Sequence
atgc intronic sequence ATGC exonic sequence...tggcggatgatcctgctccatacttattttaatgaacttgtgtacatttacaataatcctaatgagcttgaactctccgttttattgaaattttctccagGATATTGAATTGTCAAAGGAAATCAACGAGTCATTCAAACAATCTTCCCAGGCCAGAACAAAACTGCCATCGGGAATTGAGATGAGTGTCCACGTTTTAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G46210.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G10180.1 (Glycine max), 3'ss of exon 9
-tggcggatgatcctgctccatacttattttaatgaacttgtgtacatttacaataatcctaatgagcttgaactctccgttttattgaaattttctccagGATATTGAATTGTCAAAGGAAATCAACGAGTCATTCAAACAATCTTCCCAGGCCAGAACAAAACTGCCATCGGGAATTGAGATGAGTGTCCACGTTTTAA
| | | | | | || ||||| | | || || | ||| | | ||| || || | | | | ||||| |||||||| ||||| ||||| || |||||||||||||| || || ||||| || ||||||| |||| || ||||| |||||||| || |||||||
ttattgttttgtgtgatgatctgacaaacttcatgaattattata-gttcttattaacatcacagcttctgacaactatgtctcaaattgttgtgaatcagGACATTGAATTATCAAAAGAAATAAATGAGTCATTCAAACAGTCATCACAGGCGAGGTCAAAACTTGCATCAGGGATTGAAATGAGTGTTCATGTTTTAA
upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA05G27240.1 (Glycine max), 3'ss of exon 9
---tggcggatgatcctgctccatacttattttaatgaacttgtgtacatttacaataatcctaatgagcttgaactctccgttttattgaaattttctccagGATATTGAATTGTCAAAGGAAATCAACGAGTCATTCAAACAATCTTCCCAGGCCAGAACAAAACTGCCATCGGGAATTGAGATGAGTGTCCACGTTTTAA
| | ||||| ||||| | | || ||||| | | || || | ||| | | ||| || | | | | | | ||||| |||||||| ||||| ||||| || || ||||||||||| || || ||||| || ||||||| |||| || ||||| |||||||| || |||||||
atcttttgaatgatgatgctc--tgacaaacttcatgaattattata-gttcttattaacatcacagcttctgacaactacatctcaaatttttgtaaatcagGACATTGAATTATCAAAAGAAATAAATGATTCATTCAAACAGTCATCACAGGCGAGGTCAAAACTTGCATCAGGGATTGAAATGAGTGTTCATGTTTTAA
upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 9
--tggcggatgatcctgc-----tccatacttattttaatgaacttgtgtacatttacaataatcctaatgagcttgaactctccgttttattgaaattttctccagGATATTGAATTGTCAAAGGAAATCAACGAGTCATTCAAACAATCTTCCCAGGCCAGAACAAAACTGCCATCGGGAATTGAGATGAGTGTCCACGTTTTAA
|| ||| || ||||||| || || || |||| | ||| | ||| | ||| | || | | | | || | || ||| | ||||| |||||||| || || || || || ||||| ||||||||||| || || ||||| |||||||| ||| | ||||||||||||||||| || || ||||
aatgttatatgggtttgtaaatttccatacaagctt--at-aatttgtttgcatagataatgtt--aaattattttttatgcaacatcttgt--aacatttttacagGACATTGAATTATCTAAAGAGATAAATGAGTCCTTCAAACAATCATCGCAAGCCAGGACAAAACTTCCAACAGGAATTGAGATGAGTGTTCATGTCTTAA
upper sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ14633 (Selaginella moellendorffii), 3'ss of exon 9
tggcggatgatcctgctccatacttattttaatgaacttgtgtacatttacaataatcctaatgagcttgaactctccgttttattgaaattttctccagGATATTGAATTGTCAAAGGAAATCAACGAGTCATTCAAACAATCTTCCCAGGCCAGAACAAAACTGCCATCGGGAATTGAGATGAGTGTCCACGTTTTAA
| | ||| | ||| | | ||| ||| | || | | ||||| | |||||| |||||| | |||| |||||| |||||||| || || ||||| || || ||||| ||||| || ||| | ||||||||||||| ||| || || || |
-------------------------------gtacgcctgtatttttttgta-----tccaatcagcat---ctttgccgagcattgag----ttcccagGACATTGAACTTTCAAGGGAAATAAACGAGTCCTTTAAGCAATCCTCACAAGCCAGGACAAAGCTACCAGCTGGAATTGAGATGAATGTGCATGTGTTGAMapped 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|164207711|gb|ES016950.1|ES016950EST: AGACTGAGTGTGGTAGCCAGTTTACAAACAAGCTCGAAGGGATGTTCAAG GATATTGAATTGTCAAAGG
genomic: AGACTGAGTGTGGTAGCCAGTTTACAAACAAGCTCGAAGGGATGTTCAAGgtatcctttc ... ttttctccagGATATTGAATTGTCAAAGG
EST:
gi|125297081|gb|EL311166.1|EL311166EST: AGACTGAGTGTGGTAGCCAGTTTACAAACAAGCTCGAAGGGATGTTCAAG GATATTGAATTGTCAAAGGAAATCAACGAGTCATTACAAA
genomic: AGACTGAGTGTGGTAGCCAGTTTACAAACAAGCTCGAAGGGATGTTCAAGgtatcctttc ... ttttctccagGATATTGAATTGTCAAAGGAAATCAACGAGTCATT-CAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttacaataatcctaatgagcttgaactctccgttttattgaaattttctccagGATATTGAATTGTCAAAGGAAATCAACGAGTCATTCAAACAATCTTCCCAGGCCAGAACAAAACTGCCATCGGGAATTGAGATGAGTGTCCACGTTTTAA
tcctaat putative branch site (score: 2)
ttttctcc putative PPT
ttttattgaaattttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggcggatgatcctgctccatacttattttaatgaacttgtgtacatttacaataatcctaatgagcttgaactctccgttttattgaaattttctccagGATATTGAATTGTCAAAGGAAATCAACGAGTCATTCAAACAATCTTCCCAGGCCAGAACAAAACTGCCATCGGGAATTGAGATGAGTGTCCACGTTTTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - -ccatact
- - - - - - - - - - - - - - - - - - - - - - - - -acaataa