Sequence
atgc intronic sequence ATGC exonic sequence...atatagactaagaatgacagggaagtctgggttgggtgtggttatattaactggttgagttgggggatctttttccgggtttcttgtttggtaattgaagGGCCATGTTTGGGAGCGGGGGGTACGAGGTGGGATCAAAGAGACAAAGAATGATGCAATCAAATCCCTACTTGGCAGTTGGCACTGGACCTACCAGCTTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G66010.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G66010.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G22290.1 (Glycine max), 3'ss of exon 1
-atatagactaagaatgacagggaagtctgggttgggtgtggttatattaactg--gttgagttgggggatctttttccgggtttcttgtttggtaatt-gaagGGCCATGTTTGGGAGCGGGGGG------------TACGAGGTGGGATCAAAGAGACAAAGAATGATGCAATCAAATCCCTACTTGGCAGTTGGCACTGGACCTACCAGCTTT
|| | | |||| | | ||||| | |||||||| ||| | ||||||| ||||||| ||||||| |||| ||| || ||| |||| ||||||| ||||| || ||||||||| |||||||| || ||||||||||||||||||||| |||| ||||| ||||| ||||| ||| |||
aattaaaattaagtgtca-ggggaaaacaaggttgggtttggctttattaacgtatgttgagt-gggggatgttttgttt--ttttgggtatggaaatttgaagGGCAATGTTGGGAAGCGGGGGGGTTTCGGACGGGTACGAGGTTGGCTCAAAGAGACAAAGAATGATGGAATCCAATCCATACTTCGCAGTGAGCAGCGGA------------
upper sequence: AT5G66010.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G33090.1 (Glycine max), 3'ss of exon 1
-atatagactaagaatga----cagggaagtctgggttgggtgtggttatattaact--ggttgagttgggggatctttttccgggtttcttgtttggtaattgaagGGCCATGTTTGGGAGCGGGGGG------------TACGAGGTGGGATCAAAGAGACAAAGAATGATGCAATCAAATCCCTACTTGGCAGTTGGCACTGGACCTACCAGCTTT
||| | ||| | | | ||||||| | ||||||||| ||| | ||||||| ||||||| ||||||| ||||| |||| | | | ||||||||| ||||| || ||||||||| |||||||| || ||||||||||||||||||||| |||| ||||| ||||| ||||| ||| |||
aataggaattaaaattaagtgtcagggaaaacagggttgggtttggctttattaacgtatgttgagt-gggggatttttttttgggtatg------gaaatttgaagGGCAATGTTGGGAAGCGGGGGGGTTTCAGACGGGTACGAGGTTGGCTCAAAGAGACAAAGAATGATGGAATCCAATCCATACTTCGCAGTGAGCAGCGGA------------
upper sequence: AT5G66010.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv04s0044g00080.t01 (Vitis vinifera), 3'ss of exon 1
-atatagactaagaatgacagggaagtctgggttgggtgtggttatattaactggttgagttgggggatctttttccgggtttcttgtttggtaattgaagGGCCATGTTTGGGAGCGGGGGG------------TACGAGGTGGGATCAAAGAGACAAAGAATGATGCAATCAAATCCCTACTTGGCAGTTGGCACTGGACCTACCAGCTTT
||| |||| || |||| || |||||||||| ||||| ||||||| |||||||| ||||||| ||||| | | ||| | | |||||||||||| ||||| || ||||||||| |||||| | || ||||||||||||||||||||| |||||||||||||||| ||||| ||| |
aataaagacattaggtgtcaggaaaacgtgggttgggtttggttttattaacaggttgagt-gggggattttttttctgttttgggtatggataattgaagGGCAATGTTGGGAAGCGGGGGGGTTTCGGACGGGTACGAGATCGGCTCAAAGAGACAAAGAATGATGGAATCAAATCCCTACTTCGCAGTGAGCAGCAGT------------Mapped 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|164216990|gb|ES029574.1|ES029574EST: CGTGGTCGAAAACGAAGACTTTGGCGGCAGGTCATGTACGGATCTAGGGG GGCCATGTTTGGGAG
genomic: CGTGGTCGAAAACGAAGACCTTGGCGGCAGGTCATGTACGGATCTAGGGGgtatgtattc ... gtaattgaagGGCCATGTTTGGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attaactggttgagttgggggatctttttccgggtttcttgtttggtaattgaagGGCCATGTTTGGGAGCGGGGGGTACGAGGTGGGATCAAAGAGACAAAGAATGATGCAATCAAATCCCTACTTGGCAGTTGGCACTGGACCTACCAGCTTT
tattaac putative branch site (score: 1)
atcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatagactaagaatgacagggaagtctgggttgggtgtggttatattaactggttgagttgggggatctttttccgggtttcttgtttggtaattgaagGGCCATGTTTGGGAGCGGGGGGTACGAGGTGGGATCAAAGAGACAAAGAATGATGCAATCAAATCCCTACTTGGCAGTTGGCACTGGACCTACCAGCTTT
- - - -ctaagaa
- - - - - - - - - - - - - - - - - ggtgtgg