Sequence
atgc intronic sequence ATGC exonic sequenceCTATCGTGCCCCAGAGCTCATTTTTGGAGCCACCGAGTACACAACTGCAATAGACATATGGTCCACAGGTTGTGTGATGGCTGAACTGCTGCTTGGACAGgttggagcactatatttgcattagctatatgcttgttattctatttcttcaccctcttactcatttttgctctcgcggacttgttttacag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G57870.1 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA12G28730.2 (Glycine max), 5'ss of exon 8
CTATCGTGCCCCAGAGCTCATTTTTGGAGCCACCGAGTACACAACTGCAATAGACATATGGTCCACAGGTTGTGTGATGGCTGAACTGCTGCTTGGACAGgt-tggagcactatatttgcattagctatatgcttgttattcta---tttcttcaccctcttactcatttt---tgctctcgcgg----acttgttttacag
||| ||||| || || || || ||||| |||||||| || |||||||| ||||| |||||||| || |||||||| ||||||||| | || ||||||||||| | | || || || | | || || | ||| | ||||| ||| || |||| | || | | | ||| ||| |||
CTACCGTGCTCCGGAACTTATATTTGGGGCCACCGAATATACAACTGCCATAGATATATGGTCAACTGGTTGTGTAATGGCTGAATTACTTCTTGGACAGgtatttggttctttaaaaaaatgtgacaaatttttctcatttcatcatttctctgttttctgtcttcttttgcattttcctgaagttcaagttgatttgcag
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA16G00400.1 (Glycine max), 5'ss of exon 7
CTATCGTGCCCCAGAGCTCATTTTTGGAGCCACCGAGTACACAACTGCAATAGACATATGGTCCACAGGTTGTGTGATGGCTGAACTGCTGCTTGGACAGgt-tggagcactatatttgcattagctatatgcttgttattcta---tttcttcaccctcttactcatttttgctctcgc-------ggacttgttttacag
||| ||||| || || || || ||||| ||||| || || |||||||| ||||| |||||||| || |||||||| ||||||||| | || ||||||||||| | | | | | || | | || || | ||| | |||||| ||| || ||||| | | | | | ||| ||| |||
CTACCGTGCTCCGGAACTTATATTTGGGGCCACTGAATATACAACTGCCATAGATATATGGTCAACTGGTTGTGTAATGGCTGAATTACTTCTTGGACAGgtatttggtgcaagaaaaaaatgtgacaaatttttctcatttcatcatttctttgttttctgtcttctttttcattttcctgaagttgaagttgatttgcag
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 5'ss of exon 7
CTATCGTGCCCCAGAGCTCATTTTTGGAGCCACCGAGTACACAACTGCAATAGACATATGGTCCACAGGTTGTGTGATGGCTGAACTGCTGCTTGGACAGgt--tggagcactatatttgcat-tagcta---tatgcttgttattc--tatttcttcaccctcttactcat-ttttgctctcgcggacttgttttacag
|| ||||||||||| ||||| ||||| ||||| || || || ||||| ||||| || ||||| || || ||||||||||||||| |||| || |||||||| | | || || || ||| | | | | | ||| ||||| ||| ||| | | ||| ||| | ||| | |||||
TTACCGTGCCCCAGAACTCATATTTGGTGCCACTGAATATACGACTGCTATAGATATTTGGTCTACTGGCTGTGTGATGGCTGAATTGCTTCTGGGACAGgtagtacactgttaatttcagatgtagttgacttgccttcgcttttcatcatttccaagtcctgttatttaggcttttatctaaccatcttctggtacag
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 5'ss of exon 7
CTATCGTGCCCCAGAGCTCATTTTTGGAGCCACCGAGTACACAACTGCAATAGACATATGGTCCACAGGTTGTGTGATGGCTGAACTGCTGCTTGGACAGgt-----tggagcactatatttgcattagctatatgcttgttattctatttcttcaccctcttactcatttttgctctcgcggacttgttttacag-----------------------------------------------------------------------------------------
|| ||||| || ||||| || |||||||| || || ||||||||||| || ||||||||||| | ||||| |||||||| ||||| || || |||||||| || || | | | | ||| || | || | || || | || | | | | | | || | |
TTACCGTGCTCCCGAGCTGATATTTGGAGCTACAGAATACACAACTGCGATTGACATATGGTCGATGGGTTGCGTGATGGCGGAACTTCTCCTAGGACAGgtacttatgtagttcctggtagatggtgaattcatggagattctattactcctgagtactatggttcggaatggagatagatcattgtgttgattgtaatgagatgtaagtggttggtgaagtgatcattgttggtttagttagatgatatgaattctgtctggacaatttcgatgttggtgcag
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 5'ss of exon 6
CTATCGTGCCCCAGAGCTCATTTTTGGAGCCACCGAGTACACAACTGCAATAGACATATGGTCCACAGGTTGTGTGATGGCTGAACTGCTGCTTGGACAGgttggagcac--tatatttgcattagcta-tatgctt-gttattctatttcttcaccctcttactcatttttgctctcgcggacttgttttacag-----
|| ||||| || ||||| || |||||||| || || ||||| ||||| |||||||||||||| | |||||||||||||| || || || || || ||||| | || | || | ||||| || | |||| | | || | || | | || | ||| | | |
TTACCGTGCTCCTGAGCTGATATTTGGAGCGACGGAATACACCACTGCGATAGACATATGGTCGATGGGTTGTGTGATGGCGGAGCTTCTTCTAGGGCAGgtacgcccatagtttaggggaggtagctggtacaatcagttaacttgctcctgcttactagcattgtttaaaatgaaggtggatcactgtgtcgatggaa
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S60_85V6.1 (Physcomitrella patens), 5'ss of exon 7
CTATCGTGCCCCAGAGCTCATTTTTGGAGCCACCGAGTACACAACTGCAATAGACATATGGTCCACAGGTTGTGTGATGGCTGAACTGCTGCTTGGACAGgttggagcactatatttgcattag---ctatatgcttgttattctatttcttcaccc-tcttactcatttttgctctcgcggacttgttttacag-----
||| ||||| || ||||| ||||||||||| || |||||||| ||||| || || |||||||| | || || |||||||||||||| || || |||||||| | | | || | || | || || || ||| | | ||| ||| | | | | | |
CTACCGTGCTCCTGAGCTGATTTTTGGAGCGACAGAGTACACGACTGCCATCGATATATGGTCGATGGGATGCGTGATGGCTGAACTTCTTCTGGGACAGgtactggtagcgtggctgtggtgaggtctgttggcctgagatgatatggttgagtggatgccgaggattgttgattccttgcatcgagtcagtggcagtc
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 5'ss of exon 7
CTATCGTGCCCCAGAGCTCATTTTTGGAGCCACCGAGTACACAACTGCAATAGACATATGGTCCACAGGTTGTGTGATGGCTGAACTGCTGCTTGGACAGgttggagcactatatttgcattag---ctatatgcttgttattctatttcttcaccc-tcttactcatttttgctctcgcggacttgttttacag-----
||| ||||| || ||||| ||||||||||| || |||||||| ||||| || || |||||||| | || || |||||||||||||| || || |||||||| | | | || | || | || || || ||| | | ||| ||| | | | || |
CTACCGTGCTCCTGAGCTGATTTTTGGAGCGACAGAGTACACGACTGCCATCGATATATGGTCGATGGGATGCGTGATGGCTGAACTCCTTCTGGGACAGgtactggtagcgtggctgtggtgaggtctgttggcctgagatgatatggttgagtggatgccgaggattgttgattctttgcatcaagttagtggcggtc
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 5'ss of exon 6
CTATCGTGCCCCAGAGCTCATTTTTGGAGCCACCGAGTACACAACTGCAATAGACATATGGTCCACAGGTTGTGTGATGGCTGAACTGCTGCTTGGACAGgt--tggagcactatatttgcattagctatatgcttgttattctatttcttcaccctcttactcattt-ttgctctcgcggacttgttttacag--------
||| ||||| || ||||| ||||||||||| || |||||||| ||||| ||||| |||||||| | ||||| |||||||| || || || || |||||||| | | | | || || | | | || | | | || | || || || | || ||||||| ||
CTACCGTGCTCCGGAGCTTATTTTTGGAGCGACGGAGTACACGACTGCCATAGATATATGGTCGATGGGTTGCGTGATGGCAGAGCTTCTACTAGGACAGgtactcggtcgccg-atgggctctcttccacttcgaagagttgtttcaagtgacgcggggggtcgttgactggggctgttga-ttgttttgtagcaagctaa
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: EFJ10962 (Selaginella moellendorffii), 5'ss of exon 7
CTATCGTGCCCCAGAGCTCATTTTTGGAGCCACCGAGTACACAACTGCAATAGACATATGGTCCACAGGTTGTGTGATGGCTGAACTGCTGCTTGGACAGgttggagcactatatttgcattagctatatgcttgttattctatttcttcaccctcttactcatttttgctctcgcggacttgttttacag
||| || || || ||||| ||||| || ||||| || |||||||| ||||| || || ||||| | || |||||| ||||||||||||| ||||| ||||| | || | ||| | || ||| | || ||| | || ||
CTACCGAGCGCCCGAGCTGATTTTCGGTGCCACGGAATACACAACAGCAATTGATATCTGGTCGATGGGATGTGTGTTGGCTGAACTGCTACTTGGTCAGgt----gtgctttgcttgtttgaggtattagaagacatccttaccacttgtgaatgttctacag---------------------------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|116422944|gb|EG465536.1|EG465536EST: TAGACGTATGGTCCACAGGTTGTGTGATGGCTGAACTGCTGCTTGGACAG CCTCTGTTTCCTGGCGAAAGTGGAGTCGATCAACTTGTTGAAATCATAAAG
genomic: TAGACATATGGTCCACAGGTTGTGTGATGGCTGAACTGCTGCTTGGACAGgttggagcac ... tgttttacagCCTCTGTTTCCTGGCGAAAGTGGAGTCGATCAACTTGTTGAAATCATAAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTATCGTGCCCCAGAGCTCATTTTTGGAGCCACCGAGTACACAACTGCAATAGACATATGGTCCACAGGTTGTGTGATGGCTGAACTGCTGCTTGGACAGgttggagcactatatttgcattagctatatgcttgttattctatttcttcaccctcttactcatttttgctctcgcggacttgttttacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT