Sequence
atgc intronic sequence ATGC exonic sequencegtatgtactcataagttttttcttatcttcttagtaaaaaatagcacattgaaccaaaacctcatgtacatgaatgaatatgcagATGACAGCGCTAAAATCTGCTAACAAGGAGCTGAAAGGAATGATGAAAACCGTCAAGATTCAAGATATAGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G04850.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G04850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g01250.1 (Oryza sativa), 3'ss of exon 3
gtatgtactcataagttttttctta--tcttcttagtaaaaaatagcacat--tgaaccaaaacctcatg-tacatgaatgaatat----gcagATGACAGCGCTAAAATCTGCTAACAAGGAGCTGAAAGGAATGATGAAAACCGTCAAGATTCAAGATATAGAT
|||| || ||| | | | | || || | | | |||| ||| | || || ||| |||| | | || ||||||||| || | || | || || || ||||||||||||||||||||||| |||||| || |||||||||||
gtatatagctatagtatactcaagaagttttatttccatgatgttttacatcctgattcccaaacttatgatacaagtgttttcatttgggcagATGACTGCAATGAAGGCAGCCAATAAAGAGCTGAAAGGAATGATGAAAACTGTCAAGCTTGAAGATATAGAT
upper sequence: AT5G04850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G33960.1 (Glycine max), 3'ss of exon 3
---------gtatgtactcataagtt-ttttcttatcttcttagtaaaaaatagcacattgaaccaaaac-----ctcatgtacatgaatgaatatgcagATGACAGCGCTAAAATCTGCTAACAAGGAGCTGAAAGGAATGATGAAAACCGTCAAGATTCAAGATATAGAT
| ||| |||| || | |||| | || | || ||| | | | | ||| | | | | | | | ||||||||||| | || ||||| ||||||||| |||| |||||||||||||| || ||||| ||||| || |||
tcagaaatcggatgacctcaaaaaatattttttcatgctgatataaaatttaaattcgattgtttacaacttgttccttttttcccctttcctttttcagATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT
upper sequence: AT5G04850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G33630.1 (Glycine max), 3'ss of exon 3
-----------gtatgtactcataagttttttcttatcttcttagtaaaaaatagcacattgaaccaaaac----ctcatgtacatgaatgaatatgcagATGACAGCGCTAAAATCTGCTAACAAGGAGCTGAAAGGAATGATGAAAACCGTCAAGATTCAAGATATAGAT
| | | || |||||| | || | || ||| | || | ||| || | | | | | |||||||||| | || ||||| ||||||||| |||| |||||||||||||| || ||||| ||||| || |||
gttttcaaaaatcagatgacctcaatttttttttcatgctgatataaaatttaaattcaattgtttgcaacttttttctttttttcccttccctttttagATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT
upper sequence: AT5G04850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0007g02300.t01 (Vitis vinifera), 3'ss of exon 3
-gtatgtactcataagttttttct---tatcttcttagtaaaaaata---gcacattgaaccaaaacctcatgtacatgaatgaatatgc--------agATGACAGCGCTAAAATCTGCTAACAAGGAGCTGAAAGGAATGATGAAAACCGTCAAGATTCAAGATATAGAT
| | || || ||| ||| | || ||| | | | || | || || | | ||| | ||||| |||||||||| | ||| |||| ||||||||| | |||||||||||||| || || |||||| |||||||||||
aatgtttaatctcttttttattccaaatgcatttttattttgcggttttcattcgtttggctgaagtttctttgaatctaattattatgcttcttttcagATGACAGCTTTGAAAGCTGCAAACAAGGAGTTAAAAGGAATGATGAAGACTGTGAAGATTGAAGATATAGATMapped 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|124812479|gb|EH897345.1|EH897345EST: TTCATTTGCTGCTGAAGGCCTTAAAGATGCTCAACAAACT ACGACAGCGCTAAAATCTGCTAACAAGG
genomic: TTCATTTGCTGCTGAAGGCCTTAAAGATGCTCAACAAACTgtatgtactc ... gaatatgcagATGACAGCGCTAAAATCTGCTAACAAGG
EST:
gi|124974213|gb|EL047788.1|EL047788EST: TTGATCAAGTTTCATTTGCTGCTGAAGGCCTTAAAGATGCTCAACAAACT ATGACAGCGCTAAAATCTG
genomic: TTGATCAAGTTTCATTTGCTGCTGAAGGCCTTAAAGATGCTCAACAAACTgtatgtactc ... gaatatgcagATGACAGCGCTAAAATCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagtaaaaaatagcacattgaaccaaaacctcatgtacatgaatgaatatgcagATGACAGCGCTAAAATCTGCTAACAAGGAGCTGAAAGGAATGATGAAAACCGTCAAGATTCAAGATATAGAT
aaaaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtactcataagttttttcttatcttcttagtaaaaaatagcacattgaaccaaaacctcatgtacatgaatgaatatgcagATGACAGCGCTAAAATCTGCTAACAAGGAGCTGAAAGGAATGATGAAAACCGTCAAGATTCAAGATATAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA