Sequence
atgc intronic sequence ATGC exonic sequenceGTTGGATTACAATGGATGCTATCGTTGTATAATAACAAATTAAACGGGATCTTGGCTGATGAGATGGGTCTTGGAAAAACTGTTCAGgttaaatctgttcccgatttgcagggattcctggatttacttttctttcgcctttggtgaccaataaattattatattgtcctatcataatatactaattgttttgtacag
Basic information
species | Arabidopsis thaliana |
transcript | AT2G46020.2 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G46020.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os02g02290.1 (Oryza sativa), 5'ss of exon 6
GTTGGATTACAATGGATGCTATCGTTGTATAATAACAAATTAAACGGGATCTTGGCTGATGAGATGGGTCTTGGAAAAACTGTTCAGgt-taaatctgtt--cccgatttgcagg---gattcctggatttacttttctttcgcctttggtgaccaataaattattatattgtcctatcataatatactaattgttttgtacag-------------------
|| || | ||||||||||| || ||||| ||||| || || || || || ||||||||||||||||||||||| || || || ||||| | || | || ||| | | | | || | || || | || | ||| | | || ||| | | | || ||| ||| | |
GTGGGCCTTCAATGGATGCTTTCCTTGTACAATAATAAGTTGAATGGTATTTTGGCTGATGAGATGGGTCTTGGCAAGACCGTACAGgtgtggatttcttattccgttctacctgctagacttttgctatttcacaatattttcttttattatctcatttgcctccccatttccttttgccctgctagtaacatctttttgtggccaccaattgaataaatag
upper sequence: AT2G46020.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G163849_T01 (Zea mays), 5'ss of exon 6
GTTGGATTACAATGGATGCTATCGTTGTATAATAACAAATTAAACGGGATCTTGGCTGATGAGATGGGTCTTGGAAAAACTGTTCAGgttaa-----atctgttcccgatt--tgcagggattcctgg-atttacttttctttcgcctttggtgaccaataaattattatatt-gtcctatcataatatactaattgttttgtacag-----------------
|| || |||| |||||||| || ||||| ||||| || || || || || ||||||||||||||||||||||| || ||||| ||||| | | ||| | || | | | ||||| ||| | | ||| | | || | | | || ||| | || || | ||| ||| | ||| |
GTGGGCCTACAGTGGATGCTTTCTTTGTACAATAATAAGTTGAATGGCATTTTGGCTGATGAGATGGGTCTTGGCAAGACTGTACAGgtcattccttgcttattcttgtttactttctgtactcctgttattcatgatattttttattatcgtcaatgcttcctcttttcattcgaccaatggccaggaacttatttgtatgtctatgctatttgttgtaatag
upper sequence: AT2G46020.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA09G39380.1 (Glycine max), 5'ss of exon 7
GTTGGATTACAATGGATGCTATCGTTGTATAATAACAAATTAAACGGGATCTTGGCTGATGAGATGGGTCTTGGAAAAACTGTTCAGgttaaatctgttcccgatttgcagggattcctggatttacttttctttcgcctttggtgaccaataaattattatattgtcctatcataatatactaattgttttgtacag-
||||| || ||||||||||| || |||||||| ||||||||||| || || ||||| ||||||||||||||||| |||||||| ||||||| | | | ||||| | | | |||| | || ||| ||| | | || ||| | || || | | | |
GTTGGTTTGCAATGGATGCTTTCCTTGTATAACAACAAATTAAATGGAATTTTGGCAGATGAGATGGGTCTTGGCAAAACTGTACAGgttagtgttat----gttttgctgtgttgtt--------ctttaaaactaaaatgggaagaaaatctattgtgttcttttccagccgagtgattttacacatcatattaaat
upper sequence: AT2G46020.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA18G46930.1 (Glycine max), 5'ss of exon 5
GTTGGATTACAATGGATGCTATCGTTGTATAATAACAAATTAAACGGGATCTTGGCTGATGAGATGGGTCTTGGAAAAACTGTTCAGgttaa----atctgttcccgatttg--cagggattcctggatttacttttctttcgcctttggtgaccaataaattattatattgtcctatcataatatactaattgttttgtacag
||||| || ||||||||||| || |||||||| ||||||||||| || || ||||| ||||||||||||||||| |||||||| ||||||| || | || | | ||| | | | | | | | | | | |||| ||| | ||| ||| | | || ||| | | | | |
GTTGGTTTGCAATGGATGCTTTCCTTGTATAACAACAAATTAAATGGAATTTTGGCAGATGAGATGGGTCTTGGCAAAACTGTACAGgttagtgttatgttttgctgtgttgttctttaacacgggaagaaaatctgttgtgttcttttccaaccgagtgatt-ttacact-tcatattaaagtttgtt---------------
upper sequence: AT2G46020.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA07G07550.1 (Glycine max), 5'ss of exon 5
GTTGGATTACAATGGATGCTATCGTTGTATAATAACAAATTAAACGGGATCTTGGCTGATGAGATGGGTCTTGGAAAAACTGTTCAGgtta--aatctgttcccgatttgcagggattcctggatttacttttctttcgcctttggtgaccaataaattattatattgtcctatcataatatactaattgttttgtacag
||||| || ||||||||||| || |||||||| ||||| ||||| || || ||||| ||||||||||||||||| |||||||| ||||||| | | |||| | ||| || || || || || || | || | | | || |||| ||| | | | | | | | | | ||
GTTGGTTTGCAATGGATGCTTTCTTTGTATAACAACAAGTTAAATGGAATTTTGGCGGATGAGATGGGTCTTGGTAAAACTGTACAGgttagtattatgtttttgtttttt-----tttttg---ttgctcttgcttaga-ttggaaaaaatgtttatcatta-attttgtttttggagctgagtgacttcatagtt---
upper sequence: AT2G46020.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA16G03950.1 (Glycine max), 5'ss of exon 6
GTTGGATTACAATGGATGCTATCGTTGTATAATAACAAATTAAACGGGATCTTGGCTGATGAGATGGGTCTTGGAAAAACTGTTCAGgttaaatctgttcccgatttgcagggattcctggatttacttttctttcgcctttggtgaccaataaattattatattgtcctatcataatatactaattgttttgtacag
||||| || ||||||||||| || |||||||| ||||| ||||| || || ||||| ||||||||||||||||| |||||||| ||||||| | | | ||| || || || |||| || | || || |||| | | ||| | | | || || ||| |
GTTGGTTTGCAATGGATGCTTTCTTTGTATAACAACAAGTTAAATGGAATTTTGGCGGATGAGATGGGTCTTGGCAAAACTGTACAGgttagtattatgcttttttt-------ttgttgctcttgctttgattggacaaaatgtttatcattaattttgtttttgcagctgagtgacttcatagttcctttct----
upper sequence: AT2G46020.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv15s0046g02290.t01 (Vitis vinifera), 5'ss of exon 6
GTTGGATTACAATGGATGCTATCGTTGTATAATAACAAATTAAACGGGATCTTGGCTGATGAGATGGGTCTTGGAAAAACTGTTCAGgttaaatctgttcccgatttgcagggattcctggatttacttttctttcgcctttggtgaccaataaattattatattgtcctatcataatatactaattgttttgtacag
||||| || ||||||||||| || ||||| || |||||| | || || || ||||||||||||||||||||||| |||||||| ||||| ||| | | | | | || | ||| | |||||| | ||| || || || ||| |||| | | | | | || | ||| ||||
GTTGGGTTGCAATGGATGCTTTCCTTGTACAACAACAAACTGAATGGAATTTTGGCTGATGAGATGGGTCTTGGGAAAACTGTACAGgt-gaatttctgcatattccttatggcatactgcaactacttt-----caaattttatgtttaacaa-ttaagggtttgtgcagtgtttgattgtttctt-tattggacagMapped 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|125211838|gb|EL226792.1|EL226792EST: TCTTGGAAAAACTGTTCAG GTAATGGCACTGATTGCTTACCTTATGGAGTTTAAAGGGAATTATGGATCG
genomic: TCTTGGAAAAACTGTTCAGgttaaatctg ... ttttgtacagGTAATGGCACTGATTGCTTACCTTATGGAGTTTAAAGGGAATTATGGACCG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTTGGATTACAATGGATGCTATCGTTGTATAATAACAAATTAAACGGGATCTTGGCTGATGAGATGGGTCTTGGAAAAACTGTTCAGgttaaatctgttcccgatttgcagggattcctggatttacttttctttcgcctttggtgaccaataaattattatattgtcctatcataatatactaattgttttgtacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG