Sequence
atgc intronic sequence ATGC exonic sequence...tttcactagcaagctcatgtttaatgtggaatgggtaccatctgatctatttacatatgtctttcggtttagttgattgtttacttctttcttgttttagGGAGACAGTATTCTTGCAGATTCTGGTACTGAGCAGCTTGAATTTATTGCCCTTTCCCAGAGGACAGGGGACCCAAAATATCAGCAAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G21160.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G128914_T02 (Zea mays), 3'ss of exon 6
tttcactagcaagctca-tgtttaatgtggaa---tgggtaccatctgatctatttacatatgtctttcggtttagttgattgtttacttctttcttgttttagGGAGACAGTATTCTTGCAGATTCTGGTACTGAGCAGCTTGAATTTATTGCCCTTTCCCAGAGGACAGGGGACCCAAAATATCAGCAAAAG
|| | | ||| | | |||| || || | |||||| | | | | | || | ||| ||| | | |||| |||||||| ||||||||||||||||| ||||| |||||||| || || || || |||||||| ||||| || ||||| ||||| |||
aaacattcattaattcagtttgtaatttgaggctttgatttccatctaactcaggattggaaacaaa--aaatgaatt--ccacatgctttgttccttctgcagGGTGACAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCTCTGTCACAGAGGACTGGGGATCCCAAATACCAGCAGAAG
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G130889_T02 (Zea mays), 3'ss of exon 5
tttcactagcaagctca-tgtttaatgtggaa-tgggtaccatctgatc-tatttacatatgtctttcggtttagttgat------tgtttacttctttcttgttttagGGAGACAGTATTCTTGCAGATTCTGGTACTGAGCAGCTTGAATTTATTGCCCTTTCCCAGAGGACAGGGGACCCAAAATATCAGCAAAAG
| | || | | || | | || | ||| ||||| ||||| | | || | || | | ||| ||| | |||| || ||||| ||||||||||||||||| ||||| |||||||| || || || || |||||||| || || || ||||| ||||| |||
---------tatgatcgctatctattttaaaaacattttccacctgattatatttctttctaactcagaaaacaaagaataaattccatatgctttgttccatctgcagGGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAG
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G06600.1 (Glycine max), 3'ss of exon 6
tttcactagcaagctcatgtttaatgtggaatgggtaccatctga-tctatttacatatgtct--ttcggtttagttgattgtttacttctttcttgtt-ttagGGAGACAGTATTCTTGCAGATTCTGGTACTGAGCAGCTTGAATTTATTGCCCTTTCCCAGAGGACAGGGGACCCAAAATATCAGCAAAAG
| | | ||| | || | | | ||| || | || | | || | | | ||| | || | || || | || |||| |||||| ||||||||||||| ||||||||| | ||||| |||||||||||||| || || || |||||| ||||| || || || |||||
----gcaatgattttcaagatttgtctagcgcacccacctatagactatagtgaaatttttgtagctcgttctatgttcttaattgatcgttctctgttactagGGAAACAGTATTCTTGCGGATTCTGGTTCAGAGCAACTTGAATTTATTGCTCTCTCTCAAAGGACAAATGACCCCAAGTACAAGGAAAAG
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G00470.1 (Glycine max), 3'ss of exon 6
tttcactagcaagct-catgtttaatgtggaatgggtaccatctg--atctatttacatatgtctttcggtttagttgattgtttacttctttcttgttttagGGAGACAGTATTCTTGCAGATTCTGGTACTGAGCAGCTTGAATTTATTGCCCTTTCCCAGAGGACAGGGGACCCAAAATATCAGCAAAAG
||| | | || | || || | | | | || || | |||| || || || | | || |||| | |||| | | | ||| | |||||||||||| ||||||||| | ||||| |||||||||||||| || || || ||||| ||||| || || || |||||
tttaagcaataattttcaaaatttgtctagtacacctatagactatagtgaatttttgtagctcactctatgttcttaattgatcg-ttctctatcact--agGAAAACAGTATTCTTGTGGATTCTGGTTCAGAGCAACTTGAATTTATTGCTCTCTCTCAACGGACAAATGACCCCAAGTACAAGGAAAAG
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv09s0054g00230.t01 (Vitis vinifera), 3'ss of exon 1
tttcactagcaagctcatgtttaatgtggaatgggtaccatctgatctatttacat----atgtctttcg--gtttagttgattgtttacttctttcttgttttagGGAGACAGTATTCTTGCAGATTCTGGTACTGAGCAGCTTGAATTTATTGCCCTTTCCCAGAGGACAGGGGACCCAAAATATCAGCAAAAG
|| || |||| | | || | ||| | ||| | ||| || |||| |||| | | ||| || || | | | ||||| |||||||| || || ||||| || || |||||||| || |||||||||||||| || ||||| || || ||||| |||||| |||||
-----ttaataaatacatgaa-atggaaaaaaaaaaaaaatcaaacatatatccatggtaattgatttcattgttttttaaaatgtataattttccttgttcctagGGTGACAGTATCCTAGCCGATTCCGGCACAGAGCAGCTGGAGTTTATTGCCCTTTCTCAAAGGACTGGTGATCCAAAGTATCAGAAAAAG
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv11s0052g00140.t01 (Vitis vinifera), 3'ss of exon 6
tttcactagcaagctcatgtttaatgtggaa--tgggtaccatct---gatctatttacatatgtctttcggtttagttgattgtttacttctttcttgttttagGGAGACAGTATTCTTGCAGATTCTGGTACTGAGCAGCTTGAATTTATTGCCCTTTCCCAGAGGACAGGGGACCCAAAATATCAGCAAAAG
| | || | | || | | || | | ||| | | || || ||||| | |||| || ||| || | | | ||| | |||||| ||||| | || ||||||||||| || |||||||||||||||||||| | || || |||||| ||||||| || || ||| | |||
tatagacagagaattaggcattgagattgatactttgcaccttttctggagctgtttactcttttcttc---ttctgttaatc--taaagagtcccttttcctagGGAAACAGTGTCCTGGCAGATTCTGGAACAGAGCAGCTTGAATTTATTGCTTTATCTCAAAGGACAAGGGACCCCAAGTACCAGAAGAAG
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv09s0054g00370.t01 (Vitis vinifera), 3'ss of exon 6
tttcactagcaagctcatgtttaatgtggaatgggtaccatctgatctatttacatatgtctttcggtttagttgattgtt------tacttctttcttgttt-tagGGAGACAGTATTCTTGCAGATTCTGGTACTGAGCAGCTTGAATTTATTGCCCTTTCCCAGAGGACAGGGGACCCAAAATATCAGCAAAAG
| || || |||| |||| || || | | | || || ||| | | ||| ||| || || || |||| |||| ||||| || ||||| || || ||||| || || |||||||| || |||||||||||||| || ||||| || || ||||| |||||| |||||
----attaataaatacatga--aatg-aaaaaaaataaaaaatcaaacatatatccatggtaattgatttcattgttttttaaaatgtataattttcctgttcctagGGTGATAGTATCCTAGCGGATTCCGGCACAGAGCAGCTGGAGTTTATTGCCCTTTCTCAAAGGACTGGTGATCCAAAGTATCAGAAAAAGMapped 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|124944804|gb|EL020870.1|EL020870EST: ATATTATCAACTTGAAGCATGGAAATGCTCACAATCCTACATGGGCGGGG GGAGACAGTATTCTTGCAGATT
genomic: ATATTATCAACTTGAAGCATGGAAATGCTCACAATCCTACATGGGCGGGGgtaagtccta ... cttgttttagGGAGACAGTATTCTTGCAGATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctatttacatatgtctttcggtttagttgattgtttacttctttcttgttttagGGAGACAGTATTCTTGCAGATTCTGGTACTGAGCAGCTTGAATTTATTGCCCTTTCCCAGAGGACAGGGGACCCAAAATATCAGCAAAAG
agttgat putative branch site (score: 5)
ttgtttacttctttct CT-rich tract
ttacatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttcactagcaagctcatgtttaatgtggaatgggtaccatctgatctatttacatatgtctttcggtttagttgattgtttacttctttcttgttttagGGAGACAGTATTCTTGCAGATTCTGGTACTGAGCAGCTTGAATTTATTGCCCTTTCCCAGAGGACAGGGGACCCAAAATATCAGCAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - -ctgatct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtttag