Sequence
atgc intronic sequence ATGC exonic sequencegtatgttaaatgtgtggcattttcttttctttaccggatttgggttttattgcttcttgtatgaccataaccatctttgagttgttgcttcagTTGTTTGCAGATCGCAAGGGCTTTTGGAGCCTCGGATATCATTGCTGTGGATGTTCAGGATGATAAATTACAGAAGGCCAAGACACTTGGTGCTACTCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G63620.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G63620.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G00740.1 (Glycine max), 3'ss of exon 5
-gtat-gttaaatgtgtggcattttcttttctttaccggatttgggttttattgcttcttgtatgaccataaccatctttga-gttgttgc----ttcagTTGTTTGCAGATCGCAAGGGCTTTTGGAGCCTCGGATATCATTGCTGTGGATGTTCAGGATGATAAATTACAGAAGGCCAAGACACTTGGTGCTACTCAT
|||| ||| | | |||| | | || || | | | | | ||||| ||| | | | ||| | || | | | ||||||||| ||||| || || || ||||| ||||| ||||| |||||||||||||| | |||||| || ||||||| || |||||| |||||||||||||
ggtatagttgggaatcagtagatttcctatgttgactgtgtatcagctctattggctctaatcaaattgtgtttccttttaacattatcacccattccagTTGTTTACAGATAGCTAGAGCCTTTGGTGCCTCAGATATAATTGCTGTGGATGTACGGGATGAAAAGCTACAGAAAGCAAAGACATTTGGTGCTACTCAC
upper sequence: AT5G63620.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G33140.1 (Glycine max), 3'ss of exon 5
-gtatg-ttaaatgtgtggcattttcttttctttaccggatttgggttttattgcttcttgtatgaccata-accatctttgagttgttgc----ttcagTTGTTTGCAGATCGCAAGGGCTTTTGGAGCCTCGGATATCATTGCTGTGGATGTTCAGGATGATAAATTACAGAAGGCCAAGACACTTGGTGCTACTCAT
|||| || | |||| | | || ||| | | | | ||||| ||| | | | | | | || |||| | | ||||||||| ||||| || || || ||||| ||||| ||||| |||||||||||||| | |||||| || ||||||| || |||||| |||||||||||||
ggtataattgggaaccagtagatttcctatgttgaccatgtatcagctctattggctctaatcaaattgtgtatccttttaactttgtcacccattccagTTGTTTACAGATAGCTAGAGCCTTTGGTGCCTCAGATATAATTGCTGTGGATGTACGGGATGAAAAGCTACAGAAAGCAAAGACATTTGGTGCTACTCAC
upper sequence: AT5G63620.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0031g03150.t01 (Vitis vinifera), 3'ss of exon 5
------gta-tgttaaatgtgtggcattttcttttctttaccggatttgggttttattgcttcttgtatgaccataaccatctttgagttgttgcttcagTTGTTTGCAGATCGCAAGGGCTTTTGGAGCCTCGGATATCATTGCTGTGGATGTTCAGGATGATAAATTACAGAAGGCCAAGACACTTGGTGCTACTCAT
||| | ||||||| | ||||| || | | | | | | | | | | | ||| | || | | |||| |||||| |||||||| ||| |||| ||||| ||||| ||||| ||||||||||||||| | ||||| ||| | |||| || ||| ||||||| | ||||
gttcttgtaattttaaatgcaagattgtttctgttaatccacaattccttttgacgtggatctctttttcatcattatgattaaaaattacatgctccagTTGCTTGCAGATAGCACGGGCATTTGGTGCCTCTGATATTATTGCTGTGGATGTTAATGATGAAAAACTGGAGAATGCGAAGGTTTTTGGTGCCAGTCATMapped 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|86085730|gb|DR381489.1|DR381489EST: CGTCCTGGAGATTCTA-TGCAGTTATTGGAATTGGTGGTGTTGGCTCCAG TTG-TTGCAGATCGCAA-GGCTTTTGGAGCCTCGGATATAATTGCTGTGGA
genomic: CGTCCTGGAGATTCTATTGCAGTTATTGGAATTGGTGGTGTGGGCTCCAGgtatgttaaa ... gttgcttcagTTGTTTGCAGATCGCAAGGGCTTTTGGAGCCTCGGATATCATTGCTGTGGA
EST:
gi|164087198|gb|ES016049.1|ES016049EST: CGTCCTGGAGATTCTATTGCAGTTATTGGAATTGGTGGTGTTGGCTCCAG TTGTTTGCAGATCGCAAGGGCTTTTGGAGCCTCGGATA
genomic: CGTCCTGGAGATTCTATTGCAGTTATTGGAATTGGTGGTGTGGGCTCCAGgtatgttaaa ... gttgcttcagTTGTTTGCAGATCGCAAGGGCTTTTGGAGCCTCGGATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgggttttattgcttcttgtatgaccataaccatctttgagttgttgcttcagTTGTTTGCAGATCGCAAGGGCTTTTGGAGCCTCGGATATCATTGCTGTGGATGTTCAGGATGATAAATTACAGAAGGCCAAGACACTTGGTGCTACTCAT
ccataac putative branch site (score: 3)
ttgcttc putative PPT
ttttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttaaatgtgtggcattttcttttctttaccggatttgggttttattgcttcttgtatgaccataaccatctttgagttgttgcttcagTTGTTTGCAGATCGCAAGGGCTTTTGGAGCCTCGGATATCATTGCTGTGGATGTTCAGGATGATAAATTACAGAAGGCCAAGACACTTGGTGCTACTCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG