Sequence
atgc intronic sequence ATGC exonic sequencegtaaggcaaaactcaattctctcttgtatttgccttccactaatggtgtgatgcttatgggtgagtctcctttagGCCCATTTAGCTCCAGGAAGAAAGTTCGACTTCCAGAAGTATATCAAAAGATCATTGGAAGACGATTTCAAGGTGGTAGTTGGAATAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G65970.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G65970.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os05g09050.1 (Oryza sativa), 3'ss of exon 3
------gtaaggcaaaactcaattctctctt-gtatttgccttccactaatggtgtga------------tgcttatgggtgagt-------ctcctttagGCCCATTTAGCTCCAGGAAGAAAGTTCGACTTCCAGAAGTATATCAAAAGATCATTGGAAGACGATTTCAAGGTGGTAGTTGGAATAAG
|| ||| | || ||||| | || ||| | | | || | | ||||| || ||| | | | ||| ||||||||||| || || |||||||| ||||||||||| |||||| | || | || |||||||||||||| | || ||||| ||
gtgagtacaacacaagcttggatgatctctcagcatctgcgtgcaaaacatattatatcccagataatcttgcttttgagtggttaataatgtttttgcagGTTCATTTAGCTCCTGGCAGCAAGTTCGATTTCCAGAAGTACATCAAACGGTCTCTCGAGGACGATTTCAAGGTCATTGTCGGAATCAG
upper sequence: AT5G65970.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA01G36170.1 (Glycine max), 3'ss of exon 7
---------------gtaaggcaaaactcaattctctct----tgtatttgccttccactaatggtgtgatgcttatgggtgagtctcctttagGCCCATTTAGCTCCAGGAAGAAAGTTCGACTTCCAGAAGTATATCAAAAGATCATTGGAAGACGATTTCAAGGTGGTAGTTGGAATAAG
|| || | || | |||| | || |||| |||| | | | ||| ||||| | | | ||| ||| | ||||| ||||| || || | ||||| |||||||||||||||||||| ||||| || ||||||||||| || ||| | ||
gtaagtcaacccttcttatggaacaattatgttcttttcacagtggatttaccttatattgacagtgaa----ttatgaatatatat-----agGTCCACCTGGCTCCTGGAAGTAAATTTAATTTCCAAAAGTATATCAAAAGATCATTAGAAGATGACTTCAAGGTGGTCGTGGGAGTTAG
upper sequence: AT5G65970.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA16G21510.1 (Glycine max), 3'ss of exon 7
gtaaggcaaaactcaattctctcttgtatttgccttccactaatggtgtgatgcttatgggtgagtctcctttagGCCCATTTAGCTCCAGGAAGAAAGTTCGACTTCCAGAAGTATATCAAAAGATCATTGGAAGACGATTTCAAGGTGGTAGTTGGAATAAG
|| || | | || | | ||| | | | | | ||| || | | |||| ||| | ||||| ||||| || || ||||||| ||||||||||||||||| ||||| || || |||||||| || |||||| | ||
gtgagtcctactccacaagacatgttcttttaacactgaattttccttcctcttttacaa-tgcattatgtgtagGTCCACCTGGCTCCTGGAAGTAAATTTAACTTCCAAAAGTATATCAAAAGATCCTTGGAGGATGACTTCAAGGTAGTTGTTGGAGTCAG
upper sequence: AT5G65970.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA09G32920.1 (Glycine max), 3'ss of exon 3
gtaaggcaaaactcaattctctcttgtatttgccttccactaatggtgtgatgcttatgggtgagtctcctttagGCCCATTTAGCTCCAGGAAGAAAGTTCGACTTCCAGAAGTATATCAAAAGATCATTGGAAGACGATTTCAAGGTGGTAGTTGGAATAAG
|| || | | || | | || | | | | | | | | || | | |||| || | ||||| ||||| || || ||||||| ||||||||||||||||| ||||| || || |||||||| || |||||| | ||
gtgagtcctactccacaagacatgttctttaacactgaatttgcttccctcttttgacag-tgcattatgtgtagGTTCACCTGGCTCCTGGAAGTAAATTTAACTTCCAAAAGTATATCAAAAGATCCTTGGAGGATGACTTCAAGGTAGTTGTTGGAGTCAG
upper sequence: AT5G65970.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA11G09270.1 (Glycine max), 3'ss of exon 7
-----------------gtaaggcaaaactcaattctctct-tgtatttgccttccactaatggtg--tgatgcttatgggtgagtctcctttagGCCCATTTAGCTCCAGGAAGAAAGTTCGACTTCCAGAAGTATATCAAAAGATCATTGGAAGACGATTTCAAGGTGGTAGTTGGAATAAG
|| ||| | || ||| || |||| |||| | || || || ||||| || | | ||| ||| | ||||| ||||| || | | ||||| |||| ||||||||||||||| ||||| || ||||||||||| || ||| | ||
gtgagtcaacacttcttatagaacaatatgttcttttcttagtggatttacctttcttctatattgactgtgaattatgtgtatatat-----agGTCCACCTGGCTCCTGGAAGTAAATATAATTTCCAAAAGTTTATCAAAAGATCATTAGAAGATGACTTCAAGGTGGTTGTGGGAGTCAGMapped 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|125210606|gb|EL225560.1|EL225560EST: AGGACTGACTACTTAACTCTGCGCCATGGCTTCATCGCT GCCCATTTAGCTCCAGGAAGAAAGTTCGACTTCCAGAAGTATATCAAAAGA
genomic: AGGACTGACTACTTAACTCTGCGCCATGGCTTCATCGCTgtaaggcaaa ... tctcctttagGCCCATTTAGCTCCAGGAAGAAAGTTCGACTTCCAGAAGTATATCAAAAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcttgtatttgccttccactaatggtgtgatgcttatgggtgagtctcctttagGCCCATTTAGCTCCAGGAAGAAAGTTCGACTTCCAGAAGTATATCAAAAGATCATTGGAAGACGATTTCAAGGTGGTAGTTGGAATAAG
cactaat putative branch site (score: 2)
tctccttt putative PPT
tattt TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggcaaaactcaattctctcttgtatttgccttccactaatggtgtgatgcttatgggtgagtctcctttagGCCCATTTAGCTCCAGGAAGAAAGTTCGACTTCCAGAAGTATATCAAAAGATCATTGGAAGACGATTTCAAGGTGGTAGTTGGAATAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA