Sequence
atgc intronic sequence ATGC exonic sequenceTCCATTGATCGGATCATCCATACAATCAGCTACTGGTGTCGTCTACAACATCACTGGTGGAAAAGACATAACTTTGCAGGAAGTGAACCGAGTATCACAGgtacggtatttttgtcttggtttactcggctttgtttcaattgggtatacactgtattataatgcagtcttctcatgttttgggggggttttgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G55280.1 |
intron # | 5 |
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 5
lower sequence: LOC_Os04g56970.1 (Oryza sativa), 5'ss of exon 5
TCCATTGATCGGATCATCCATACAATCAGCTACTGGTGTCGTCTACAACATCACTGGTGGAAAAGACATAACTTTGCAGGAAGTGAACCGAGTATCACAGgtacg-gtatt-tttgtcttggtttactcggctttgtttcaattgggtat-acactgtattataatgcagtct-tctcatgttttgggggggttttgcag--------------------------------------------------------------------------------------------
||| || ||||| || || || | | ||||||||||| || ||||| |||||||||||||| |||||||| ||||| ||||| ||| ||| || ||||| || ||| | ||| | || || | | || | |||| | | | | | |||| | || | || | | | ||
TCCTTTAATCGGGTCGTCTATTGAGGCGGCTACTGGTGTTGTGTACAATATCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACAAAGTCTCTCAGgtgcgtgtaatatttcttgccattgtcttgaactgtctttgaagaagtatgatatagcactgtaatatgttaagtcgaaaaacttaagatgctattatcacgatcatactccacaatttagggctactggaattatgtggcctaggtgattgaagtgctttgttttgaccaatgcttatgcacgttttgcag
upper sequence: AT5G55280.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA08G43500.1 (Glycine max), 5'ss of exon 6
TCCATTGATCGGATCATCCATACAATCAGCTACTGGTGTCGTCTACAACATCACTGGTGGAAAAGACATAACTTTGCAGGAAGTGAACCGAGTATCACAGgtac---ggtatttt--tgtcttggtttactcggctttgtttcaattgggtatac-actgtattataatgcagtcttctcatgttttgggggggttttgcag---------
||| || || || ||||| || || ||||||||||| || || || ||||| ||||| ||||||||||||||| | |||||||||||| |||| || ||||||| || ||||| || | || | | || ||| || | | | || || || | | || |||||| || |
TCCTTTAATTGGCTCATCTATTCAGTCAGCTACTGGGGTAGTGTATAACATTACTGGAGGAAAAGACATAACTCTACAGGAAGTGAACAGAGTGTCTCAGgtacctcggaattttattggcagaaagaacatttcagtattctttttgatcttatgaatttgttgcaa-acatttgtatcctgttttcaaaa--cttcataactgttgtag
upper sequence: AT5G55280.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA18G10030.1 (Glycine max), 5'ss of exon 6
TCCATTGATCGGATCATCCATACAATCAGCTACTGGTGTCGTCTACAACATCACTGGTGGAAAAGACATAACTTTGCAGGAAGTGAACCGAGTATCACAGgtac---ggtatttttgtcttggtttactcggctttgt-ttcaattgggtatac-actgtattataatgcagtcttctcatgttttgggggggttttgcag----------
|| || || || || || || || ||||||||||| || || || ||||| ||||| || | |||||||||| |||| ||||||||| |||| || ||||||| | ||||| | | | | | | ||| ||| || | | | || | | || | | || |||||| || |
-CCTTTAATTGGCTCTTCTATTCAGTCAGCTACTGGAGTAGTGTATAACATTACTGGGGGGAGAGACATAACTCTGCAAGAAGTGAACAGAGTGTCTCAGGtacttaagaattttattgtcagaaggaacatttcagcattcttttgatcttatgaatttgttgtga-acatttgtatcctgttttcaaaa--cttcataactgctgtagg
upper sequence: AT5G55280.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA14G02110.1 (Glycine max), 5'ss of exon 5
TCCATTGATCGGATCATCCATACAATCAGCTACTGGTGTCGTCTACAACATCACTGGTGGAAAAGACATAACTTTGCAGGAAGTGAACCGAGTATCACAGgtacggtatttttgtcttggtttactcgg------ctttgttt--caattgggtatacac-tgtattataatgcagtcttctcatgttttgggggggttttgcag
||| || || |||||||| || || ||||||||||| || || || || || ||||| ||||| |||||||| |||||||||||||| | || || |||||| | ||||| || || ||||||| | ||| | | | | || || | | | | |||||| | |||||
TCCTTTAATTGGATCATCTATTCAGTCAGCTACTGGGGTAGTGTATAATATTACTGGAGGAAAGGACATAACCCTGCAGGAAGTGAACAGGGTTTCTCAGgtatttaaagattgtcaccactttcttaagaaacattttgtttttcctttgatcttgtaaatttgttgcaaactaaccatataatgtttcttga---ttttgt--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|86039265|gb|DR335020.1|DR335020EST: TCACTGGTGGAAAAGACATAACTTTGCAGGAAGTGAACCGAGTATCACAG GTCGTGACAAGTTTGGCAGACCCATCGGCCAACATCATATTTGGAGCTGTT
genomic: TCACTGGTGGAAAAGACATAACTTTGCAGGAAGTGAACCGAGTATCACAGgtacggtatt ... ggttttgcagGTCGTGACAAGTTTGGCAGACCCATCGGCCAACATCATATTTGGAGCTGTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TCCATTGATCGGATCATCCATACAATCAGCTACTGGTGTCGTCTACAACATCACTGGTGGAAAAGACATAACTTTGCAGGAAGTGAACCGAGTATCACAGgtacggtatttttgtcttggtttactcggctttgtttcaattgggtatacactgtattataatgcagtcttctcatgttttgggggggttttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA