Sequence
atgc intronic sequence ATGC exonic sequence...ctcttctttaagttgtttcatcttttgttagaaattgttaacatgagcattaagtttagaatgattgtaattataagtttgtgtttatttttatgtgtagAGGTACGCGGATTAAGACCCGCAAAAGGAATATTGCTGCTCCTCTCGACCCTGCTGCTTTTTCTGATGCACTAGTTCAGATTTATCTGGATAATGCTGGT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G65220.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G65220.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os11g21990.1 (Oryza sativa), 3'ss of exon 2
ctcttctttaagttgtttcatc-ttttgttagaaattgttaacatgagcattaa-----gtttagaatgattgtaattataagtttgtgtttatttttatg-tgtagAGGTACGCGGATTAAGACCCGCAAAAGGAATATTGCTGCTCCTCTCGACCCTGCTGCTTTTTCTGATGCACTAGTTCAGATTTATCTGGATAATGCTGGT
|| || ||||| | |||| ||| || | | | | || | ||| | | | | | || | ||| | | | | ||| || ||||| ||||||||||||||||||| ||||||||||||||||| | |||||||| | || ||||||||| | || |||||||||||||||||||||||
-------ttgtgtcaattcatagtattgtgtgaagttttcagctttctttgcaactatcatatagtaaggctatcttaatgattttttttgttatgctatactgcagAGGCCAGCGGATTAAGACCCGCAAACGGAATATTGCTGCTCCTTTGGACCCTGCATCATTCTCTGATGCAATTGTCCAGATTTATCTGGATAATGCTGGA
upper sequence: AT1G65220.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G012416_T04 (Zea mays), 3'ss of exon 2
ctcttctttaagttgtttcatcttttgttagaaattgtt---aacatgagcatta-agtttagaatgat--tgtaatt--ataagtttgtgtttatttttatgtgtagAGGTACGCGGATTAAGACCCGCAAAAGGAATATTGCTGCTCCTCTCGACCCTGCTGCTTTTTCTGATGCACTAGTTCAGATTTATCTGGATAATGCTGGT
|||| ||| | | | | ||| ||||| || || | | |||| ||| | | ||| | |||||| | ||| | ||| |||| || ||||| |||||||||||||||||||| |||||||||| |||||| | |||||||| | || ||||||||| | |||||||| ||| ||||||||| |||
------tttatgtttatac-tgtattggtagaacttatttggagagtttgcatggcagtattgcatgttcatgtaatccactttattttcctcaattattat-tgcagAGGCACGCGGATTAAGACCCGCAAGCGGAATATTGCAGCTCCTTTGGACCCTGCATCATTCTCTGATGCAATTGTTCAGATCTATTTGGATAATGGTGGA
upper sequence: AT1G65220.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM5G877316_T03 (Zea mays), 3'ss of exon 2
-----ctcttctttaagttgtttcatcttttgttagaaattgttaacatgagcattaagt-ttagaatgattgtaattataagtttgtgtttatttttatgtgtagAGGTACGCGGATTAAGACCCGCAAAAGGAATATTGCTGCTCCTCTCGACCCTGCTGCTTTTTCTGATGCACTAGTTCAGATTTATCTGGATAATGCTGGT
| | || || || | | ||| | || | | | | | || ||| | || | ||| || | ||| || ||| |||| || ||||| |||||||||||||||||||| |||| ||||| |||||| | |||||||| | || ||||||||| | || ||||||||||||||||||| |||
catgtttatactatataatggtaaaacttat-ttgcagagtttgcatggcagtattgcatgttcaggtaattcaccttgt---tttctgca-attattat-tgcagAGGCACGCGGATTAAGACCCGCAAGCGGAACATTGCAGCTCCTTTGGACCCTGCATCATTCTCTGATGCAATTGTCCAGATTTATCTGGATAATGGTGGA
upper sequence: AT1G65220.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G38530.1 (Glycine max), 3'ss of exon 2
ctcttctttaagttgtttcatcttttgttagaaattgttaacatgagcat-taagtttagaatg-attgtaattataagtttgtgtttatttttatgtgtagAGGTACGCGGATTAAGACCCGCAAAAGGAATATTGCTGCTCCTCTCGACCCTGCTGCTTTTTCTGATGCACTAGTTCAGATTTATCTGGATAATGCTGGT
|| | || | | || ||| | | ||||| | | ||| || || || | ||| | | || ||||||| | || || || ||||||||||||||||||||| ||||||||||||| || || |||||||| || || || |||||| | || ||||||||| ||||||||||||||
--attttgtaggctattgcatgtagcttctattattgtgttatttatcatgtatgtataatttatgttgaggctcttttcttttgtttatctcaatccccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCTGCGCCGCTGGACCCTGCAGCATTCTCGGATGCAGTGGTCCAGATTTATTTGGATAATGCTGGT
upper sequence: AT1G65220.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G47780.1 (Glycine max), 3'ss of exon 2
ctcttctttaagttgtttcat-----cttttgtta--gaaattgttaacatgagcattaagtttagaatgattgtaattataagtttgtgtttatttttatgtgtagAGGTACGCGGATTAAGACCCGCAAAAGGAATATTGCTGCTCCTCTCGACCCTGCTGCTTTTTCTGATGCACTAGTTCAGATTTATCTGGATAATGCTGGT
|| | || | | || ||| ||| | ||| | | ||| |||| || | |||| || | | |||| || ||||||| | || || || ||||||||||||||||||||| | ||||||||||| || || |||||||| || || || |||||| | || ||||||||| |||||||||||||
---ttttgtaggctattgcatgtgagcttatattattgtgttatttatcatgtatgtttaatttatgttgtgggcacttat---cttttgtttatctccatccccaGTGGCACGCGGATTAAGACCCGCAAACGAAATATTGCTGCGCCGCTGGACCCTGCAGCATTCTCGGATGCAGTGGTCCAGATTTATTTGGATAATGCTGG-
upper sequence: AT1G65220.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv04s0023g00670.t01 (Vitis vinifera), 3'ss of exon 3
ctcttctttaagttgtttcatcttttgttagaaattgttaacatgagcattaagtttagaatgattgtaattataagtttgt----gtttatttttatgtgt----agAGGTACGCGGATTAAGACCCGCAAAAGGAATATTGCTGCTCCTCTCGACCCTGCTGCTTTTTCTGATGCACTAGTTCAGATTTATCTGGATAATGCTGGT
|||| | || | | ||| || || || | || | | ||| |||| ||||| ||| ||| ||| ||| | | || || ||||||||||||||||||||| |||||||||| || || || |||||||| | ||| | |||||| | || ||||||||||||||||||||||||
--tggtggaaagtaactacag----tagcgaacattcttgacgtgtgtttttgttatcaaat--ttgttgacataagcctgttgtcatttgtttctatttttttccagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCAGCGCCGCTGGACCCTGCAACATTTGCAGATGCAGTGGTCCAGATTTATCTGGATAATGCTGGT
upper sequence: AT1G65220.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ06557 (Selaginella moellendorffii), 3'ss of exon 2
ctcttctttaagttgtttcatcttttgttagaaattgttaacatgagcattaagtttagaatgattgtaattataagtttgtgtttatttttatgtgtagAGGTACGCGGATTAAGACCCGCAAAAGGAATATTGCTGCTCCTCTCGACCCTGCTGCTTTTTCTGATGCACTAGTTCAGATTTATCTGGATAATGCTGGT
|| || || | ||||| ||| | || || | | ||| || || | ||| ||| || ||||||||||||||||||||| |||||||||| ||| | ||||| || |||| | ||||| |||| ||||| || ||||| ||||||||
--------------------------gtaagggctttgagattcttgcattggttttggtttggtt----tggtttgttcatgatt-tgggcgtgtatagTGGCACGCGGATTAAGACCCGCAAACGGAATATTGCAATTCCGTTGGACCCATCTTCTTTCGCGGATGCTATAGTCCAGATCTACTTGGATCATGCTGGTMapped 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|124934835|gb|EL011870.1|EL011870EST: GCTCAAAGGAGAAGCCCACTCTCGG AGGTACGCGGATTAAGACCCGCAAAAGG
genomic: GCTCAAAGGAGAAGCCCACTCTCGGgtatgtgaat ... ttatgtgtagAGGTACGCGGATTAAGACCCGCAAAAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcattaagtttagaatgattgtaattataagtttgtgtttatttttatgtgtagAGGTACGCGGATTAAGACCCGCAAAAGGAATATTGCTGCTCCTCTCGACCCTGCTGCTTTTTCTGATGCACTAGTTCAGATTTATCTGGATAATGCTGGT
tttattttt CT-rich tract
aatgattgtaattata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcttctttaagttgtttcatcttttgttagaaattgttaacatgagcattaagtttagaatgattgtaattataagtttgtgtttatttttatgtgtagAGGTACGCGGATTAAGACCCGCAAAAGGAATATTGCTGCTCCTCTCGACCCTGCTGCTTTTTCTGATGCACTAGTTCAGATTTATCTGGATAATGCTGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
ctcttct
- - - - - - - - - - - - - - - - - - - -aacatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agtttgt