Sequence
atgc intronic sequence ATGC exonic sequencegtacttcaaaattttcacgtatggcgattgcattttatgtatattgaggtataaatctgactcttttctctttgggtttgattttgtagGTTGAGAACCAGGAAGGTGTGATTAACTTTGATGAGATCTTGCGTGAAACAGATGCGTTCATGGTTGCCCGTGGTGATCTCGGGATGGAGATTCCGATAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G08570.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G08570.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os04g58110.1 (Oryza sativa), 3'ss of exon 2
---gtacttcaaaattttcacgtatggcgattg-catttta------tgtatattgaggtataaatctgactcttttct---ctttgggtttgattttgtagGTTGAGAACCAGGAAGGTGTGATTAACTTTGATGAGATCTTGCGTGAAACAGATGCGTTCATGGTTGCCCGTGGTGATCTCGGGATGGAGATTCCGATAG
|| | | | || | || | || | |||| || ||| | | | ||| | | ||||| |||| ||| |||| ||||||| ||||| || ||||| | ||||| |||||||||||| | ||||| ||||| || |||||||| | |||||||| || ||||||||||| | |
ttcgtgatgatgataatacatatgaggtgcctggtaatttaccatgctggttatgttgctgtgcgtctaatttctttcttaactttttccttgttttt--agGTTGAAAACCAAGAGGGTGTTGTAAACTTCGATGAGATCTTGAGGGAAACGGATGCATTTATGGTTGCTAGAGGTGATCTTGGAATGGAGATTCCAGTTG
upper sequence: AT5G08570.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G150098_T01 (Zea mays), 3'ss of exon 2
gtacttcaaaattttcac---gtatggcgattgcattttatgtatattgaggta--------taaatctgact-cttttctctttgggtttgattttgtagGTTGAGAACCAGGAAGGTGTGATTAACTTTGATGAGATCTTGCGTGAAACAGATGCGTTCATGGTTGCCCGTGGTGATCTCGGGATGGAGATTCCGATAG
| | | |||| ||| ||| | | || | || ||| | || | |||||| | | || | | |||| | || ||||||||||||| || ||||| | |||||||||||||||||| | || || ||||| || |||||||| | |||||||| || ||||||||||| | |
-tgacgctacatttccacctggtaggctgttttactcctaaccgaattctgttaacttcacatggatctgatttccttaatgatatggttctgctatgcagGTTGAGAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTGGGAATGGAGATTCCAGTCG
upper sequence: AT5G08570.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G008714_T01 (Zea mays), 3'ss of exon 2
------gtacttcaaaatttt-cacgtatggcgattgcatt--ttatgtatattgaggtataaatctgactcttttctc--tttgggtttgattttgtagGTTGAGAACCAGGAAGGTGTGATTAACTTTGATGAGATCTTGCGTGAAACAGATGCGTTCATGGTTGCCCGTGGTGATCTCGGGATGGAGATTCCGATAG
||| ||| || | || ||| | || | | || ||| | || |||||| || |||| | ||| || | || ||||||| ||||| || ||||| | |||||||||||||||||| | || || ||||| || |||||||| | |||||||| || ||||||||||| | |
ttcatattacatcatgataatgtacatatagaacttatgatcgtgttggttatgctgtcatggatctgattcctttcatgatatggtttccgctatgcagGTTGAAAACCAAGAGGGTGTTGTAAACTTTGATGAGATCTTGAGGGAGACTGATGCTTTTATGGTTGCTAGAGGTGATCTTGGAATGGAGATTCCTGTTG
upper sequence: AT5G08570.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv10s0071g01060.t01 (Vitis vinifera), 3'ss of exon 2
-------------gtacttcaaaattttcacgtatggcgatt-gcattttatgtatattgaggtataaatctgactcttttctctttgggtttgattttgtagGTTGAGAACCAGGAAGGTGTGATTAACTTTGATGAGATCTTGCGTGAAACAGATGCGTTCATGGTTGCCCGTGGTGATCTCGGGATGGAGATTCCGATAG
| ||| || | | | || |||||| || | ||| ||| | | | || | | || | | | ||| ||||||||||||| || ||||| || ||||| ||||| || || ||||| || || | |||||||||||||| ||||||||||| |||||||| || | |
atgagaaattactgagtttctgtggttcttcaaggagtgttttgcatttcttggtcactgaatgatatgttt---ttttctttgttgagctgaaaattttcagGTTGAGAACCAAGAGGGTGTTATCAACTTCGATGAAATATTACGTGAGACTGACTCCTTCATGGTTGCCCGAGGTGATCTCGGAATGGAGATCCCAGTGG
upper sequence: AT5G08570.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0056g00190.t01 (Vitis vinifera), 3'ss of exon 2
--gtacttcaaaattt-tcacgtatggcgattgcattttatgtatattgaggtataa-------atctgactcttttctctttgggtttgattt-tgtagGTTGAGAACCAGGAAGGTGTGATTAACTTTGATGAGATCTTGCGTGAAACAGATGCGTTCATGGTTGCCCGTGGTGATCTCGGGATGGAGATTCCGATAG
|| |||| || | | | | || ||| || | || | | | | || | | | ||| ||| | | ||| || |||| ||||||||||| ||||| || ||||||||||| || ||||||| || ||| | || |||||||||||||||||||| || |||||||| || | |
gcttatttcatggttggttgtgcaatttgcttacatgtttctttgataaatatgtcatagcctcatggcatcttcctttctgtggctgtaattcctgaagGTGGAGAACCAGGAGGGTGTTATCAACTTTGATGAAATACTGCGTGAGACCGATTCATTTATGGTTGCCCGTGGTGATCTTGGAATGGAGATCCCAGTGGMapped 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|124972914|gb|EL046579.1|EL046579EST: GCTCATGTCAAAG GTTGAGAACCAGGAAGGTGTGATTAACTTTGATGAGATCTTGCGTGAAACA
genomic: GCTCATGTCAAAGgtacttcaaa ... gattttgtagGTTGAGAACCAGGAAGGTGTGATTAACTTTGATGAGATCTTGCGTGAAACA
EST:
gi|124848657|gb|EH933094.1|EH933094EST: CCGCAAGGTTCTTGGTATCTCATGCTAAAAGCATAATGCTCATGTCAAAG GTTGAGAACCAGGAAGGTGTGATTAACTTTGA
genomic: CCGCAAGGTTCTTGG-ATCTCATGCTAAAAGCATAATGCTCATGTCAAAGgtacttcaaa ... gattttgtagGTTGAGAACCAGGAAGGTGTGATTAACTTTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatgtatattgaggtataaatctgactcttttctctttgggtttgattttgtagGTTGAGAACCAGGAAGGTGTGATTAACTTTGATGAGATCTTGCGTGAAACAGATGCGTTCATGGTTGCCCGTGGTGATCTCGGGATGGAGATTCCGATAG
tataaatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttcaaaattttcacgtatggcgattgcattttatgtatattgaggtataaatctgactcttttctctttgggtttgattttgtagGTTGAGAACCAGGAAGGTGTGATTAACTTTGATGAGATCTTGCGTGAAACAGATGCGTTCATGGTTGCCCGTGGTGATCTCGGGATGGAGATTCCGATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT