Sequence
atgc intronic sequence ATGC exonic sequencegtactttgattctgctccatacgctgtgaaatttggattctatattactattattagacatggagcaatcatacagaataacagtttcaattcatcatttccgtagactttatatttgatcttccaggtatagaggatacttaatttgattgtttttgtttcccttcagGGTATTCGAAGACCATGGAAAGGAGTTCTCATGTTTGGTCCTCCTGGGACAGGTAAAACCCTGTTGGCAAAAGCTGTTGCAACTGAGTGTGGTACCACCT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G80350.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G80350.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g49000.1 (Oryza sativa), 3'ss of exon 3
gtactttgattctgctccatacgctgtgaaatttggattctatattactattattagacatggagcaatcatacagaataacagtttcaattcatcatttccgta---gactttatatttgatcttccaggtatagaggatacttaatttgattgt-----ttttgtttcccttcagGGTATTCGAAGACCATGGAAAGGAGTTCTCATGTTTGGTCCTCCTGGGACAGGTAAAACCCTGTTGGCAAAAGCTGTTGCAACTGAGTGTGGTACCACCT
|| ||||| | | || | | ||| || | || | || | | | | || || | | | | | |||| ||||||||||| |||| |||||||| ||||| ||||||||||| ||||| || || || || || || || || || || || || || ||||| || || |
----------------------------------------------------------------------------cgtattcatttcagtcttttcttcttgcatgtgaccttgttattcagtttaaatttgttttg-atcctcatcctatccatgctcactctatttctgaccagGGTATTCGCCGACCTTGGAAAGGGGTTCTAATGTTTGGTCCACCTGGTACTGGAAAGACTCTTTTAGCGAAGGCAGTAGCTACAGAATGTGGCACAACAT
upper sequence: AT1G80350.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G017305_T01 (Zea mays), 3'ss of exon 3
gtactttgattctgctccatacgctgtgaaatttggattctatattactattattagacatggagcaatcatacagaataacagtttcaattcatcatttccgtagactttat-atttgatcttccaggtatagaggatacttaatttgattgtttttgtttcccttcagGGTATTCGAAGACCATGGAAAGGAGTTCTCATGTTTGGTCCTCCTGGGACAGGTAAAACCCTGTTGGCAAAAGCTGTTGCAACTGAGTGTGGTACCACCT
| ||||| | | || | | || | |||| |||| | || || ||| ||| | | ||||| | ||| | | |||||||||||| |||| |||||||||||||| ||||||||||| || || || || || || || |||||||| || || || || || ||||| || || |
---------------------------------------------------------------aatgatcatgaacccaaccaatcttttctc-----tcttgtagcctttttcatctggtctaaacttgatacatagtggctaattatgtccacttt--tccttatcagGGTATTCGTCGACCTTGGAAAGGAGTTCTTATGTTTGGTCCACCAGGCACGGGAAAGACTCTTTTGGCAAAGGCAGTGGCCACCGAATGTGGAACAACAT
upper sequence: AT1G80350.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G054715_T01 (Zea mays), 3'ss of exon 3
gtactttgattctgctccatacgctgtgaaatttggattctatattactattattagacatggagcaatcatacagaataacagtttcaattcatcatttcc-gtagactttat-atttgatcttccaggtatagaggatacttaatttgattgtttttgtttcccttcagGGTATTCGAAGACCATGGAAAGGAGTTCTCATGTTTGGTCCTCCTGGGACAGGTAAAACCCTGTTGGCAAAAGCTGTTGCAACTGAGTGTGGTACCACCT
| |||| ||| ||| || | || |||| |||| | |||| ||| |||| | | ||||| || | || |||||||||||| |||| |||||||||||||| ||||||||||| || || || || || || || |||||||| || || || || || ||||| || || |
---------------------------------------------------------------aatggtcatg------aacccaactaatctattctctcttgtagcctttctcatttagtctaaactctatacatagtggctaatt--atgtccactcttctttatcagGGTATTCGTCGACCTTGGAAAGGAGTTCTTATGTTTGGTCCACCAGGCACGGGAAAGACTCTTTTGGCAAAGGCAGTGGCTACAGAATGTGGAACAACAT
upper sequence: AT1G80350.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv09s0002g05260.t01 (Vitis vinifera), 3'ss of exon 3
gtactttgattctgctccatacgctgtgaaatttggattctatattactattattagacatggagcaatcatacagaataacagtttcaattcatcatttccgtagactttatatttgatcttc-caggtatagaggatacttaatttgattgtttttgtttcccttcagGGTATTCGAAGACCATGGAAAGGAGTTCTCATGTTTGGTCCTCCTGGGACAGGTAAAACCCTGTTGGCAAAAGCTGTTGCAACTGAGTGTGGTACCACCT
| || | | || | || |||| | |||| | ||| | || || || | | | | | ||| ||||||| | || | ||||| ||| | |||||||||||||| ||||| ||||||||||||||||| || || || || || ||||| ||||||||||| |||||||||||||| || |
------------------------------------------------------------------gcttat-ctcactatta--ttaaattaagaatttaagggacttttgtgttggaagtttgtattttttattcaggtcaagttttattgtttct-ttacttaacagGGAATTAGGAGACCATGGAAAGGTGTTCTTATGTTTGGTCCTCCTGGTACTGGCAAGACACTTTTGGCTAAAGCTGTTGCTACTGAGTGTGGTACAACATMapped 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|125086452|gb|EL145920.1|EL145920EST: TGCTTGAGGAGGCAGTTGTCCTTCCTTTATGGATGCCCGAATACTTTCAG GGTATTCGAAGACCA
genomic: TGCTTGAGGAGGCAGTTGTCCTTCCTTTATGGATGCCCGAATACTTTCAGgtactttgat ... ttcccttcagGGTATTCGAAGACCA
EST:
gi|125027774|gb|EL100043.1|EL100043EST: TGCTTGAGGAGGCAGTTGTCCTTCCTTTATGGATGCCCGAATACTTTCAG GGTATTCGAAGACCATGGAAAGGA
genomic: TGCTTGAGGAGGCAGTTGTCCTTCCTTTATGGATGCCCGAATACTTTCAGgtactttgat ... ttcccttcagGGTATTCGAAGACCATGGAAAGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgatcttccaggtatagaggatacttaatttgattgtttttgtttcccttcagGGTATTCGAAGACCATGGAAAGGAGTTCTCATGTTTGGTCCTCCTGGGACAGGTAAAACCCTGTTGGCAAAAGCTGTTGCAACTGAGTGTGGTACCACCT
ttgtttttgtttccct CT-rich tract
atacttaatttgattg TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactttgattctgctccatacgctgtgaaatttggattctatattactattattagacatggagcaatcatacagaataacagtttcaattcatcatttccgtagactttatatttgatcttccaggtatagaggatacttaatttgattgtttttgtttcccttcagGGTATTCGAAGACCATGGAAAGGAGTTCTCATGTTTGGTCCTCCTGGGACAGGTAAAACCCTGTTGGCAAAAGCTGTTGCAACTGAGTGTGGTACCACCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT