Sequence
atgc intronic sequence ATGC exonic sequencegtaacctctagacactcttagtggattggtttttaaaaaattgcaatcctaatttatgatttcggtaatctttaatgcaattcccagCCTCAAGCGAGAGAGAAAGCTGAGAAAGAGGGATTCAAAGTAAGTATCGCCAAGACAAGTTTCAAGGCAAACACAAAGGCCCTAGCCGAAAATGAAGGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G16155.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 11
-----------------------------------------------------------------------------------------------gtaacctctagacactcttagtggattggtttttaaaaaattgcaatcctaa-tttatgatttcggtaatctttaatgcaattcccagCCTCAAGCGAGAGAGAAAGCTGAGAAAGAGGGATTCAAAGTAAGTATCGCCAAGACAAGTTTCAAGGCAAACACAAAGGCCCTAGCCGAAAATGAAGGAG
||| || || || | | ||| | |||| || | |||| || | | || || ||| || ||||| || || || ||||| ||||| || || ||||| || ||||| | | ||||| ||||| ||||| |||||||||||||| || || ||||||||||
gtaagtgagataccattctccaatattacattctctgttcaacatagttgaaatctgcttggtaaagttaatttgactagtacactttcttaagtataaaatcacaacttgtttccaactcttgctttgcttggctagcaaaccaatctttacgactctaatcattgttcctgct-tttgcagCCACAGGCTAGGGAGAAGGCTGACAAGGAAGGATTTGAAATAAGTGTTGTAAAGACCAGTTTTAAGGCTAACACAAAGGCCCTGGCAGAGAATGAAGGAG
upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA07G37050.1 (Glycine max), 3'ss of exon 11
-gtaacctctagacactcttagtggattggtttttaaaaaattgc-----aatcctaatttatgatttcg------gtaatctttaatgcaattcc-cagCCTCAAGCGAGAGAGAAAGCTGAGAAAGAGGGATTCAAAGTAAGTATCGCCAAGACAAGTTTCAAGGCAAACACAAAGGCCCTAGCCGAAAATGAAGGAG
| |||| | || || | | | ||| | ||| | || | | || | || | ||| || ||| | ||||||||||| || ||||||| ||| |||||||| || |||||||| | ||||| |||||||| || || ||||||||||| ||||| ||||| |||||||
tccatactcttttcccttatattatttatacaataaaattactgcctctcattcttcacttgaattctcatgtgttgcgatcaaacataaaatcctgcagCCTCAAGCAAGGGAGAAAGGTGAAAAAGAGGGGTTTGAAGTAAGTGTTGCCAAAACAAGTTTTAAAGCTAACACAAAGGCTCTAGCAGAAAACGAAGGAG
upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 6
---------gtaacctctagacactcttagtggattgg---tttttaaaaaattgcaatcct---aatttatgatttcggtaatctttaatgcaattcccagCCTCAAGCGAGAGAGAAAGCTGAGAAAGAGGGATTCAAAGTAAGTATCGCCAAGACAAGTTTCAAGGCAAACACAAAGGCCCTAGCCGAAAATGAAGGAG
|| ||| | | | | | | ||| | | | || || | || | ||| || | ||| || || ||||||||||| || ||||||||||| || ||||| || |||||||| | ||||| |||||||| || || |||||||||||| |||| ||||| ||||| |
ttctgatctgttacccccttatattatatatatattaaaattactcattgtccctcactcatatgaactcatggatt--atgatcaaacattatatatgcagCCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGTTTTGAAGTAAGTGTTGCCAAAACAAGTTTTAAAGCTAACACAAAGGCCTTAGCTGAAAACGAAGGGG
upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 11
gtaacctctagacactcttagtggattggtttttaaaaaattgc-----aatcctaatt--tatgatttcggtaatcttta------atgcaattcccagCCTCAAGCGAGAGAGAAAGCTGAGAAAGAGGGATTCAAAGTAAGTATCGCCAAGACAAGTTTCAAGGCAAACACAAAGGCCCTAGCCGAAAATGAAGGAG
| || || | || || | | | | ||| | ||| | | | | ||||| || || | | || || ||||||||||| || ||||||||||| || ||||| || |||||||| | ||||| |||||||| || || |||||||||||| |||| ||||| ||||| |
tcaccccctttccccttatattatttatataataaaattactgcttgttgtccttcactcgtatgaactcatgtattatgataaaacatattatatgcagCCTCAAGCAAGGGAGAAAGCTGAAAAGGAGGGTTTTGAAGTAAGTGTTGCCAAAACAAGTTTTAAAGCTAACACAAAGGCCTTAGCTGAAAACGAAGGGG
upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 11
------------------------------------------------------------------------------------------------------------gtaacctctagacactcttagtggattggt-ttttaaaaaattgcaatcctaatttatgatttcg----gtaatctttaatgcaattcccagCCTCAAGCGAGAGAGAAAGCTGAGAAAGAGGGATTCAAAGTAAGTATCGCCAAGACAAGTTTCAAGGCAAACACAAAGGCCCTAGCCGAAAATGAAGGAG
| || | | | || | ||| ||| ||| | | | || | | | || ||| | ||| ||||||||||| || | ||||| ||| |||||||| || |||||||| | ||||| |||||||| || || ||||||||||| ||||| ||||| |||||||
gtatatcataattttattttgtttgatgtgtcattcactgcaacaatttacaatgaatgagttctcttttatgtgtggttaactttctctccattcttcttttccatcctcttttccttatattatttatacattaaaatttctgcctcttgtccttcacttgaattctcttgtgttgtgatcaaacttaaaatctgcagCCTCAAGCAAGGGTGAAAGGTGAAAAAGAGGGGTTTGAAGTAAGTGTTGCCAAAACAAGTTTTAAAGCTAACACAAAGGCTCTAGCAGAAAACGAAGGAG
upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 11
------------------------------------gtaacct--ctagacactcttagtggattggttttta------aaaaattgca-atcctaatttatgatttcggtaatctttaatgcaattcc---------cagCCTCAAGCGAGAGAGAAAGCTGAGAAAGAGGGATTCAAAGTAAGTATCGCCAAGACAAGTTTCAAGGCAAACACAAAGGCCCTAGCCGAAAATGAAGGAG
|||| | | || ||||| || | | | || ||| | || | |||||| || || ||| | ||||| || ||||| ||||| |||| | ||||||||||| |||||||| ||| | |||||||| || ||||| || ||||| ||||| || || || |||||||| |
gtatagcaatccttttgtttcacaatttactttttaataacttgatttgaacctctttgtaatgtagctcttgtgactggaaagcttcacagcctaatccatttttcaggtgaaagttaatttctttttattctctggcagCCACAAGCAAGAGCACTGGGAGAGAAAGAGGGTTTCAAAGTTAGTGTTGCCAAGACTAGCTTCAAAGCCAACACTAAGGCTCTCGCTGAGAATGAAGGCGMapped 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|86087012|gb|DR382771.1|DR382771EST: GCTTGTTTTACTCATCCTGAAATAAGTATGGTGGGATTGACAGAG CCTCAAGCGAGAGAGAAAGCTGAGAAAGAGGGATTCAAAGTAAGTATCGCC
genomic: GCTTGTTTTACTCATCCTGAAATAAGTATGGTGGGATTGACAGAGgtaacctcta ... caattcccagCCTCAAGCGAGAGAGAAAGCTGAGAAAGAGGGATTCAAAGTAAGTATCGCC
EST:
gi|164155496|gb|ES048292.1|ES048292EST: CAGCTGCTTGTTTTACTCATCCTGAAATAAGTATGGTGGGATTGACAGAG CCTCAAGCGAGAGAGAAAGCTGAGAAAGAGGGATTC
genomic: CAGCTGCTTGTTTTACTCATCCTGAAATAAGTATGGTGGGATTGACAGAGgtaacctcta ... caattcccagCCTCAAGCGAGAGAGAAAGCTGAGAAAGAGGGATTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaaaaattgcaatcctaatttatgatttcggtaatctttaatgcaattcccagCCTCAAGCGAGAGAGAAAGCTGAGAAAGAGGGATTCAAAGTAAGTATCGCCAAGACAAGTTTCAAGGCAAACACAAAGGCCCTAGCCGAAAATGAAGGAG
ttccc CT-rich tract
taatttatgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacctctagacactcttagtggattggtttttaaaaaattgcaatcctaatttatgatttcggtaatctttaatgcaattcccagCCTCAAGCGAGAGAGAAAGCTGAGAAAGAGGGATTCAAAGTAAGTATCGCCAAGACAAGTTTCAAGGCAAACACAAAGGCCCTAGCCGAAAATGAAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG