Sequence
atgc intronic sequence ATGC exonic sequencegttcctttcaaatctttttaggttttagtgtaatgtggtcaaggagacaagttgtgggtttaagttaccttgcacttgaatacagGTTAATTCAAAAGCAGCAGAATCTTTGGCTGATCCTGAGGAGTACTCAAATCTTTTTGAAGATTGGCAAGTTGCTCTTTCTGTGGAAGCTAAAGCTGTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G52360.2 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 12
-----------gttcctttcaaatctttttaggttttagt-gtaatgtggtcaaggaga-caagttgtgggtttaagttaccttgcacttgaat--acagGTTAATTCAAAAGCAGCAGAATCTTTGGCTGATCCTGAGGAGTACTCAAATCTTTTTGAAGATTGGCAAGTTGCTCTTTCTGTGGAAGCTAAAGCTGTAG
| | | || |||| || ||| | ||||| | | | || || ||| || | ||| || | | |||| || | |||||||||||||| ||||| |||||||| |||||| |||| | |||||||| |||||| ||||||| ||| |||||||| | |
tcttattttcagacttacgcgacactgtttaatttgtaggagctatgtgttttattatctcaccatgccttttttccttctcatgccattatctttatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 21
-------------------------------------------------------------------------------------------------------------------gttcctttcaaatctttttaggttttagtgtaatgtggtcaaggagacaagttgtgggtttaagttaccttgcacttgaatacagGTTAATTCAAAAGCAGCAGAATCTTTGGCTGATCCTGAGGAGTACTCAAATCTTTTTGAAGATTGGCAAGTTGCTCTTTCTGTGGAAGCTAAAGCTGTAG
||| || || ||| | || || | | || | ||| || ||| | |||||||||| ||||||| || ||||| |||||||||||||||||||| | ||| | ||||| |||||||||||||| ||| |||| ||| |||||||| ||
gtaatgttatatatatatatatatatatatatataatttagcaacggaatagcctgacatttatgttgtgcacatgatactgtgggtaggaacttctgttctcattccattggcctgccctgtcctggattcttatcatgctacatattgcatgtgaaataaaaatataaattcttatatttatttgttaatatgcacagGTTAATCCAAAAGCCGCCGAATCATTGGCTGATCCTGAGGAGTATCCTAATTTGTTTGATGATTGGCAAGTTGCACTTGCTGTTGAATCTAAAGCTACAG
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 21
---------gttcctttcaaatctttttaggttttagtgtaatgtggtcaaggagacaagttg----tgggtttaagttac--cttgcacttgaatacagGTTAATTCAAAAGCAGCAGAATCTTTGGCTGATCCTGAGGAGTACTCAAATCTTTTTGAAGATTGGCAAGTTGCTCTTTCTGTGGAAGCTAAAGCTGTAG
| || | || ||| | || | ||| | | ||| | ||| ||| | ||| || ||| | | | | || | | ||||||||| ||||||| || ||||| |||||||||||||| || || ||||| | |||||||||||||| ||||| || |||| ||| |||||||||| |
ggtaggagcatcagttctcattcatttgccttgtttgagtagtcttatcatgttgacgagtggctcatggattaaagagagtacatatattttattgcagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAGGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 10
------------------gttcctttcaaatctttttaggttttagtgta-atgtggt-caaggagacaagttgtgggtttaagttaccttgcacttgaatacagGTTAATTCAAAAGCAGCAGAATCTTTGGCTGATCCTGAGGAGTACTCAAATCTTTTTGAAGATTGGCAAGTTGCTCTTTCTGTGGAAGCTAAAGCTGTAG
| | | |||| | | | | || | ||||| || | | || || ||| || ||| | |||||||||| ||||||| || ||||| ||||||||||||||||| || | ||| | ||||| |||||||||||||| || |||| ||| |||||||| |
ctcattccattggcctgccctgtcctggattcttatcatgctacagattgcatgtgaaataaaaatataaatt-----cttatatttagttgttaatatgcacagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAGGAATATCCTAATTTGTTTGATGATTGGCAAGTTGCACTAGCTGTTGAATCTAAAGCTACGG
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA13G43680.1 (Glycine max), 3'ss of exon 21
---gttcctttcaaatctttttaggttttagtgtaatgtggtcaaggagacaagt----tgtgggtttaagt---tacct-----tgcacttgaatacagGTTAATTCAAAAGCAGCAGAATCTTTGGCTGATCCTGAGGAGTACTCAAATCTTTTTGAAGATTGGCAAGTTGCTCTTTCTGTGGAAGCTAAAGCTGTAG
| | || | || ||| | || | ||| | | ||| | ||||||| | ||| || ||| ||| | | | || | ||||| ||| ||||||| || ||||| |||||| ||||||| || || ||||| | |||||||||||||||||||| || |||| ||| |||||||||| |
agcatccgttctcattcatttgccttgtttgggtagtcttatcatgttgacaagtgacttatggattaaagagagtacgtatacgtatattttgttgcagGTCAATCCAAAAGCTGCTGAATCATTGGCTAATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAAGTTGCACTAGCTGTCGAATCTAAAGCTGTGG
upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 21
----------------gttcctttcaaatctttttaggttttagtgtaatgtggtcaaggagacaagttgtgggtttaagttaccttgcacttgaatacagGTTAATTCAAAAGCAGCAGAATCTTTGGCTGATCCTGAGGAGTACTCAAATCTTTTTGAAGATTGGCAAGTTGCTCTTTCTGTGGAAGCTAAAGCTGTAG
| || | | |||| |||| ||| || | || |||||| | | || |||| || ||||||||| ||||||| || |||||||||||||||||||| ||||| | ||| | ||||| || |||||||||| |||| | | ||| |||||| || |
atatgcctgcttgggtagttggatctatttcatttaacttttcttgtgatttaaagaaagagacacatatctaatcctgtttgatcaacact-atatgcagGTTAATCCAAAAGCTGCTGAATCTTTGGCTGATCCTGAAGAGTATCCTAATTTATTTGAGGACTGGCAAGTTGGTCTTGCCATTGAATCTAAAGTTGCCGMapped 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|124705343|gb|EH796745.1|EH796745EST: CGAGCAAAGTTTCTGAGATAGTAGCTCTTTGGAGGAAAGATCTCAGCAAG GTTAATTCAAAAGC
genomic: CGAGCAAAGTTTCTGAGATAGTAGCTCTTTGGAGGAAAGATCTCAGCAAGgttcctttca ... ttgaatacagGTTAATTCAAAAGC
EST:
gi|124809032|gb|EH894842.1|EH894842EST: CGAGCAAAGTTTCTGAGATAGTAGCTCTTTGGAGGAAAGATCTCAGCAAG GTTAATTCAAAAG
genomic: CGAGCAAAGTTTCTGAGATAGTAGCTCTTTGGAGGAAAGATCTCAGCAAGgttcctttca ... ttgaatacagGTTAATTCAAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatgtggtcaaggagacaagttgtgggtttaagttaccttgcacttgaatacagGTTAATTCAAAAGCAGCAGAATCTTTGGCTGATCCTGAGGAGTACTCAAATCTTTTTGAAGATTGGCAAGTTGCTCTTTCTGTGGAAGCTAAAGCTGTAG
tttaagtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcctttcaaatctttttaggttttagtgtaatgtggtcaaggagacaagttgtgggtttaagttaccttgcacttgaatacagGTTAATTCAAAAGCAGCAGAATCTTTGGCTGATCCTGAGGAGTACTCAAATCTTTTTGAAGATTGGCAAGTTGCTCTTTCTGTGGAAGCTAAAGCTGTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG