Sequence
atgc intronic sequence ATGC exonic sequenceTGCACCTGTGGTAGCTCAGATTTCGAAGGATGCTGGTTATTTGACTGTTGGTGTTGTTACCTATCCGTTTAGCTTTGAAGGACGTAAAAGATCTTTGCAGgtaatgtgtgttgacaccgtttcttgttgaatgggtttaagtttaaagtcttgttatggatctatgcctgatttggttatttcctctag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G55280.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G55280.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os04g56970.2 (Oryza sativa), 5'ss of exon 3
TGCACCTGTGGTAGCTCAGATTTCGAAGGATGCTGGTTATTTGACTGTTGGTGTTGTTACCTATCCGTTTAGCTTTGAAGGACGTAAAAGATCTTTGCAGgtaa-----tgtgtgttgaca--ccgtttcttgttga-atgggtttaagtttaaagtcttgttatggatctatgcctgatttggttatttcctctag-----
||| || || || |||||||| || ||||| || |||||| | || ||||| |||||||||||||| || || ||||||||||| || | ||| | |||| || || || || | |||| | || | ||| ||| ||| | | ||| ||| || || || ||||||| |
TGCTCCAGTTGTTGCTCAGATATCAAAGGAAGCCGGTTATCTCACCGTTGGAGTTGTTACCTATCCATTCAGTTTTGAAGGACGCAAGCGCTCTCTTCAGgcaagtgtttgagtcttctccacccgtatacaattaatgtggcgttacatttgataaatagttttgg--ttaagcatggaacaaacatttccttaggggagc
upper sequence: AT5G55280.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os04g56970.1 (Oryza sativa), 5'ss of exon 3
TGCACCTGTGGTAGCTCAGATTTCGAAGGATGCTGGTTATTTGACTGTTGGTGTTGTTACCTATCCGTTTAGCTTTGAAGGACGTAAAAGATCTTTGCAGgtaa-----tgtgtgttgac--accgtttcttgttga-atgggtttaagtttaaagtcttgttatggatctatgcctgatttggttatttcctctag-----------
|| || |||||||| || ||||| || |||||| | || ||||| |||||||||||||| || || ||||||||||| || | ||| | |||| || || || || | |||| | || | ||| ||| ||| | | ||| ||| || || || ||||||| |
------AGTTGTTGCTCAGATATCAAAGGAAGCCGGTTATCTCACCGTTGGAGTTGTTACCTATCCATTCAGTTTTGAAGGACGCAAGCGCTCTCTTCAGGCAAGTgtttgagtcttctccacccgtatacaattaatgtggcgttacatttgataaatagttttgg--ttaagcatggaacaaacatttccttaggggagctgtgag
upper sequence: AT5G55280.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G119773_T01 (Zea mays), 5'ss of exon 3
TGCACCTGTGGTAGCTCAGATTTCGAAGGATGCTGGTTATTTGACTGTTGGTGTTGTTACCTATCCGTTTAGCTTTGAAGGACGTAAAAGATCTTTGCAGgtaatgtgtgttgacaccgtttc-ttgttgaat--gggtttaagtt-taaagtcttgttatggatctatgcctgatttggttatttcctctag---------
||| || || || || ||||| || ||||| ||||||||| | |||||||||||||| |||||||| || || || || || ||||| | ||| | |||| || || | | | || ||| | ||||| || || | | | ||| ||| || || | | | | | | | |||
TGCTCCAGTTGTTGCCCAGATATCAAAGGAAGCTGGTTATCTTACTGTTGGTGTTGTCACCTATCCATTCAGTTTCGAGGGCCGTAAGCGCTCTGTACAGgcaa-gtatctgagccccccttcactcctgaattttaattcaaactgtcatatctcgttctgcgactttcttttgctcgatggaagcat-tagtttgtagtc
upper sequence: AT5G55280.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA02G46530.1 (Glycine max), 5'ss of exon 3
TGCACCTGTGGTAGCTCAGATTTCGAAGGATGCTGGTTATTTGACTGTTGGTGTTGTTACCTATCCGTTTAGCTTTGAAGGACGTAAAAGATCTTTGCAGgtaa-tgtgtgttgacaccgtttcttgttgaatgggtttaagtttaaagtcttgttatggatcta---tgcctgatttggttatttcctctag----------
||| || || ||||| || || || || || || ||||| |||||||| ||||||||||||||||| || || |||||||||||||| ||||| ||||||| | ||| || |||| ||| ||||| | || | ||||| | | | || | | ||| ||| ||||| | |
TGCCCCAGTTGTAGCCCAAATATCAAAAGAGGCAGGTTACTTGACTGTAGGTGTTGTTACCTATCCCTTCAGTTTTGAAGGACGTAAGAGATCCTTGCAGgcaggtgtccttttttctcgttatttgg-gaatgtggcta--ctgaaagttctactcttaattaatattaccttctttctttattatgttgaaaaatatcact
upper sequence: AT5G55280.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA14G02110.1 (Glycine max), 5'ss of exon 3
TGCACCTGTGGTAGCTCAGATTTCGAAGGATGCTGGTTATTTGACTGTTGGTGTTGTTACCTATCCGTTTAGCTTTGAAGGACGTAAAAGATCTTTGCAGgtaatgtgtgttgacaccgtttcttgttgaatgggtttaagtttaaagtcttgttatggatctatg---cctgatttggttatttcctctag---------
||| || || ||||| || || || || || || ||||| |||||||| ||||||||||||||||| || || |||||||||||||| |||| ||||||| | |||| | | || || ||||| | || ||| || | | || || ||| ||| ||| | | |
TGCCCCAGTTGTAGCCCAAATATCAAAAGAGGCAGGTTACTTGACTGTAGGTGTTGTTACCTATCCCTTCAGTTTTGAAGGACGTAAGAGATGCTTGCAGgcag-gtgtcctttttctcgttatttgggaatgtgactactgaattagttttactcttaattaatactaccttctttctttaatatgttgaaaaatatcac
upper sequence: AT5G55280.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA18G10030.1 (Glycine max), 5'ss of exon 3
TGCACCTGTGGTAGCTCAGATTTCGAAGGATGCTGGTTATTTGACTGTTGGTGTTGTTACCTATCCGTTTAGCTTTGAAGGACGTAAAAGATCTTTGCAGgtaatgtgtgttgacaccgtttcttgttgaatgggtttaagtttaaagtcttgttatggatctatgcctgatttggttatttcctctag
|| || || || | || | || || || ||||| ||||| || ||||||||||||||||| || || ||||||||||| |||||||| |||||| | |||| | | | || ||| || | || | |||
----CCAGTAGTGGCCCGAATAGCTAAAGAGGCAGGTTACTTGACAGTAGGTGTTGTTACCTATCCCTTCAGTTTTGAAGGACGCAAAAGATCACTGCAGGCAG-
upper sequence: AT5G55280.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv19s0090g01320.t01 (Vitis vinifera), 5'ss of exon 3
TGCACCTGTGGTAGCTCAGATTTCGAAGGATGCTGGTTATTTGACTGTTGGTGTTGTTACCTATCCGTTTAGCTTTGAAGGACGTAAAAGATCTTTGCAGgtaatgtgtgttgacaccgtttcttg---ttgaatgggtttaagtttaaagtct-tgttatggatctatgcctgatttggttatttcctctag-------
||| || || || || || || || ||||| || ||||||||||||||||| || || ||||| || || ||||||||||||||||||||||| |||||| | || | || ||| | || || | | ||| || | | | | |||| || ||| | | |
TGCCCCAGTTGTTGCCCAAATATCTAAGGAAGCGGGTTATTTGACTGTTGGGGTGGTCACCTACCCTTTCAGCTTTGAAGGACGTAAAAGATCACTGCAGgcaggtgccattttggtctttatttgaaatcaaagggaaattattttgttgtttgtctggtcttactatatatgtaacaattaacttccaaatgacaggcMapped 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|301501112|gb|HO206652.1|HO206652EST: GTGTTGTTACCTATCCGTTTAGCTTTGAAGGACGTAAAAGATCTTTGCAG GCACTGGAAGCTAT
genomic: GTGTTGTTACCTATCCGTTTAGCTTTGAAGGACGTAAAAGATCTTTGCAGgtaatgtgtg ... tttcctctagGCACTGGAAGCTAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGCACCTGTGGTAGCTCAGATTTCGAAGGATGCTGGTTATTTGACTGTTGGTGTTGTTACCTATCCGTTTAGCTTTGAAGGACGTAAAAGATCTTTGCAGgtaatgtgtgttgacaccgtttcttgttgaatgggtttaagtttaaagtcttgttatggatctatgcctgatttggttatttcctctag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG