Sequence
atgc intronic sequence ATGC exonic sequencegtattcattaacgcaaacaaataattgttcctatctttgattccttttttctgagtgatatctttcttggttctttgtgcttattccaacgattttgctcatctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTACCAGTACTGCCGTATTGATGGAAATACTGGTGGTGACGAACGAGATGCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G18620.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 10
gtattcattaacgcaaacaaataattgttcctatctttgattccttttttctgagtgatatctttcttggttctttgtgcttattccaacgattttgctcatctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTACCAGTACTGCCGTATTGATGGAAATACTGGTGGTGACGAACGAGATGCTT
| | | |||||||||| || | | | | | | | | | | | ||| | | | || || || ||| || |||||||| |||||||||||||| | || ||||| || ||||| | || || ||||| ||||| || ||||||||||||||||| || || || ||||| |
--------tgatctgagttctctattgttcctaagcatgttaacgtcacacataatttggtttcttcaaatcttgtgt-ttgactttgacatttatgtccattc-ta-cagATGACCAGGCTTTTGGATATATTGGAAGATTATCTTATGTACAGAGGCTATCAGTATTGCCGGATAGATGGAAATACTGGTGGAGAAGATCGTGATGCAT
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 10
gtattcattaacgcaaacaaataattgttcctatctttgattccttttttctgagtgatatctttcttggttctttgtgcttattccaacgattttgctcatctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTACCAGTACTGCCGTATTGATGGAAATACTGGTGGTGACGAACGAGATGCTT
| | | || ||||||| || | | | | | | | | | | ||| | | | || || || ||| || |||||||| |||||||||||||| | || ||||| || ||||| | || || ||||| ||||| || ||||||||||||||||| || || || ||||| |
--------tgatctgagttctctatggttcctaagcatgttaacgtcacacataatttggtttcttcaaatctcgtgt-ttgactttgacatttatgtccattc-ta-cagATGACCAGGCTTTTGGATATATTGGAAGATTATCTTATGTACAGAGGCTATCAGTATTGCCGGATAGATGGAAATACTGGTGGAGAAGATCGTGATGCAT
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 7
-------------------------------------------------gtattcattaacgcaaacaaataattgttcctatctttgatt-------ccttttttctgagtgatatctttcttggttctttgtgcttattccaacgattttgctcatctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTACCAGTACTGCCGTATTGATGGAAATACTGGTGGTGACGAACGAGATGCTT
|| | ||| | | | | || ||| | | || | | | | ||| ||| | ||||| || | || | | |||||||| |||||||||||||| | || ||||| || |||||| | || || ||||| || || |||||||||||||| ||||| || || || ||||| |
gtgtgttttccaatcccatgcagatttgaatgcattatttatttagcaagtgtgtgttaggagatatcagacaccactctggatggtgagcatgtgcacagtgcacctcattaaaaacttggttgtcctagaatttttatttgcctgacatagcaccatcctg-cagATGACCAGGCTTTTGGATATCTTGGAAGATTATCTTATGTATAGGGGATATCAGTATTGTCGAATTGATGGAAATACAGGTGGAGAAGATCGTGATGCAT
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 10
--------------------------------------------------gtattcattaacgcaaacaaataattgttcct---------atctttgattccttttttctgagtgatatctttcttggttctttgtgcttattccaacgattttgc-tcatctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTACCAGTACTGCCGTATTGATGGAAATACTGGTGGTGACGAACGAGATGCTT
|| | ||| | | | | | || | | | | | | || | | | || |||| | | | || || | || ||||| |||||||| |||||||||||||| | || ||||| || |||||| | ||||| ||||| || || ||||| |||||||| ||||| || || || ||||| |
gtgattgttttccattgccatgcagatttgaatgcattattcgttagcaagtgtgtattgggagatatcagacaccgctcgtgggatgctgagcatgtgcacagtgcacctcattaagcactcgcttgtcctataattttcctttgtctgacatcgcatcatcctg--cagATGACCAGGCTTTTGGATATCTTGGAAGATTATCTTATGTATAGAGGTTATCAGTATTGTCGAATTGACGGAAATACAGGTGGAGAAGATCGTGATGCAT
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 10
gtattcattaacgcaaacaaataattgttcctatctttgattccttt---tttctgagtgatatctttcttggttctttgtgcttattccaacgattttgctcatctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTACCAGTACTGCCGTATTGATGGAAATACTGGTGGTGACGAACGAGATGCTT
||| | | | ||||| ||| | | | || || | | | | | | ||| || | | ||||| | | | | | || ||| |||||||| ||||| | || || || || ||||| || |||| |||||| ||||| || || || |||||||||||||||||||| ||||| ||||||||||
---gtcagttctgtgtaggaataag-attcttggcactaatagctatgactgtgttatttcaatcagcctagtgtatttgttccattctcgcttaatctgtggttcttctccagATGACTAGGCTGCTAGACATACTTGAAGATTATCTCATGTTTCGTGGATACCAATATTGTCGCATTGATGGAAATACTGGTGGAGACGATCGAGATGCTT
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 10
-----------------------------gtattcattaacgcaaacaaataattgttcctatctttgattccttttttctgagtgatatctttcttggttctttgtgcttattccaacgattttgctcatctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTACCAGTACTGCCGTATTGATGGAAATACTGGTGGTGACGAACGAGATGCTT
| | || | | || | | || || | | | || ||| ||| | | || ||| ||| ||| | | || | | | | | ||| |||||||| ||||| | || || ||||| ||||| || ||| |||||| || || || ||||| |||||||||||||||||||| || || ||||||||||
gtcagttctgtcagagtgtgtgattcttgtcactgatgattgtgaataccttatattttgcaacctgtttttgtttgctctcatttatttctgccttttgaattttcttctgtgcctaatttgtggtttttctcc-ccagATGACTAGGCTACTAGACATACTCGAAGATTATTTAGTGTTTCGTGGATATCAATATTGCCGCATTGATGGAAATACTGGTGGGGATGATCGAGATGCTT
upper sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 10
---------------------------gtattcattaacgcaaacaaataattgttcctatctttgattccttttttctgagtgatatctttcttggttctttgtgcttattccaacgattttgctcatctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTACCAGTACTGCCGTATTGATGGAAATACTGGTGGTGACGAACGAGATGCTT
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gtcagttctgtcagaatgtgattcttgtcgctgatgattgtgaatgccttatattttgcaacctgtttttgtttgctctcatttatttctgccttttgaattttcttctgtacctaatttgtggcttttctcc-ccagATGACTAGGCTGCTAGACATACTCGAAGATTATTTAATGTTTCGTGGATATCAATATTGTCGCATTGATGGAAATACTGGTGGGGATGATCGAGATGCTTMapped 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|125065242|gb|EL132547.1|EL132547EST: TTGAAGGATCGAGATTCAAGGGTTCTGATATTTTCTCAG ATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTAC
genomic: TTGAAGGATCGAGATTCAAGGGTTCTGATATTTTCTCAGgtattcatta ... tctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatatctttcttggttctttgtgcttattccaacgattttgctcatctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTACCAGTACTGCCGTATTGATGGAAATACTGGTGGTGACGAACGAGATGCTT
ctcatct CT-rich tract
ttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattcattaacgcaaacaaataattgttcctatctttgattccttttttctgagtgatatctttcttggttctttgtgcttattccaacgattttgctcatctgtatcagATGACAAGGCTTTTGGATATTCTCGAGGATTACCTAATGTATCGTGGTTACCAGTACTGCCGTATTGATGGAAATACTGGTGGTGACGAACGAGATGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG