Sequence
atgc intronic sequence ATGC exonic sequenceGAAAAGAATGAAGTAATCGTTGCGGATAATTACTTCACAGGATCAAAAGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTAATTCGTCATGgtatagtatcttcttaattaatcaaacttacttaatactcattaaccaaaacaatgcattaatactcattcttgtgattttttcag
Basic information
species | Arabidopsis thaliana |
transcript | AT2G28760.3 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G28760.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 5'ss of exon 4
GAAAAGAATGAAGTAATCGTTGCGGATAATTACTTCACAGGATCAAAAGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTAATTCGTCATGgtatag-tatcttcttaattaatcaaacttac------ttaatactcattaaccaaaacaatgcattaatactcattcttgtgattt----tttcag---
|| || || || || || | ||||| || ||||||||||| || ||||| ||||| || || ||||||||||||||||| ||||||||||| | || |||| | | || | | | || ||| | || | || | | | || | | || | || ||| ||
------------GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctacattctcagtgcatttagttcatgaactattgttacatactagtaataaagttttactgctagcaagttttttcgttcaaaatttgagaaa
upper sequence: AT2G28760.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 3
GAAAAGAATGAAGTAATCGTTGCGGATAATTACTTCACAGGATCAAAAGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTAATTCGTCATGgtatagtatcttcttaattaatcaaactta------cttaatactcattaaccaaaacaatgcattaatactcattcttgtgattttttcag----------
|| || ||||| ||||| | ||||| || ||||||||||| || ||||| |||||||| || |||||||||||||| || |||||||||| | || || ||| || || | ||| |||| || | || | | | | | | | || ||| | |
------------GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgta-aataactagttagctatgcacatttaagatattttaagtcttctctttcagaggatcctgaaagttatgaaccctg-gatagtcaatgataaataaac
upper sequence: AT2G28760.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA12G06990.1 (Glycine max), 5'ss of exon 4
GAAAAGAATGAAGTAATCGTTGCGGATAATTACTTCACAGGATCAAAAGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTAATTCGTCATGgtatagtatcttcttaatta--atcaaacttacttaatactcattaaccaaaacaatg--cat-taatac--tcattcttgtgattttttcag-------
|| || ||||| ||||| |||||||| |||||||| ||||| ||||| ||||||||||||||||||||||| ||||| ||||||||||||||| || || || || || ||| | | || || || ||| || ||| | ||| | | || | | || |
------------GTCATTGTTGCTGATAACTACTTCACTGGATCAAAGGACAACCTCAAAAAATGGATTGGTCATCCAAGATTCGAGCTTATTCGTCATGgtatactacattttttcgtactattcaacgtgtcaactatctataaattaaattgttgggcatatgatagagtgaaggttagattatattttgtctcatt
upper sequence: AT2G28760.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA11G15020.1 (Glycine max), 5'ss of exon 4
GAAAAGAATGAAGTAATCGTTGCGGATAATTACTTCACAGGATCAAAAGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTAATTCGTCATGgtatagt--atcttcttaattaatcaaacttacttaatactcattaaccaaaacaatgcattaatactcattcttgtgattttttcag--------------
|| || ||||| || || |||||||| |||||||| ||||| ||||| ||||||||||||||||||||||||||||| || |||||||||||| | || || || | || |||| ||| | | | || ||| | || || | | || |||| | |
------------GTCATTGTTGCTGACAACTACTTCACTGGATCAAAGGACAACCTCAAAAAATGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatactccattttgtttactattcaa-cttctcaaccatctaaaaattaaattattgtgcatatgat-agactgaagattagattatattttgtctcattt
upper sequence: AT2G28760.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA11G15010.1 (Glycine max), 5'ss of exon 4
GAAAAGAATGAAGTAATCGTTGCGGATAATTACTTCACAGGATCAAAAGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTAATTCGTCATGgtatagtat--cttcttaattaatcaaacttacttaatactcattaaccaaaacaatgcattaatactcattcttgtgattttttcag-------------
|| || ||||| || || |||||||| ||||| |||||||| || || | ||||||||| ||||||||||||||||||||||||||||||||| | | || | || || | | | | | | | || ||| ||| | ||| || | | | | |
------------GTCATTGTTGCTGACAACTACTTCACTGGATCTAAAGACAACCTTAAAAGATGGATTGGCCATCCAAGATTTGAGCTAATTCGTCATGgtataattttactattctcttcattgcaatcattcacagtttgg-gattaatttgatggtttattctcaattgttctaaatcagttaccaatgtagagcag
upper sequence: AT2G28760.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA13G40960.1 (Glycine max), 5'ss of exon 5
GAAAAGAATGAAGTAATCGTTGCGGATAATTACTTCACAGGATCAAAAGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTAATTCGTCATGgtatagtatcttcttaattaatcaaacttacttaatactcattaaccaaaacaatgcattaatactcattcttgtgattttttcag------------------
||||| ||||| || || |||||||| ||||| || ||||| ||||| |||||||| |||||||||||||||||||| || |||||||||||||| | |||| || | | | || | |||||| || ||||| || ||| |||| |
------------GTAATTGTTGCTGACAACTACTTCACTGGATCCAAGGACAACCTCAAAAAATGGATAGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatagtctaatctttgtttactatcaactatcaa-aggcattaa---aattgtcacattaggcagtatctccttgagcttttaaatttagtttgtcaactggt
upper sequence: AT2G28760.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA12G06980.2 (Glycine max), 5'ss of exon 3
GAAAAGAATGAAGTAATCGTTGCGGATAATTACTTCACAGGATCAAAAGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTAATTCGTCATGgtatagtat--cttcttaattaatcaaacttacttaatactcattaaccaaaacaatgcattaatactcattcttgtgattttttcag-------------
|| || ||||| || || | |||||| ||||| |||||||| || || ||||||||||| ||||||||||| ||||||||||||||||||||| | | || | || || | | | | | | | | || ||| ||| | ||| || | | | |||
------------GTCATTGTTGCTGACAACTTCTTCACTGGATCTAAAGACAACCTTAAAAAATGGATTGGCCATCCAAGATTCGAGCTAATTCGTCATGgtataattttactgttctcttcattgcaatcattca-cagactgggattaatttgatggtttattctcaattgttctaaatcagtcaccaatgtagagcag
upper sequence: AT2G28760.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA15G04500.2 (Glycine max), 5'ss of exon 5
GAAAAGAATGAAGTAATCGTTGCGGATAATTACTTCACAGGATCAAAAGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTAATTCGTCATGgtatagtatct---tcttaattaatcaaacttacttaatactcat-taaccaaaacaatgcattaatactcattcttgtgattttttcag----------
|| || ||||| || || |||||||| ||||| || || || ||||| || |||||||||||||||||||||||||| || |||||||||||||| | | || ||| | | || | || || | |||| | | || || | ||||| |
------------GTCATTGTTGCTGACAACTACTTCACTGGATCCAAGGATAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatagtctttcatctttgtttactgtcaactatcaactatcaatgccattaaaattgtcacatgttagatgcactaaagttttttattgatttatcttt
upper sequence: AT2G28760.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 5'ss of exon 4
GAAAAGAATGAAGTAATCGTTGCGGATAATTACTTCACAGGATCAAAAGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTAATTCGTCATGgtatagtatcttcttaattaatcaaacttacttaatactcattaaccaaaacaatgcattaatactcattcttgtgattttttcag----------------
||||| ||||| ||||| |||||||| || || || ||||||||||||||||||||||||||||||||||||||||| ||||||||||||| | | | | ||| || | ||| || || | ||| | | | || | ||| | || |||||
------------GTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtaagttttttatctttttactccattttattttat-cacatatgcatatgcgtcat-ttgtttggaatttgggatatcccttcagatgaatcctgattggtMapped 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|86060668|gb|DR356425.1|DR356425EST: CAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTAATTCGTCATG ATGTGGCTGAACCTCTTTTCGTCGAGGTTGATCAAATCTACCATTTAGCAT
genomic: CAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTAATTCGTCATGgtatagtatc ... attttttcagATGTGACTGAACCTCTTTTCGTCGAGGTTGATCAAATCTACCATTTAGCAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GAAAAGAATGAAGTAATCGTTGCGGATAATTACTTCACAGGATCAAAAGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTAATTCGTCATGgtatagtatcttcttaattaatcaaacttacttaatactcattaaccaaaacaatgcattaatactcattcttgtgattttttcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA