||||||||||||| ||| | |||||||| | | || || || |||| || || | | || | | | | | | || | ||||| || ||| || | || ||
ATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAGCAAGATGTTGATATTGAGAATCAATATTACAATTCAAAAGgtatttcc--------aacaactattatt----actt-----ttgcttcttgttagttgcaagaagcaaaaagataattccttgcatttatgaattgggaaattttatc---tttttttg----------------------------------------------
upper sequence: PP1S124_47V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA19G17660.2 (Glycine max), 5'ss of exon 2
ATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAGgtatgcgttgacacgaagccgctgttttttgcaacttatcgtctgatttacctcatttttatggtggtatggtttatattctaaatttaaacatggggcgatcatcctgaacaattatgtcgaaacggttcgatatttgttataaccatgctgcaaacactatag
|||| |||||||| || ||||| |||||||| || || ||||| | || |||||||| |||||||| |||||||||||||| ||| | |||||| | ||| ||| ||||| | || | || || | || | | | | || | ||| || || |||||| | | | | || |
ATGCTGACATGGAGGACTATGGCTTCGAGTACTCTGATGAGGAGCAAGAAGAGCAAGACGTTGATATCGAGAATCAATATTACAATTCAAAAGgt-tctgtt------------ctgctttttactg-ttgttgtttgg-------cgttgctgaattagga--attgaagccagaaacttgttttgcggttgatcatt----atcactgtatcagtgtg--------------------------------------
upper sequence: PP1S124_47V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA03G00670.1 (Glycine max), 5'ss of exon 2
ATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAGgtatgcgttgacacgaagccgctgttttttgcaacttatcgtctgatttacctcatttttatggtggtatggtttatattctaaatttaaacatggggcgatcatcctgaacaattatgtcgaaacggttcgatatttgttataaccatgctgcaaacactatag
|||| || ||||| || ||||| || ||||| || || ||||| | ||||| || |||||||||||||||||||||||||| ||| | |||||||| || |||| |||| || | ||||| ||| | | || | | | || ||| | || | | |
ATGCTGATATGGAGGACTATGGATTTGAGTACTCAGATGAGGAGCAAGAGGAACAGGATGTTGATATTGAGAATCAATATTACAATTCAAAAGgtat--------------------ttccctgca-tttatgaattgggaaaatgtctttttttgggaatctagtgttcaat-tagattgtgttgaaaactactttgttcaaatcagtgttcta-------------------------------------------
upper sequence: PP1S124_47V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA05G14170.1 (Glycine max), 5'ss of exon 2
ATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAGgtatgcgttgacacgaagccgctgttttttgcaacttatcgtctgatttacctcatttttatggtggtatggtttatattctaaatttaaacatggggc-gatcatcctgaacaattatgtcgaaacggttcgatatttgttataaccatgctgcaaacactatag
|||| |||||||| || || || |||||||| || || ||||| | ||||||||| |||||||| |||||||||||||| ||| | |||||| | ||| ||| || || || | | | |||| | || ||| || | || | | || || ||| ||||| | | | | ||||
ATGCTGACATGGAGGACTACGGTTTCGAGTACTCCGATGAGGAGGAAGTGGAGCAAGACGTTGATATCGAGAATCAATATTACAATTCAAAAGgt-tctgtt------------ctgcttattattgtttttgttgttatttggcg-----ttgtggaattaggaattggaggcacaagcctgttttgtggctgatca----gtatcactgtgtc--------------------------------------------
upper sequence: PP1S124_47V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT2G26990.1 (Arabidopsis thaliana), 5'ss of exon 2
ATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAGgtatgcgttgacacgaagccgctgttttttgcaacttatcgtctgatttacctcatttttatggtggtatggtttatattctaaatttaaacatggggcgatcatcctgaacaattatgtcgaaacggttcgatatttgttataaccatgctgcaaacactatag
|||| |||||||| || ||||| ||||||||||| || ||||| | ||||| ||||||||||| |||||||| || |||||||| | |||||| | | ||| || | ||| || ||| | ||| | | | || | ||| ||||| | || | | | | | ||
ATGCTGACATGGAGGACTATGGATTCGAGTATTCTGATGAGGAGCAAGAGGAACAAGATGTTGACATTGAGAACCAGTATTATAACTCTAAAGgt----------------tagttttttcttacgttctattgt---gtttgc---attctcaaacttgtgctgcg---attataaatcttgactcctagtggtttccttctttaag--------------------------------------------------
upper sequence: PP1S124_47V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 5'ss of exon 2
ATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAGgta-tgcgttgacacgaagccgctgttttttgcaacttatcgtctgatttacctcatttttatggtggtatggtttatattctaaatttaaacatggggcgatcatcctgaacaattatgtcgaaacggttcgatatttgttataaccatgctgcaaacactatag
|||| |||||||| |||||||| || ||||| || || ||||| || |||||||| |||||||||||||||||||||||||| ||| | ||||||| | | || | | | || | ||| || | | | ||| || | ||| | || | | || | ||| || | || |
ATGCAGACATGGAGGATTATGGATTTGAGTACTCAGAAGAGGAGCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAGgtacttctgtggcctataacttct-tgtttgaaaattccttagaagtcttatcta--tattagagaagttttctgaatgcttcaaaattttttttcggaattt---------------------------------------------------------------
upper sequence: PP1S124_47V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EDP09792 (Chlamydomonas reinhardtii), 5'ss of exon 1
--ATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAGgtatgcgttgacacgaagccgctgt--tttttgcaacttatcgtctgatttacctcatttttatgg-tggtatggtttatattctaaatttaaacatggggcgatcatcctgaacaattatgtcgaaacggttcgatatttgttataaccatgctgcaaacactatag
| | || ||||| |||||||| |||||||| ||||||||||| ||||| ||| |||| || ||||| ||||| || || |||||| | || |||| | | || || ||| || | | | | | || || | | | || || | | | | || | |
CGACGATGAAATGGAGGATTATGGCTTCGAGTACTCGGACGAGGACCCCGAAGAGGAAGACGTCGATATCGAGAACCAGTACTATAATGCGAAGGgtagg-gctggggcgcagcgaatgcagccccggttgcacgttattgggctttatacagatctgggcctgaccgggcctgcaggccggggtcaagacagcag-------------------------------------------------------------------
upper sequence: PP1S124_47V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ29478 (Selaginella moellendorffii), 5'ss of exon 2
ATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAGgtatgcgttgacacgaagccgctgttttttgcaacttatcgtctgatttacctcatttttatggtggtatggtttatattctaaatttaaacatggggcgatcatcctgaacaattatgtcgaaacggttcgatatttgttataaccatgctgcaaacactatag
| || ||||||||||||||||| || ||||| ||||| || || ||||||||||||||||| ||||| |||||||| || || || | ||||||| ||| | || || | || || | | | | |
ACGCGGACATGGAAGATTATGGCTTTGAGTACTCGGAAGAAGACCCCGAGGAGCAAGATGTCGATATCGAGAATCAGTACTACAACTCTAAAGgta-gcgat---------tttcttttctgtgaaagaaaacaatggtatcggcag---------------------------------------------------------------------------------------------------------------
upper sequence: PP1S124_47V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ28052 (Selaginella moellendorffii), 5'ss of exon 2
ATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAGgtatgcgttgacacgaagccgctgttttttgcaacttatcgtctgatttacctcatttttatggtggtatggtttatattctaaatttaaacatggggcgatcatcctgaacaattatgtcgaaacggttcgatatttgttataaccatgctgcaaacactatag
| || ||||||||||||||||| || ||||| ||||| || || ||||||||||||||||| ||||| |||||||| || || || | ||||||| || || || | || || | | | | |
ACGCGGACATGGAAGATTATGGCTTTGAGTACTCGGAAGAAGACCCCGAGGAGCAAGATGTCGATATCGAGAATCAGTACTACAACTCTAAAGgtagagatt----------ttcttttctgtgaaagaaaacaatggtatcggcag---------------------------------------------------------------------------------------------------------------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|162204804|gb|FC381161.1|FC381161EST: ACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAG GATTGGTAGAAGCTGATCCTGAAGGAGCACTGAAGGGATTTGCAGAGGTTG
genomic: ACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAGgtatgcgttg ... aacactatagGATTGGTAGAAGCTGATCCTGAAGGAGCACTGAAGGGATTTGCAGAGGTTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAGgtatgcgttgacacgaagccgctgttttttgcaacttatcgtctgatttacctcatttttatggtggtatggtttatattctaaatttaaacatggggcgatcatcctgaacaattatgtcgaaacggttcgatatttgttataaccatgctgcaaacactatag
- - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG