Sequence
atgc intronic sequence ATGC exonic sequencegtaagattgtgtatgaattttgttacagatcgcttgggaactaattttaatgtgaaaaccccctcaattttttacgactgtgtgatcagGAATGTGAATCTGAAGGAGCCAATAAAATGATCGAGTATCTTAGAGAAATCTTGTCTAAGAGCAAGGCCGGTGACGTTTATG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G51820.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA10G38590.1 (Glycine max), 3'ss of exon 17
-------------gtaagattgtgtatgaattttgttacagatcgcttgggaactaattttaatgtgaaaaccccctcaatttttta---cgactgtgtgatcagGAATGTGAATCTGAAGGAGCCAATAAAATGATCGAGTATCTTAGAGAAATCTTGTCTAAGAGCAAGGCCGGTGACGTTTATG
| |||| | | |||||| || || || | |||| || | ||| || | | | ||| | | | | | ||||||||||||||||||| |||||||| ||||| || || || |||| || ||||||||||||||| | ||||| ||||
gtaggtatcattgctgcaattgaagtttagttttgtaacctatt-ctgagatactaggttaagtgt-aatgtttctttattttaacaaatcaagtcgttatatagGAATGTGAATCTGAAGGTGCCAATAAGATGATAGAATACCTACGAGATATTTTGTCTAAGAGCAAGCCTGGTGATCAGTATG
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA20G29230.1 (Glycine max), 3'ss of exon 17
-------------gtaagattgtgtatgaattttgttacagatcgcttgggaactaattttaatgtgaaaaccccctcaatttttta--cgactgtgtgatcagGAATGTGAATCTGAAGGAGCCAATAAAATGATCGAGTATCTTAGAGAAATCTTGTCTAAGAGCAAGGCCGGTGACGTTTATG
| |||| | |||| ||| || || || | |||| || | ||| | | || || | | | | | | ||||||||||||||||||| |||||||| ||||| || | || |||| || |||||||||||||| | ||||| ||||
gtaggcatcattgctgcaattgaagtttaattctgtaacctatt-ctgagctactaggttaagtgtaatgtttctctattttaacaaatcaagtctatatatagGAATGTGAATCTGAAGGTGCCAATAAGATGATAGAACACCTACGAGATATTGTGTCTAAGAGCAAGCCTGGTGATCAGTATG
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 17
----------------------------------------------------gtaagattgtgtatgaattttgttacagatcg---cttgggaactaattttaatgtgaaaaccccctcaattttt----tacgactgtgtgatcagGAATGTGAATCTGAAGGAGCCAATAAAATGATCGAGTATCTTAGAGAAATCTTGTCTAAGAGCAAGGCCGGTGACGTTTATG
|| |||||| | |||| | | | || | ||| || || | ||| | | | | | ||||||||||||||||||||| |||||||||||||| || ||||||||||| | | |||||||||||||| ||||| ||||
gtgagcatgtacatctaatttgtattgaattatactggctcaacttttgctgtcaattttgtgttttctggaacatacacactagaattagatgtatagtcttagagtagcaattttttttttttgactaattcaaatccttattcagGAATGTGAATCTGAAGGTGCCAATAAAATGATAGAATATCTTAGAGATTTGGTCTCTAAGAGCAAGGCAGGTGAAAAGTATGMapped 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|86088359|gb|DR384118.1|DR384118EST: AGTATTGGGCGACATACGGAAGGAACNNNNNNNCAAGATACGACTATGAA GAATGTGAATCTGAAGGAGCCAATAAAATGATCGAGTATCTTAGAGAAATC
genomic: AGTATTGGGCGACATACGGAAGGAACTTTTTTTCAAGATACGACTATGAAgtaagattgt ... gtgtgatcagGAATGTGAATCTGAAGGAGCCAATAAAATGATCGAGTATCTTAGAGAAATC
EST:
gi|124783658|gb|EH873484.1|EH873484EST: CAAGATACGACTATGAA GAATGTGAGTCTGAAGGAGCCAATAAAATGATCGAGTATCTTAGAGAAATC
genomic: CAAGATACGACTATGAAgtaagattgt ... gtgtgatcagGAATGTGAATCTGAAGGAGCCAATAAAATGATCGAGTATCTTAGAGAAATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgggaactaattttaatgtgaaaaccccctcaattttttacgactgtgtgatcagGAATGTGAATCTGAAGGAGCCAATAAAATGATCGAGTATCTTAGAGAAATCTTGTCTAAGAGCAAGGCCGGTGACGTTTATG
taattttaatgtgaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagattgtgtatgaattttgttacagatcgcttgggaactaattttaatgtgaaaaccccctcaattttttacgactgtgtgatcagGAATGTGAATCTGAAGGAGCCAATAAAATGATCGAGTATCTTAGAGAAATCTTGTCTAAGAGCAAGGCCGGTGACGTTTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG