Sequence
atgc intronic sequence ATGC exonic sequenceCTTCCTCCTTTACCTTCATATGGATATGGAAGAGAGCATCATGGACCTCGTTATGGAAGTTTCATTCATGGACAGAATCTTAGAGATGTTGTTGTTACAGgttagttgattggtttgtgaattttgcttctggggactattcttgtgtttgcaatgtaactcttcttgtgtttgcattgtccttgttgagctttttaggc...
Basic information
species | Arabidopsis thaliana |
transcript | AT3G42950.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G42950.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA09G08270.1 (Glycine max), 5'ss of exon 2
CTTCCTCCTTTACCTTCATATGGATATGGAAGAGAGCATCATGGACCTCGTTATGGAAGTTTCATTCATGGACAGAATCTTAGAGATGTTGTTGTTACAGgttagt---tgattggtttgtgaattttgcttctggggactattcttgtgtttgcaatgtaactcttcttgtgtttgcattgtccttgttgagctttttaggc
| || | || ||||||||||| |||||||| ||||||| ||| ||||| ||| | ||||| |||||||| || ||||||||||||||||| | |||||| || | | | | | | ||| || || || ||| || || | | | ||| | | | | | | |
ATGCCCGCATTGCCTTCATATGGGTATGGAAGGGAGCATCCTGGTCCTCGATATAGCAGTTTAATTCATGGTCAAAATCTTAGAGATGTTGTCATAACAGgtcaggataaaaaaaggcatcgtcctctatctagaacaactgtttttac-ttaaaaatttagatcatttcttcttttaagtatttatatataagagaagaa--
upper sequence: AT3G42950.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA17G05550.1 (Glycine max), 5'ss of exon 2
CTTCCTCCTTTACCTTCATATGGATATGGAAGAGAGCATCATGGACCTCGTTATGGAAGTTTCATTCATGGACAGAATCTTAGAGATGTTGTTGTTACAGgttagttgattggtttgtgaattttgcttctggggactattcttgtgtttgcaat--gtaactcttcttgtgtttgcatt---gtccttgttgagctttttaggc
| ||||| || ||||||||||| ||||| || ||||||| ||| ||||| ||||| ||||| |||||||| || |||||| ||||||||| | |||||| || || | || | | || | | | | | | | ||| | | | | | |||| ||| || | || |
ATGCCTCCATTGCCTTCATATGGGTATGGGAGGGAGCATCCTGGGCCTCGATATGGCAGTTTGATTCATGGTCAACATCTTAAAGATGTTGTGATAACAGgtgaggatttttcatcctgcttccaatgtatgtgaaggaatacaaaagtcatacttggtatccaatgtcattgtcacattcaagtctttatcttgcagtg-----
upper sequence: AT3G42950.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA13G17170.1 (Glycine max), 5'ss of exon 2
CTTCCTCCTTTACCTTCATATGGATATGGAAGAGAGCATCATGGACCTCGTTATGGAAGTTTCATTCATGGACAGAATCTTAGAGATGTTGTTGTTACAGgttagttgattggtttgtgaattttgcttctggggactattcttgtgtttgcaa--tgtaactcttcttgtgtttgcattgtccttgttgagctttttaggc-----
| ||||| || ||||||||||| ||||| || ||||||| ||| ||||| ||||| ||||| |||||||| || |||||| ||||||||| | |||||| || | || | || |||||| | | | | | || || |||| | | ||| || | || | | |
ATGCCTCCATTGCCTTCATATGGGTATGGGAGGGAGCATCCTGGGCCTCGATATGGCAGTTTGATTCATGGTCAACATCTTAAAGATGTTGTGATAACAGgtgag-------gatttttcatcctgcttccaatgtatgtgaagggatacaaaagtcgtcactcactcttcatgacagaggtctttacttagtatccaatgtcattg
upper sequence: AT3G42950.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA15G19820.1 (Glycine max), 5'ss of exon 2
CTTCCTCCTTTACCTTCATATGGATATGGAAGAGAGCATCATGGACCTCGTTATGGAAGTTTCATTCATGGACAGAATCTTAGAGATGTTGTTGTTACAGgttag--ttgattggtttgtgaattttgcttctggg-gactattcttgtgtttgcaatgtaactcttcttgtgtttgcattgtccttgttgagctttttaggc
| ||| | || ||||||||||| |||||||| ||||||| || ||||| ||| | ||||| |||||||| || |||||| ||||||||| | |||||| || | | | | | | || || ||| || || | | | | | || || ||| | | | || |
ATGCCTGCATTGCCTTCATATGGGTATGGAAGGGAGCATCCCGGTCCTCGATATAGTAGTTTAATTCATGGTCAAAATCTTGTAGATGTTGTCATAACAGgtaaggataaaaaaagtcattatcctctctcgaggacaactgtttttacttcaggatttagataattttttcttttaagaatttaattataagagaagaa---
upper sequence: AT3G42950.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv11s0016g00720.t01 (Vitis vinifera), 5'ss of exon 2
CTTCCTCCTTTACCTTCATATGGATATGGAAGAGAGCATCATGGACCTCGTTATGGAAGTTTCATTCATGGACAGAATCTTAGAGATGTTGTTGTTACAGgttagttgattggtttgtgaatt-ttgcttctggggactattcttgt---gtttgcaatgtaactcttcttgtgtttgcattgtccttgttgagctttttaggc
| ||||| || ||||||||||| ||||| |||||||||| |||| |||| ||||| ||||| |||||||| || ||||||| ||||||||| | |||||| || | || | | || | | ||||||| ||| | ||| || | |||| | | | || ||
ATGCCTCCCTTGCCTTCATATGGGTATGGGAGAGAGCATCGTGGAGCTCGATATGGGAGTTTGATTCATGGTCAAAATCTTAAGGATGTTGTTATAACAGgtcagatatttcttccttttgccactgagttgaagtactattcctgttaaatggccaaagtgtagacttggatgttgactaaaaaatattcacatttgtt----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|164090913|gb|ES067712.1|ES067712EST: TGGAAGTTTCATTCATGGACAGAATCTTAGAGATGTTGTTGTTACAG GGAATAATGGTAGCATCAACGGGCAGGGACAAACGTGGTGGAAGAAGTATC
genomic: TGGAAGTTTCATTCATGGACAGAATCTTAGAGATGTTGTTGTTACAGgttagttgat ... tggaaaacagGGAATAATGGTAGCATCAACGGGCAGGGACAAACGTGGTGGAAGAAGTATC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTTCCTCCTTTACCTTCATATGGATATGGAAGAGAGCATCATGGACCTCGTTATGGAAGTTTCATTCATGGACAGAATCTTAGAGATGTTGTTGTTACAGgttagttgattggtttgtgaattttgcttctggggactattcttgtgtttgcaatgtaactcttcttgtgtttgcattgtccttgttgagctttttaggc
- - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcttctt