Sequence
atgc intronic sequence ATGC exonic sequenceTGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGATGTTTACACAGCTCTTGGAAGTGAGgtaacatgatgtttctgtactaatgatattactttagtacgactttgtgatgttgtgtccttgtacttgagattgtaataactgcaattagcaatgttct...
Basic information
species | Arabidopsis thaliana |
transcript | AT3G16950.2 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 5'ss of exon 5
TGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGATGTTTACACAGCTCTTGGAAGTGAGgtaacatgatgtttctgtactaatgatattactttagtacgactttgtgatgttgtgtccttgtacttgagat--tgtaataactgcaattagcaatgttct--
||| | ||| | ||||||||||| || ||||| ||||| || |||||||| || ||||| ||||| ||||||||||| || ||||||||||||||||||||| | ||| || | | | ||| | || | ||| | || | | | || | || || || ||| | |||| | || |||||
TGCACTAAAACTTGAGTCTGTCCCGGACTGGATAGCAATCGTTGGAAGTGGATACATTGGGCTTGAATTCAGTGATGTATATACAGCTCTTGGAAGTGAGgtacatgaaagttcttgctgtgaataaatt-caaggatatggcttagaga-atcata-cagtgagcatggaatcatgcaattattgcaga-aacatggttctac
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 5
TGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGATGTTTACACAGCTCTTGGAAGTGAGgtaacatgatgtttctgtactaatgatattactttagtacg-actttgtgat-gttgtgtccttg-tacttgagattgtaataactgcaattagcaatgttct
||| | ||| | ||||| || ||||| |||||||| || || ||||| ||||| ||||| || || ||||||||||| ||||| ||||| |||||||||||| ||||| | || | || | | || || | | | | | ||| | | | | | | || || || ||
TGCACTAAAACTTGAGTCAGTTCCTGACTGGATTGCTATCGTGGGAAGCGGTTACATTGGACTGGAATTCAGTGATGTATACACGGCTCTGGGAAGTGAGgta-catgaacagttcctaagatgcatcattttctaacacatgcatagaaacagacatgttttgggtgcatacatgttctgcaagtgtcttttcttggctt--
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G145595_T02 (Zea mays), 5'ss of exon 4
TGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGATGTTTACACAGCTCTTGGAAGTGAGgtaacatgatgtttctgtactaatgatattactttagtacgactttgtgatgttgtgtccttgtacttgagattgtaataactgcaattagcaatgttct-
||| | ||| | ||||| |||||||| |||||||| ||||| ||||||||||| ||||| ||||| ||||||||||| ||||||||||| |||||||||||| |||| || | ||| ||| | ||| || | || || | || || | | | | | | | || | |
TGCACTAAAACTTGAGTCAGTCCCTGAATGGATTGCTATTGTTGGAAGTGGTTACATTGGACTTGAATTCAGTGATGTATACACAGCTCTAGGAAGTGAGgta-tatgaacaatcattcaagccatcattgcttaaatacatgcttagggagtctaatcgtgttagttattttagcgaatattcctctgtcatatatcatg
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G073774_T01 (Zea mays), 5'ss of exon 5
TGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGATGTTTACACAGCTCTTGGAAGTGAGgta-acatgatgtttctgtactaatgatattactttagtacgactttgtgatgttgtgtccttgtacttgagattgtaataactgcaattagc-aatgttct-
||| ||||| | ||||| || || || ||||| || ||||| ||||||||||| ||||| ||||||||||||||||| |||||||||||||||||||||||| | || | | || | || || || || | | || || | | | |||| | | || || | || | | | ||||
TGCACTGAAACTTGAGTCAGTTCCAGACTGGATAGCTATTGTTGGAAGTGGTTACATTGGACTTGAGTTCAGTGATGTATACACAGCTCTTGGAAGTGAGgtacattagaagctcttgctcggattat-ttgctatgct--gatttctccaagaaccattcttggcaacaccagagaaacaatgaaacttgcccagtattcta
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA17G03560.1 (Glycine max), 5'ss of exon 5
TGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGATGTTTACACAGCTCTTGGAAGTGAGgtaacatgatgtttctgtactaatgatat--tactttagtacgactttgtgatgttgtgtccttgtacttga--gattgtaataactgcaattagcaatgttct
|| | ||| | |||||||| ||||| ||||| ||||||||||||||||| |||||||||||||| ||||||||||| || ||||| ||||||||||||||| || || |||| | | | | || | ||| || | || | | || || | | ||| | || || || |||
CGCACTCAAACTGGAGTCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGATGTATATACAGCACTTGGAAGTGAGgtagcacatctttgtgatactgtttctttcttttttcattaccttttgttcttgataaatatttataaataatcgatcccttcatttgacatcagaaata----
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA07G37050.2 (Glycine max), 5'ss of exon 5
TGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGATGTTTACACAGCTCTTGGAAGTGAGgtaacatgatgtttctgtactaatgatattactttagtacgactttgtgatgttgtgtccttgtacttgagattgtaataactgcaattagcaatgttct--
|| | ||| | || ||||| ||||| ||||| ||||||||||||||||| |||||||||||||| ||||||||||| || ||||| ||||||||||||||| || || ||| || | | ||||| | || | || | | || ||| |||| | | ||||| || || | |
CGCACTCAAACTGGAATCTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGATATATTGGTCTTGAATTCAGTGATGTATATACAGCACTTGGAAGTGAGgtagcac-atctttgtgaattt-tgatactttttctttctcttttcattaccttttgttcttgagaaatatttacaaataatcaatcctatcatttgacatc
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA15G15310.1 (Glycine max), 5'ss of exon 5
TGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGATGTTTACACAGCTCTTGGAAGTGAGgtaacatgatgtttctgtactaatg-atattactttagtacgactttgtgatgttgtgtccttgtacttgagattgtaataactg--caattagcaatgttct-----------------------------------------------------------------------------------------------
||| | ||| | ||| |||| ||||| ||||| |||||||||||||||||||||||||| ||||| ||||||||||| || || || ||||||||||||||| | |||| | || || || || |||| || | | || ||| | || | || | |||| | ||||| | |
TGCACTCAAACTGGAGACTGTTCCTGATTGGATAGCAATTGTAGGAAGTGGTTATATTGGCCTTGAATTCAGTGATGTATATACGGCCCTTGGAAGTGAGgtagtac-----ttctcttctgatatatttttttttatcctttctcaattgtattttgttcatg-agaagaactgacaatagttttccaatttttcttttatgacgtttgaaagttttttatattatctcattgtttgaaaagttagaaacctaatttgtgcagaagagatatagttggtaataatggtactctgcag
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 5'ss of exon 5
TGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGATGTTTACACAGCTCTTGGAAGTGAGgtaacatgatgtttctgtactaatgatattactttagta-cgactttgtgatgt-tgtgtccttgtacttga----gattgtaa-taactgcaattagcaatgttct-----
||| |||| | |||| |||| || |||||||| ||||| ||||||||||| ||||||||||||||||| ||||| || || || |||||||||||||||| || | || | | || ||| | || || | | | |||| || |||| || ||| |||| | | ||| | || | || ||
TGCGCTGAAGCTGGAGTGGATCCCAGACTGGATTGCCATTGTTGGAAGTGGTTACATTGGTCTTGAGTTCAGCGATGTCTATACTGCCCTTGGAAGTGAGgtaaaatt-tccttgcgcattattgacaataaaataaaagtggatgtgtggagtgcgtgtgtaattatctgacaataattggagctgacttcccttttctgtgggcttgcag
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S352_68V6.1 (Physcomitrella patens), 5'ss of exon 5
TGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGATGTTTACACAGCTCTTGGAAGTGAGgtaacatgatgtttctgtactaat--gatattactttagtacgactttgtgatgttgtgtccttgta---cttga--gattgtaataact-gcaattagcaatgttct------------
|||||||| ||||||| | || || |||||||| || || || || ||||| |||||||| |||||||||||||| ||||||||||| ||||| ||||| | |||| | | | | | ||| | | | | | | | | | ||| ||| | ||||| ||| ||| | | | || |
CGCTTTGAAGTTAGAGTGGATTCCAGACTGGATTGCGATCGTTGGCAGCGGTTACATTGGTCTAGAGTTCAGTGATGTATACACAGCTCTCGGAAGCGAGgtcagtaaccgtttgtctcacggtctaggagcatttttattttattctattttttcactttgtcgtatatcttcatcacttgtatggactcacaagttgacctcttttcgtgcccggcag
upper sequence: AT3G16950.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 5'ss of exon 5
TGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGATGTTTACACAGCTCTTGGAAGTGAGgtaacatgatgtttctgtactaatgatattactttagtacgactttgtgatgttgtgtccttgtacttgaga-ttgtaata-actgcaattagcaatgttct----------------
||| ||||| | |||| | || || ||||| | ||||| ||||||||||| ||||||||||||||||||||||||||||| || |||||||| |||||| | | || | ||||| || | | | | | || ||| || || || | | | |||| || | || | | | |||
TGCGTTGAAGCTGGAGTGGATTCCCGACTGGATCACTATTGTCGGAAGTGGTTACATTGGTCTTGAGTTCAGTGATGTTTACACTGCCCTTGGAAGCGAGgtacagttttattgaaaggaca-caatatt-tttaaaaataaaatggatatattgggttctagttttaaaaagttgtcatctagtggagcttattttcctcttgctgtgggttggcagMapped 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|125320557|gb|EL334642.1|EL334642EST: TATTGGTCTTGAGTTCAGTGATGTTTACACAGCTCTTGGAAGTGAG GTAACTTTTATAGAAGCACTGGATCAGCTAATGCCTGGATTTGATCCTGA
genomic: TATTGGTCTTGAGTTCAGTGATGTTTACACAGCTCTTGGAAGTGAGgtaacatgat ... ttttgtgcagGTAACTTTTATAGAAGCACTGGATCAGCTAATGCCTGGATTTGATCCTGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGCTTTGAAATTAGAGTCTGTCCCTGAGTGGATTGCAATTGTAGGAAGTGGTTATATTGGTCTTGAGTTCAGTGATGTTTACACAGCTCTTGGAAGTGAGgtaacatgatgtttctgtactaatgatattactttagtacgactttgtgatgttgtgtccttgtacttgagattgtaataactgcaattagcaatgttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG