Sequence
atgc intronic sequence ATGC exonic sequenceTGTTTTAGAATGTGTTCCACCTCCTGTGGCTGCTGCTGCAACCTCTGCTCTTAATATTCCAACCATTGGCATAGGAGCTGGCCCTTTCTGCAGTGGTCAGgttcgttttgatactctttacattgtcttaacgagagcaataggcttctttcggtttcatgtgcttatacatggtttgattgaataaaccatattctcagttattggcctttttgcatgattaaagagtaagatcagcacaaaaagagtgagttatctacatttctgatcaagtatgtcacatttttcttgtggattcag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G61530.2 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G61530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G010596_T01 (Zea mays), 5'ss of exon 3
TGTTTTAGAATGTGTTCCACCTCCTGTGGCTGCTGCTGCAACCTCTGCTCTTAATATTCCAACCATTGGCATAGGAGCTGGCCCTTTCTGCAGTGGTCAGgttcgttttgatactctttacattgtcttaacgagagcaatagg----cttctttcggtttcatgtgcttatacatggtttgattgaataaaccatattctcagttattggcctttttgcatgattaaagagtaagatcagcacaaaaagagtgagttatctacatttctgatcaagtatgtcacatttttcttgtggattcag
||| || || ||||| || |||| ||||| || |||||||| || || | || || |||||||||||||| || ||||| || ||||| ||||| ||||||||||| | | | | | | | | ||| | || | ||| || | | || | || | | | || | ||||| |
TGTGTTGGAGTGTGTGCCTGCTCCAGTGGCAGCAGCTGCAACATCAGCATTGAAAATCCCAACCATTGGCATTGGGGCTGGACCATTCTGTAGTGGCCAGgttcgttt-gttctttgctccgtaaaatgaggaggagaagtaagatcacttgctttgctcacagatactgagatacaagatgttgactctggtcatatcca-------------------------------------------------------------------------------------------------------
upper sequence: AT3G61530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv15s0046g02170.t01 (Vitis vinifera), 5'ss of exon 3
TGTTTTAGAATGTGTTCCACCTCCTGTGGCTGCTGCTGCAACCTCTGCTCTTAATATTCCAACCATTGGCATAGGAGCTGGCCCTTTCTGCAGTGGTCAGgttcgttttgatactctttacattgtcttaacgagagcaataggcttctttcggtttcatgtgcttatacatggtttgattgaataaaccatattctcagttattggcctttttgcatgattaaagagtaagatcagcacaaaaagagtgagttatctacatttctgatcaagtatgtcacatttttcttgtggattcag
|||| | |||||||| || | |||||||||||||| |||| || || ||| || || |||||||||||||||||||| |||||||||||||| |||||| || | ||| | || || ||| |||| | | || ||| | || || || | | || || | | |||| || || |||
TGTTCTTGAATGTGTGCCTGCACCTGTGGCTGCTGCAACAACATCAGCCCTTCGAATCCCCACCATTGGCATAGGAGCTGGACCTTTCTGCAGTGGACAGgttgatt-----attctct--atctctctactaagataaatacccgtgtt----ttttgtatgttttcttttgttgctaagaaaaaatatgaaaaccaagtt---ggtctattt--------------------------------------------------------------------------------------
upper sequence: AT3G61530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S130_272V6.4 (Physcomitrella patens), 5'ss of exon 5
TGTTTTAGAATGTGTTCCACCTCCTGTGGCTGCTGCTGCAACCTCTGCTCTTAATATTCCAACCATTGGCATAGGAGCTGGCCCTTTCTGCAGTGGTCAGgttcgttttgatactctttacattgtcttaacgagagcaataggcttctttcggtttcatgtgcttatacatggtttgattgaataaacc-atattctcagttattggcctttttgcatgattaaagagtaagatcagcacaaaaagagtgagttatctacatttctgatcaagtatgtcacatttttcttgtggattcag
|| | || || |||||| ||||| | || || |||| || || || ||||| ||||| |||||||| || || |||||||||||||| ||||| ||||| ||| | ||| ||| || |||| | | ||||| | | || | || || | || ||| |||| ||| || | | | | | || | || | | | | || | | | | | || | | || |
CGTGCTCGAGTGCGTTCCATCTCCTATTGCGGCAGCTGTTACATCCGCACTTAAAATTCCCACCATTGGGATTGGTGCTGGCCCTTTCTGTAGTGGCCAGgt-------agtacgtctctcataaccttt--------------ctcttttccttcacccatgcttgtcgacactt--gccaatcaagcctgttttggcagcatttggggctttc------tttgtggttgattttaatttctaagtttttgtttgtttgtttgtttgtttgtttgtttta-atgtgttttacag------
upper sequence: AT3G61530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ15486 (Selaginella moellendorffii), 5'ss of exon 4
TGTTTTAGAATGTGTTCCACCTCCTGTGGCTGCTGCTGCAACCTCTGCTCTTAATATTCCAACCATTGGCATAGGAGCTGGCCCTTTCTGCAGTGGTCAGgttcgt------tttgatactctttacattgt--cttaacgagagcaataggcttctttcggtttcatgtgcttatacatggtttgattgaataaaccatattctcagttattggcctttttgcatgattaaagagtaagatcagcacaaaaagagtgagttatctacatttctgatcaagtatgtcacatttttcttgtggattcag
||| | || ||| | ||| | || ||||||||||| || || | | | || |||||||| ||||| |||||||| |||||||||||||| |||||| | || | |||| | | |||| || || | |||||||| |||| |||
GGTTCTCGAGTGTATACCATCGCCAGTGGCTGCTGCCATCACTTCGTCCTTGCAGATACCAACCATCGGCATTGGAGCTGGGCCTTTCTGCAGTGGCCAGgtttataagaaacttaacgttcttcgctcggaaacttacaaaggaaaaaacgcttctttttttttccattgcag--------------------------------------------------------------------------------------------------------------------------------------
upper sequence: AT3G61530.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ24767 (Selaginella moellendorffii), 5'ss of exon 4
TGTTTTAGAATGTGTTCCACCTCCTGTGGCTGCTGCTGCAACCTCTGCTCTTAATATTCCAACCATTGGCATAGGAGCTGGCCCTTTCTGCAGTGGTCAGgttcgt------tttgatactctttacattg----tcttaacgagagcaataggcttctttcggtttcatgtgcttatacatggtttgattgaataaaccatattctcagttattggcctttttgcatgattaaagagtaagatcagcacaaaaagagtgagttatctacatttctgatcaagtatgtcacatttttcttgtggattcag
||| | || ||| | ||| | || ||||||||||| || || | | | || |||||||| ||||| |||||||| |||||||||||||| |||||| | || | || | | | | || | || || || |||| || ||
GGTTCTCGAGTGTATACCATCGCCAGTGGCTGCTGCCATCACTTCGTCCTTGCAGATACCAACCATCGGCATTGGAGCTGGGCCTTTCTGCAGTGGCCAGgtttataagaaacttaacgttcgtcgctcggaaacttacaaaggaagaaacgcttttttttccattgcag--------------------------------------------------------------------------------------------------------------------------------------------Mapped 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|86079956|gb|DR375713.1|DR375713EST: TTCCAACCATTGGCATAGGAGCTGGCCCTTTCTGCAGTGGTCAG GTTTTAGTCTACCATGATCTTCTGGGAATGATGCAGCATCCACATCACGCT
genomic: TTCCAACCATTGGCATAGGAGCTGGCCCTTTCTGCAGTGGTCAGgttcgttttg ... gtggattcagGTTTTAGTCTACCATGATCTTCTGGGAATGATGCAGCATCCACATCACGCT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGTTTTAGAATGTGTTCCACCTCCTGTGGCTGCTGCTGCAACCTCTGCTCTTAATATTCCAACCATTGGCATAGGAGCTGGCCCTTTCTGCAGTGGTCAGgttcgttttgatactctttacattgtcttaacgagagcaataggcttctttcggtttcatgtgcttatacatggtttgattgaataaaccatattctcagttattggcctttttgcatgattaaagagtaagatcagcacaaaaagagtgagttatctacatttctgatcaagtatgtcacatttttcttgtggattcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG