Sequence
atgc intronic sequence ATGC exonic sequenceCATGGAAGGTATTGTTGAGCAAGTCCGTGATGGCAGCACCATTCGGGTTTATCTTCTTCCGGAATTTCAGTTTGTTCAAGTATTTGTTGCTGGACTCCAGgtatgttatcttgtttccttgtttttactgcgtgaggagttgacattttaatttcatggtgtaagagtgctggaaattttctatgtag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G61780.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G61780.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA05G33320.1 (Glycine max), 5'ss of exon 6
CATGGAAGGTATTGTTGAGCAAGTCCGTGATGGCAGCACCATTCGGGTTTATCTTCTTCCGGAATTTCAGTTTGTTCAAGTATTTGTTGCTGGACTCCAGgtatgttatcttgtttccttgtttttactgcgtgaggagttgacattttaatttcatggtgtaagagtgctggaaattttctatgtag-
||||||||| ||||||||||| || || |||||||| ||| | || || ||| | || || || ||||||||||| ||||| |||||||||||| | ||||||||| || | | || | || || || | | |||| | | | | ||| | | || |
CATGGAAGGAATTGTTGAGCAGGTTCGCGATGGCAGTACCCTGCGTGTCTATTTGCTCCCAGAGTTTCAGTTTGTCCAAGTTTTTGTTGCTGGAATTCAGgtatgt-atatatcataaatgctgtttcta---------tttctaccct--tttctaagcatgcaaataatggttttcctttaaattag
upper sequence: AT5G61780.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA08G00910.1 (Glycine max), 5'ss of exon 6
CATGGAAGGTATTGTTGAGCAAGTCCGTGATGGCAGCACCATTCGGGTTTATCTTCTTCCGGAATTTCAGTTTGTTCAAGTATTTGTTGCTGGACTCCAGgtatgt----tatcttgtttccttgtttttactgcgtgaggagttgacattttaatttcatggtgtaagagtgctggaaattttctatgtag
||||||||| ||||||||||| | || |||||||| ||| | || || ||| | || || |||||||||||||| ||||| |||||||||||| | ||||||| | || | | | | | ||| ||| | || || | | | | | | ||| |
CATGGAAGGAATTGTTGAGCAGGCTCGCGATGGCAGTACCCTACGCGTCTATTTGCTCCCAGAATTTCAGTTTGTCCAAGTTTTTGTTGCTGGAATTCAGgtatatatcataaatgctgttcctatttctaccctttcctaagcatgcaaataattgttttcctttaaattag-------------------
upper sequence: AT5G61780.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA06G17050.4 (Glycine max), 5'ss of exon 6
CATGGAAGGTATTGTTGAGCAAGTCCGTGATGGCAGCACCATTCGGGTTTATCTTCTTCCGGAATTTCAGTTTGTTCAAGTATTTGTTGCTGGACTCCAGgtatgttatcttgtttccttgtttttactgcgtgaggagttgacattttaatttcatggtgtaa--gagtgctggaaattttctatgtag
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CATGGAGGCAGTTGTTGAGCAGGTTCGTGATGGCAGTACACTCCGAATCTATTTGCTCCCGGAGTTTCAGTTTGTTCAAGTTTTTGTTGCTGGAATTCAGgtatgt-gtcaaatgctgttgctattgctatttg-----ctaccgtctttattcacacatgcagctaattgttttacctttaccccag--
upper sequence: AT5G61780.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA04G38010.1 (Glycine max), 5'ss of exon 6
CATGGAAGGTATTGTTGAGCAAGTCCGTGATGGCAGCACCATTCGGGTTTATCTTCTTCCGGAATTTCAGTTTGTTCAAGTATTTGTTGCTGGACTCCAGgtatgttatcttgtttccttgtttttactgcgtgaggagttgacattttaatttcatggtgtaa--gagtgctggaaattttctatgtag
|||||| | |||||||||| || ||||||||||| || | || | ||| | || ||||| ||||||||||| ||||| |||||||||||| | ||||||||| | || ||| | || || || | ||| || ||| || | | || | | ||| |
CATGGAGGCAGTTGTTGAGCAGGTTCGTGATGGCAGTACACTCCGTATCTATTTGCTCCCGGAGTTTCAGTTTGTCCAAGTTTTTGTTGCTGGAATTCAGgtatgt-gccaaattctgttgctattgctatttg-----ctaccatctttattcgcacatgcagctaattgttttacctttaccgcag--
upper sequence: AT5G61780.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv00s0283g00020.t01 (Vitis vinifera), 5'ss of exon 6
CATGGAAGGTATTGTTGAGCAAGTCCGTGATGGCAGCACCATTCGGGTTTATCTTCTTCCGGAATTTCAGTTTGTTCAAGTATTTGTTGCTGGACTCCAGgtatgttatcttgtttccttgtttttactgcgtgagg-agttgacattttaatttcatggtgtaagagtgctgga--aattttctatgtag----------------
|||| |||||||||||||||| || || |||||||| ||||| ||||| ||| | ||||| ||||| |||||||||||||| |||||||| ||| ||||||||| | ||| ||| | | |||| || ||| | ||||| || ||| ||| ||| | | | |||| | |||
CATGCAAGGTATTGTTGAGCAGGTTCGAGATGGCAGTACCATCCGGGTCTATTTGCTTCCTGAATTCCAGTTTGTTCAAGTGTTTGTTGCAGGAATCCAGgtat-tgatccgcttttc--atcagcactgtactagttagtggtgattttgata----ggtataatggtgatatatcagttttattcatagttgttgactcaggaaa
upper sequence: AT5G61780.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv14s0068g00720.t01 (Vitis vinifera), 5'ss of exon 5
CATGGAAGGTATTGTTGAGCAAGTCCGTGATGGCAGCACCATTCGGGTTTATCTTCTTCCGGAATTTCAGTTTGTTCAAGTATTTGTTGCTGGACTCCAGgtatgttatct-tgtttccttgtttttactgcgtgaggagttgacattttaatttcatggtgtaagagtgctggaaattttctatgtag-------------------------------------
||| | || |||||||||||||| |||||||| || || | || |||||| | ||||| || |||||||||||||| || |||||||| ||| |||||||| | |||| | | || || ||| | | | || | | | || || | | || || ||| | | | |
TATGCAGGGCATTGTTGAGCAAGTTCGTGATGGAAGTACAGTCCGAGTTTATTTGCTTCCAGAGTTTCAGTTTGTTCAGGTTTTTGTTGCCGGAATCCAGgtaagacatctgcatgttattattattattattt--tgggtctatttgtgaagggtattgcaatggggt-ttgcctattgttttggcacatatctcaatttccataattctcttgtggtaaattagMapped 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|116396661|gb|EG439253.1|EG439253EST: ATCTTCTTCCGGAATTTCAGTTTGTTCAAGTATTTGTTGCTGGACTCCAG GCTCCATCGATGGGAAGGAGACAATCAACACAAGAAGCTGTCGTTGATCCT
genomic: ATCTTCTTCCGGAATTTCAGTTTGTTCAAGTATTTGTTGCTGGACTCCAGgtatgttatc ... ttctatgtagGCTCCATCGATGGGAAGGAGACAATCAACACAAGAAGCTGTCGTTGATCCT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CATGGAAGGTATTGTTGAGCAAGTCCGTGATGGCAGCACCATTCGGGTTTATCTTCTTCCGGAATTTCAGTTTGTTCAAGTATTTGTTGCTGGACTCCAGgtatgttatcttgtttccttgtttttactgcgtgaggagttgacattttaatttcatggtgtaagagtgctggaaattttctatgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA