Sequence
atgc intronic sequence ATGC exonic sequenceTGAATTTTACGAAGGCTTACATATGAAAGTGGAACAGCAAATTCCTATGCTTTTGGTGGAGAGATCAGCTCTAAACGAAGCTATGGAAGGAGAGAAACACgtaaaacctctatatcttattgatactatgtttatactctctctttctctctcgctcatttgtttcaacctacttctatctaattttgctgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G36860.1 |
intron # | 8 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: LOC_Os06g08400.1 (Oryza sativa), 5'ss of exon 8
TGAATTTTACGAAGGCTTACATATGAAAGTGGAACAGCAAATTCCTATGCTTTTGGTGGAGAGATCAGCTCTAAACGAAGCTATGGAAGGAGAGAAACACgtaaaacctctatatcttattgatactatgtttatactctctctttctctctcgctcatttgtttcaacctacttctatctaattttgctgcag
|||||||| |||||| || |||||||||||||||| ||| |||| ||||| | || || ||| ||| |||| ||||| |||||||||||||| ||| | | | || || | ||| || | || | | | || | || || | | || | | | || |
GGAATTTTATGAAGGCCTAAATATGAAAGTGGAACAACAAGTTCCCTTGCTTCTTGTAGAAAGACAGGCTTTAAATGAAGCCATGGAAGGAGAGAAGACTgtatgttgaccaaagctggacaat-ccatgattctcctgtttttcactat---actaatgttagtaaatattttgtttcctgtggaaaccag--
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GRMZM2G017845_T02 (Zea mays), 5'ss of exon 7
TGAATTTTACGAAGGCTTACATATGAAAGTGGAACAGCAAATTCCTATGCTTTTGGTGGAGAGATCAGCTCTAAACGAAGCTATGGAAGGAGAGAAACACgtaaaacctctatatcttattgatactatgtttatactctctctttctctctcgctcatttgtttcaacctacttctatctaattttgctgcag-
|||||||||||||| | ||||||||||||||||||| ||||| ||||| |||| ||| || |||| | || ||||| |||||||||||||| ||| |||| | | | | ||| || | ||| | | || || | | | | || | ||| ||| | | |
GGAATTTTACGAAGGACTGAATATGAAAGTGGAACAGCAGGTTCCTCTGCTTCTGGTCGAGCGACAAGCTTTGAATGAAGCCATGGAAGGAGAGAAGGCTgtatgtttactatgctcaa--aacccaaaattt---ctttttctaccccactgtactgttagctgtagctattttgtttct--tttggataccag
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA01G38640.3 (Glycine max), 5'ss of exon 5
TGAATTTTACGAAGGCTTACATATGAAAGTGGAACAGCAAATTCCTATGCTTTTGGTGGAGAGATCAGCTCTAAACGAAGCTATGGAAGGAGAGAAACACgtaaa-------------acctctatatcttattgatactatgtttatactctctctttctctctcgctcatttgtttcaacctacttctatctaattttgctgcag----
|||||||| ||||| ||| |||||||| |||| ||||||||||||||||| ||||| |||||| |||||| || || |||||||| ||||| || | |||| | || | || | ||| || || || || | | | ||| | || | ||| ||| | | || |
AGAATTTTATGAAGGTTTAAATATGAAATTGGAGCAGCAAATTCCTATGCTCTTGGTTGAGAGACAAGCTCTGAATGAGGCTATGGAGGGAGAAAAGAATgtaagtgtcaatgtgtttaactttccatttcattcatggaatattgttatttctgttctttctagtatcttgacttcgaaatgttcttttatttctcactattgaatgtag
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA16G25750.1 (Glycine max), 5'ss of exon 8
TGAATTTTACGAAGGCTTACATATGAAAGTGGAACAGCAAATTCCTATGCTTTTGGTGGAGAGATCAGCTCTAAACGAAGCTATGGAAGGAGAGAAACACgtaaaacctctatatcttattgatactatgtttatactctctctttctctctcgctcatttgtttcaacctacttctat----ctaattttgctgcag-----------
|| ||||| ||||| ||||||||||| | || |||||| |||| ||||||||||| |||||| ||| || ||||| |||||||| |||||||| | |||| | || | || | | || || | | | |||| | | || || ||| ||| ||||||| |||||| |||
AGAGTTTTATGAAGGTTTACATATGAAGATAGAGCAGCAAGTTCCAATGCTTTTGGTTGAGAGACAAGCACTGAACGAGGCTATGGAGGGAGAGAAGAATgtaag-tgttaatgtttt-caacttccattcttgaattttgccttt-tatttctcttctttacatcatatcccttctattgttctaattatgcattgctttgaatgtag
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA11G06650.2 (Glycine max), 5'ss of exon 4
TGAATTTTACGAAGGCTTACATATGAAAGTGGAACAGCAAATTCCTATGCTTTTGGTGGAGAGATCAGCTCTAAACGAAGCTATGGAAGGAGAGAAACACgtaaa-------------acctctatatcttattgatactatgtttatactctctctttctctctcgctcatttgtttcaacctacttctatctaattttgctgcag----
|||||||| ||||| ||| |||||||| |||| || |||||||||||||| ||||| |||||| ||| || || || |||||||| ||||| || | |||| | || || | ||| || ||| | || | | | ||| | | ||| || | ||| ||| | | || |
AGAATTTTATGAAGGTTTAAATATGAAATTGGAGCAACAAATTCCTATGCTCTTGGTTGAGAGACAAGCGCTGAATGAGGCTATGGAGGGAGAAAAGAATgtaagtgttaatgtgtttaacttcccatttcattcatggaatgctgttatttctattctttctagtgtcc---tgtcgaaatgttcttttatttctcactattgaatgtag
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA12G19010.1 (Glycine max), 5'ss of exon 7
TGAATTTTACGAAGGCTTACATATGAAAGTGGAACAGCAAATTCCTATGCTTTTGGTGGAGAGATCAGCTCTAAACGAAGCTATGGAAGGAGAGAAACACgtaaaacctctatatcttattgatactatgtttatactctctctttctctctcgctcatttgtttcaacctacttctat----ctaattttgctgcag------------
|| ||||| || || ||||||||||| |||| |||||| ||| ||||||||||| |||||| ||| || ||||| |||||||| |||||||| | ||||| | | || || | | | | ||| | | |||| | | || || ||| ||| | |||| || ||||||||||
AGAGTTTTATGAGGGTTTACATATGAAGATGGAGCAGCAAGTTCTGATGCTTTTGGTTGAGAGACAAGCACTGAACGAGGCTATGGAGGGAGAGAAGAATgtaaa---tgttaatgttttcaactttcattctatgttttgccttt-tatttctcttctttacatcataccccttccattgttctaattttgcattgcttttgaatgtag
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA02G06720.2 (Glycine max), 5'ss of exon 8
TGAATTTTACGAAGGCTTACATATGAAAGTGGAACAGCAAATTCCTATGCTTTTGGTGGAGAGATCAGCTCTAAACGAAGCTATGGAAGGAGAGAAACACgtaaaacctctatatcttattgatactatgtttatactctctctttctctctcgctcatttgtttcaacctacttctat----ctaattttgctgcag------------
|| ||||| || || ||||||||||| | || |||||| |||| ||||||||||| |||||| ||| || ||||| |||||||| |||||||| | ||||| | | || | | | | | ||| | | |||| | | || | |||| ||| | |||| || ||||||||||
AGAGTTTTATGAGGGTTTACATATGAAGATAGAGCAGCAAGTTCCGATGCTTTTGGTTGAGAGACAAGCACTGAACGAGGCTATGGAGGGAGAGAAGAATgtaaa---tgttaatgctttcaactttcattctatgttttgccttt-tatttctattatttacatcataccccttccattgttctaattttgcattgcttttgaatgtagMapped 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|86086879|gb|DR382638.1|DR382638EST: TTTTGGTGGAGAGATCAGCTCTAAACGAAGCTATGGAAGGAGAGAAACAC GGACATCATCATTTACCTGAAACTAGAGGACTTTGTTTGTCTGAAGAACAA
genomic: TTTTGGTGGAGAGATCAGCTCTAAACGAAGCTATGGAAGGAGAGAAACACgtaaaacctc ... tttgctgcagGGACATCATCATTTACCTGAAACTAGAGGACTTTGTTTGTCTGAAGAACAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGAATTTTACGAAGGCTTACATATGAAAGTGGAACAGCAAATTCCTATGCTTTTGGTGGAGAGATCAGCTCTAAACGAAGCTATGGAAGGAGAGAAACACgtaaaacctctatatcttattgatactatgtttatactctctctttctctctcgctcatttgtttcaacctacttctatctaattttgctgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA