Sequence
atgc intronic sequence ATGC exonic sequenceATGCTCAGGTATTGCTGGATATGTTGGAATGTGGGTGTCAGTTCGTGCTAATGTGCGGGTCTCCAGTGCTGCCAGACGATCTGCGAGAGAAGCATTGCAGgttcttctttagtttagctattttggtaacatgtcatgtacacgtttccaaatactaagtggcagatataatgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G78920.2 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G78920.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G075900_T01 (Zea mays), 5'ss of exon 5
ATGCTCAGGTATTGCTGGATATGTTGGAATGTGGGTGTCAGTTCGTGCTAATGTGCGGGTCTCCAGTGCTGCCAGACGATCTGCGAGAGAAGCATTGCAGgttcttctttagtttagctat---tttggtaacatgtcatgtacac---gtttccaaatactaagtggcagatataatgcag
||| || || || ||||| | |||||||||||||||||| || ||||| ||||| || || || |||||||| | || ||||| || ||| ||||||||||| ||| |||| || |||| | | | |||| || ||||| | || | || |||
ATGTTCTGGAATAGCTGGTTTTGTTGGAATGTGGGTGTCCGTACGTGCAAATGTACGAGTTTCAAGTGCTGCTCGTCGCTCTGCAAGGGAATCATTGCAGgtttggttttcgtttttggatgcacttggcatttgcccttctacaatagaatttcaaatcatgtctgtttcct-caaaacag
upper sequence: AT1G78920.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA07G00350.1 (Glycine max), 5'ss of exon 5
ATGCTCAGGTATTGCTGGATATGTTGGAATGTGGGTGTCAGTTCGTGCTAATGTGCGGGTCTCCAGTGCTGCCAGACGATCTGCGAGAGAAGCATTGCAGgtt----cttctttagttta------gctattttggtaaca-tgtcatgtacacgtttccaaatactaagtggcagatata-atgcag
|| || ||| ||||||||||||| || |||||||||||||||||||| ||||| | ||||| |||||||| ||||| ||||| ||||| |||||||||||| | || ||| || | | | | || |||| || || ||| | | || ||| ||| || || |||||
TTGTTCCGGTGTTGCTGGATATGTAGGGATGTGGGTGTCAGTTCGTGCCAATGTCAGAGTCTCTAGTGCTGCAAGACGGTCTGCAAGAGAGGCATTGCAGgttaaaccatcattaattcatcatcagtttctgtgaaaacaatgaacagttcac-tatttgtgtattaactggaaggaatttgtgcag
upper sequence: AT1G78920.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA08G24120.2 (Glycine max), 5'ss of exon 5
ATGCTCAGGTATTGCTGGATATGTTGGAATGTGGGTGTCAGTTCGTGCTAATGTGCGGGTCTCCAGTGCTGCCAGACGATCTGCGAGAGAAGCATTGCAGgtt----cttctttagttta------gctattttggtaaca-tgtcatgtacacgtttccaaatactaagtggcagatata-atgcag
|| || ||| ||||||||||||| || |||||||||||||||||||| ||||| | ||||| |||||||| ||||| ||||| ||||| |||||||||||| | || ||| || | | | | || |||| || || ||| | | || ||| ||| || || |||||
TTGTTCGGGTGTTGCTGGATATGTAGGGATGTGGGTGTCAGTTCGTGCCAATGTCAGAGTCTCTAGTGCTGCAAGACGGTCTGCAAGAGAGGCATTGCAGgttaaaccatcattaattcatcatcagtttctgtgaaaacaatgaacagttcac-tatttgtgtattaactggaaggaatttgtgcag
upper sequence: AT1G78920.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 5'ss of exon 5
ATGCTCAGGTATTGCTGGATATGTTGGAATGTGGGTGTCAGTTCGTGCTAATGTGCGGGTCTCCAGTGCTGCCAGACGATCTGCGAGAGAAGCATTGCAGgttcttcttta-gtttagctattttggtaacatgtcatgtacacgtttccaaatacta----agtggcagatataatgcag-------------------
|| ||||| |||||||| |||||||||||||||||||| || ||||| || || || ||||| |||||||| ||||| ||||| |||||||||||||||||| | ||| | || ||| || | | | | | ||| | | |||| | | || || |
TTGTTCAGGAATTGCTGGGTATGTTGGAATGTGGGTGTCGGTACGTGCAAACGTTCGAGTCTCAAGTGCTGCAAGACGGTCTGCAAGAGAAGCATTGCAGgttttccttcatagttcattatcaactgaaaaacacttttttattttttaagaaactactatattagcccttaaagcctgactcaagtggcaggggtttt
upper sequence: AT1G78920.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ13082 (Selaginella moellendorffii), 5'ss of exon 4
ATGCTCAGGTATTGCTGGATATGTTGGAATGTGGGTGTCAGTTCGTGCTAATGTGCGGGTCTCCAGTGCTGCCAGACGATCTGCGAGAGAAGCATTGCAGgttcttctttagtttagctattttggtaacatgtcatgtacacgtttccaaatactaagtggcagatataatgcag
||| || || || ||||| || |||||||||||||| |||||| | ||||||||||| || || || ||||| ||| ||||||| ||||| || |||| ||| | | || | | || | || | | || ||
ATGTTCTGGCATCGCTGGCTACGTTGGAATGTGGGTTTCAGTTAGAGCTAATGTGCGAGTATCAAGCGCTGCTAGAAGATCTGCCAGAGAGGCGTTGCTGgtaaacatcaaacttttgtttcttcggtctattctaaaatctttcttgcag-------------------------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|164185316|gb|ES049082.1|ES049082EST: GAAGCATTGCAG ATAGTCCGTTCGTGCTGGTGGGTTTTCAGCCCTGGTTGTTGTTGGTATGGC
genomic: GAAGCATTGCAGgttcttcttt ... tataatgcagATAG-CCGTTCGTGCTGGTGGGTTTTCAGCCCTGGTTGTTGTTGGTATGGC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATGCTCAGGTATTGCTGGATATGTTGGAATGTGGGTGTCAGTTCGTGCTAATGTGCGGGTCTCCAGTGCTGCCAGACGATCTGCGAGAGAAGCATTGCAGgttcttctttagtttagctattttggtaacatgtcatgtacacgtttccaaatactaagtggcagatataatgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC