Sequence
atgc intronic sequence ATGC exonic sequenceGTACATGGCACTTTTGCAACTGCTGGGTCAGATGGTGCTTTCAATTTCTGGGACAAAGATAGTAAACAAAGACTCAAGgtattttcctcctgcattgattttttattttgttaaccaagtaattatctaacagttttgtattctgtgtccccacag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G80670.1 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G80670.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os08g07960.1 (Oryza sativa), 5'ss of exon 9
GTACATGGCACTTTTGCAACTGCTGGGTCAGATGGTGCTTTCAATTTCTGGGACAAAGATAGTAAACAAAGACTCAAGgtattttcctc-ctgcattgattttttattt-tgttaaccaa-gtaattatctaacagtttt-----gtattctgtg--tccccacag------------
|| ||| ||| |||||||||||||| |||||||| || || ||||||||||| || ||||| ||||||||||| ||||| | | | || |||| || |||| | | | | | || | | ||| |||||| ||| | | ||
GTTCATCACACGTTTGCAACTGCTGGATCAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAGgtttgatgttggctcttttgaagttccatttgtactggttattgcacttgtatttttgttcccttgagtattcagtgatttttaatagtcataattgctt
upper sequence: AT1G80670.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 9
GTACATGGCACTTTTGCAACTGCTGGGTCAGATGGTGCTTTCAATTTCTGGGACAAAGATAGTAAACAAAGACTCAAGgta------ttttcct---cctgcattgatttt---ttattttgttaaccaagtaattatctaaca------gttttgtattctgtgtc-cccacag---
|| ||| ||| |||||||||||||| || || ||||||||||| |||||||| || ||||| || || || || |||||| ||| | | | |||||||| || | ||| || | | || | | || | | ||| ||||| || |
GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaatttccatggctttttgttgattttcacttgtgttggtagctgttgatttctgttgcatcgattatccttgattttgtgttgtttactggtt
upper sequence: AT1G80670.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA01G09290.1 (Glycine max), 5'ss of exon 8
GTACATGGCACTTTTGCAACTGCTGGGTCAGATGGTGCTTTCAATTTCTGGGACAAAGATAGTAAACAAAGACTCAAGgtattttcctcctgcattgattttttattttgttaaccaagtaattatctaacagttttgtattctgtgtccccacag------------------------
|||||| |||||||||||||||||| || ||||||||||| ||||||||||| ||||| |||||||| ||||||||||| | | | || | | | | | | | | ||| || | | | | || | | ||| |
GTACATCACACTTTTGCAACTGCTGGATCTGATGGTGCTTTTAATTTCTGGGATAAAGACAGTAAACAGAGACTCAAGgttcctgctttctctaattaatac--actcttctcacctgtcctttccttctgaaactgatctttggaatttccaaaacatacttgtgttttttttttattt
upper sequence: AT1G80670.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA02G13780.1 (Glycine max), 5'ss of exon 8
GTACATGGCACTTTTGCAACTGCTGGGTCAGATGGTGCTTTCAATTTCTGGGACAAAGATAGTAAACAAAGACTCAAGgtattttcctcctgcattgattttttattttgttaaccaagtaattatctaacagttttgtattctgtgtccccacag---------------------------
|||||| |||||||||||||||||| || ||||||||||| ||||||||||| || || |||||||| ||||||||||| | || || | | || | | | | ||| || | | | | || | | ||| |
GTACATCACACTTTTGCAACTGCTGGATCTGATGGTGCTTTTAATTTCTGGGATAAGGACAGTAAACAGAGACTCAAGgtttcttgctttctc-----tattacactcttctcacctgtcctttccttctgaaactgatctttggaatttccaaaacatacttttttttttttgtatagtata
upper sequence: AT1G80670.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA15G05740.1 (Glycine max), 5'ss of exon 8
GTACATGGCACTTTTGCAACTGCTGGGTCAGATGGTGCTTTCAATTTCTGGGACAAAGATAGTAAACAAAGACTCAAGgt------attttcctcctgcattgattttttattttgttaaccaagtaattatctaacagttttgt----attctgtgtccccacag---------------------
||||| ||| ||||||||| |||| || ||||||||||||||||| ||||| || ||||||||||| || |||||||| ||||| | || | || || | || || | | || | ||||| ||| || |
GTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGGGATAAGGATAGTAAACAGAGGCTCAAGgttattccatttttattaaacacttccattcaatcctaactgacacatattgttgcaatatttttggcataattacatgcttatctaatgcaaacttgtcttatttcag
upper sequence: AT1G80670.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA08G19260.1 (Glycine max), 5'ss of exon 8
GTACATGGCACTTTTGCAACTGCTGGGTCAGATGGTGCTTTCAATTTCTGGGACAAAGATAGTAAACAAAGACTCAAGgtattttcctcctgcattgattttttattttgttaaccaagtaat-tatctaacagttttgtattctgtgtccccacag-------------------------------
||||| ||| ||||||||| |||| || ||||||||||||||||| ||||| || ||||||||||| | |||||||| || | | | | | || || | | || || || | ||| | | || | | ||||
GTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGGGATAAGGATAGTAAACAGCGGCTCAAGgttattccatttttattaaacacttccattcaattcctaaccaacacatattgtagtgatatttttggcataatcacatgcttatctaatgcaaacgtgtcttgtttcag
upper sequence: AT1G80670.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv09s0002g09150.t01 (Vitis vinifera), 5'ss of exon 8
GTACATGGCACTTTTGCAACTGCTGGGTCAGATGGTGCTTTCAATTTCTGGGACAAAGATAGTAAACAAAGACTCAAGgtattttcctcctgcattgatttttt-attttgttaaccaagtaattatctaacagttttgtattctgtgtccccacag----------------------
|| ||| || ||||||||||| ||||| ||||||||||| ||||| |||||||| ||||||||||| ||||| ||||| | || | | || | ||||| | | | || || |||| | ||||| || | | | |||
GTGCATCATACATTTGCAACTGCAGGGTCTGATGGTGCTTTTAATTTTTGGGACAAGGATAGTAAACAGAGACTTAAGgtgcctcccaaatactttcagtttttgaatatttttcccgttctgttatttctgtgtttta-gttgtcacttcatacatgaactatcgttcctggtttcat
upper sequence: AT1G80670.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv12s0055g00900.t01 (Vitis vinifera), 5'ss of exon 9
GTACATGGCACTTTTGCAACTGCTGGGTCAGATGGTGCTTTCAATTTCTGGGACAAAGATAGTAAACAAAGACTCAAGgtattttcctcctgcattgattttttattttgttaaccaagtaattatctaacagttttg-tattctgtgtccccacag------------------------
|| ||| ||| ||||| ||||| || || || |||||||| |||||||||||||| ||||||||||| |||||||||||| | ||| | ||| ||||| | | |||| | || || || ||| | || | |||| | | | |
GTGCATCACACATTTGCCACTGCAGGCTCTGACGGTGCTTTTAATTTCTGGGACAAGGATAGTAAACAGAGACTCAAGgtaat---ctcaaggattcctttttgaatatgttcttctcgttgttttcggacactgttactcttctattattctagattctattgtttttaccctaatcggaMapped 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|125225838|gb|EL239923.1|EL239923EST: ATAGTAAACAAAGACTCAAG GCCATGTCGAGGTGCAATCAGCCAATTCCATGCAGCTCGTTCAACCACGAT
genomic: ATAGTAAACAAAGACTCAAGgtattttcct ... gtccccacagGCCATGTCGAGGTGCAATCAGCCAATTCCATGCAGCTCGTTCAACCACGAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTACATGGCACTTTTGCAACTGCTGGGTCAGATGGTGCTTTCAATTTCTGGGACAAAGATAGTAAACAAAGACTCAAGgtattttcctcctgcattgattttttattttgttaaccaagtaattatctaacagttttgtattctgtgtccccacag
- - - - - - - - - - - - - - CAGATG