Sequence
atgc intronic sequence ATGC exonic sequencegtagcagaaactttcactagtgataccttttacacatctgcttctgctgcttacactaactttttttttttgtgttgctgcttatatatagGTCAACGAAGCTGATATTGAAGAGTTTGAGGCAAACTACAGGGGATCTGAGTCAGAGAAGAAAGACTTGCTTGAGCTTTTCAACAAGTTTAAGGGTAAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G06910.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G06910.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G32480.1 (Glycine max), 3'ss of exon 4
gtagcagaaactttcactagtgataccttttacac-atctgcttctgctgcttacactaactttttttttttgtgttgctgcttata------tatagGTCAACGAAGCTGATATTGAAGAGTTTGAGGCAAACTACAGGGGATCTGAGTCAGAGAAGAAAGACTTGCTTGAGCTTTTCAACAAGTTTAAGGGTAAAA
| | ||| | ||||| | || | | | || | | | || | | || ||| ||| | |||||| | || |||| | |||||||||||||| |||||||| |||||||| |||||||||| |||||||| || || ||| |||| | | ||| |||| |||||||| |
---gtatttgttttaatatatgatatatggtattctgttttctaatccattgtggtatatttgtgttcatttatgtgg-tgcttaaaatgtgctacagGTGACTGAAGCTGATATTGAGGAGTTTGAAGCAAACTATCGGGGATCTGACTCAGAGAAAAATGATTTGATTGATTTGTACAAGAAGTGCAAGGGTAACA
upper sequence: AT5G06910.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G31080.1 (Glycine max), 3'ss of exon 4
gtagcagaaac--tttcactagtgataccttttacacatctgcttctgctgcttacactaactttttttttttgtgttgctgcttatatatagGTCAACGAAGCTGATATTGAAGAGTTTGAGGCAAACTACAGGGGATCTGAGTCAGAGAAGAAAGACTTGCTTGAGCTTTTCAACAAGTTTAAGGGTAAAA
||| || | | ||| || || |||| | || || ||| || | | || | | | || | |||||||| |||||||||||||| |||||||| |||||||| ||||| ||||| || ||||| || || ||| |||| || | ||| |||| |||||||| |
gtaacatgatccctttttctcccaatgccttatg-gtatacttgtcatctgtgtagctgatatattgtaatatatgcta----------atagGTCACTGAAGCTGATATTGAGGAGTTTGAAGCAAACTATAGGGGGTCTGACTCTGAGAAAAATGATTTGATTGATCTGTACAAGAAGTGCAAGGGTAATA
upper sequence: AT5G06910.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G12350.1 (Glycine max), 3'ss of exon 4
gtagcagaaac-tttcactagtgataccttttacacatctgcttctgctgcttacactaactttttttttttgtgttgctgcttatatatagGTCAACGAAGCTGATATTGAAGAGTTTGAGGCAAACTACAGGGGATCTGAGTCAGAGAAGAAAGACTTGCTTGAGCTTTTCAACAAGTTTAAGGGTAAAA
||| || | ||| || || |||| | || | ||| | | | | | | || | | | | ||| | |||||||| |||||||||||||| || ||||| |||||||| ||||| ||||| ||||| || || ||| |||| || | ||| |||| || ||||| |
gtacatgatccctttttctcccaatgccttgtg---atatacttgtaatctgtgtagctgatatattgtaatatat-gct------aaatagGTCACTGAAGCTGATATTGAGGAATTTGAAGCAAACTATAGGGGGTCTGACATTGAGAAAAATGATTTGATTGATCTGTACAAGAAGTGCAACGGTAATA
upper sequence: AT5G06910.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 4
---gtagcagaaactttcactagtgatacctttta--cacatctgcttctgctgcttacactaactttttttttttg---tgttgctgcttatat-----atagGTCAACGAAGCTGATATTGAAGAGTTTGAGGCAAACTACAGGGGATCTGAGTCAGAGAAGAAAGACTTGCTTGAGCTTTTCAACAAGTTTAAGGGTAAAA
|| || | | || || | || | || | | || || ||| | | | || ||| ||| || |||| | || || ||||||||||||||||| ||||||||||| |||||||| ||||||||||| || ||| |||| || | ||| |||| |||||||| |
gtcatatcattttgccttattatggaaaatttctgatttcacgtaatcctcctatttattttcagactggaaagatgacatgtgaacacttgcattggtagcagGTTACTGAGGCAGATATTGAAGAGTTTGAAGCAAACTACAGAGGATCTGATTCAGAGAAGAATGATTTGATTGACCTGTACAAAAAGTGCAAGGGTAATAMapped 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|19875304|gb|AU236135.1|AU236135EST: GAGATGCGTTTGAGAATTTGCGGGATTTCTTCCGGGACATGTNTAAGAAG GTCAACGAAGCTNATATTTGAAGAGTTTGAGGCA
genomic: GAGATGCGTTTGAGAATTTGCGGGATTTCTTCCGGGACATGTATAAGAAGgtagcagaaa ... ttatatatagGTCAACGAAGCTGATATT-GAAGAGTTTGAGGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgcttctgctgcttacactaactttttttttttgtgttgctgcttatatatagGTCAACGAAGCTGATATTGAAGAGTTTGAGGCAAACTACAGGGGATCTGAGTCAGAGAAGAAAGACTTGCTTGAGCTTTTCAACAAGTTTAAGGGTAAAA
cactaac putative branch site (score: 1)
ttacactaactttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagcagaaactttcactagtgataccttttacacatctgcttctgctgcttacactaactttttttttttgtgttgctgcttatatatagGTCAACGAAGCTGATATTGAAGAGTTTGAGGCAAACTACAGGGGATCTGAGTCAGAGAAGAAAGACTTGCTTGAGCTTTTCAACAAGTTTAAGGGTAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT