Sequence
atgc intronic sequence ATGC exonic sequencegttaacatttttctccaatttgactcttcttgttttgaaaattctttataaaacaaatgctgatgatgtgttgtggattttggaatggagtagGTGTTGGAGGAGAATCTTGATTGGGAAGATGTACAGTGGTCACAAACTGGTGTTTGGATTGCTGGAAAAGAGTACACTCTTGCTCGTGTTCATTTTCTCT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G08450.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G08450.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os07g29450.1 (Oryza sativa), 3'ss of exon 11
gttaacatttttctccaatttgactcttcttgttttgaaaattc---tttataaaaca-aatgctgatgatgtgttgtgg--attttggaatggagtagGTGTTGGAGGAGAATCTTGATTGGGAAGATGTACAGTGGTCACAAACTGGTGTTTGGATTGCTGGAAAAGAGTACACTCTTGCTCGTGTTCATTTTCTCT
|||| | | || | | || | | || ||||| | | ||| || ||| || | || || | | | | | | ||||| || |||| ||| | || ||||| ||||| |||||||| || |||||||||||| |||||||||| || || |||| || || || ||||| || |
-gtaacgtcctgctt---tctaacattaaaatggtggataattcgcatacagaaaccacaattctcacacggttttcttgttacctcgacgcaacgcagGTGCTGCAGGATAATTTGGAATGGGAGGATGTGCAGTGGTCGCAGACTGGTGTTTGGGTTGCTGGAAAGGAATATCCTCTCGCCCGAGTGCATTTCCTAT
upper sequence: AT5G08450.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA09G28530.1 (Glycine max), 3'ss of exon 9
--------gtta-acatttttctccaatttgactcttcttgttttga-aaattctttataaaacaaatgctgatgatgtgttgtggattttggaatggagtagGTGTTGGAGGAGAATCTTGATTGGGAAGATGTACAGTGGTCACAAACTGGTGTTTGGATTGCTGGAAAAGAGTACACTCTTGCTCGTGTTCATTTTCTCT
| || | ||| || | | | || | | | | ||| | | | || || | | | || || ||||| ||| ||||| | ||||| || || || |||||||||||||||||||| |||||||| ||||||||||| ||||| || || || |||||||| || ||||| | |
aatttgtggctatatattgttattctaattaatttacagaatgcaaacgtattgtgtttcaacttgattataaattcgaattctgcattttctgatg---cagGTGCTAGAGGAAAACCTGGACTGGGAAGATGTACAGTGGTCGCAAACTGGCGTTTGGATTGCAGGAAAGGAATATACCCTTGCTCGGGTGCATTTCTTGT
upper sequence: AT5G08450.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA16G33300.1 (Glycine max), 3'ss of exon 10
-gttaacat--ttttctccaatttgactcttcttgttttgaaaattc---tttataaaacaaat--gctgatgatgt--gttgtggattttggaatggagtagGTGTTGGAGGAGAATCTTGATTGGGAAGATGTACAGTGGTCACAAACTGGTGTTTGGATTGCTGGAAAAGAGTACACTCTTGCTCGTGTTCATTTTCTCT
| || | | | | ||||| | ||| | || | ||| | | ||| ||| | | | || || || ||||| |||| ||||| | ||||| || || || ||||||||||||||||||||||||||||| || |||||||| ||||| || || || |||||||| || ||||| | |
tctcaatttggtgctgtataattttattctaatgaattccagaatgcaaatgtatgtttcaacttgattaaaaattccaattctgcattttctaatg---cagGTGCTAGAGGAAAACCTGGACTGGGAAGATGTACAGTGGTCACAAACTGGCGTCTGGATTGCAGGAAAGGAATATACCCTTGCTCGGGTGCATTTCTTGT
upper sequence: AT5G08450.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA20G35720.1 (Glycine max), 3'ss of exon 10
-----------------------------------------------------gttaacatttttctccaatttgactcttct-tgttt-tgaaaattctttataaaacaaatgctgatgat--------gtgttgtggattttgga---------atggagtagGTGTTGGAGGAGAATCTTGATTGGGAAGATGTACAGTGGTCACAAACTGGTGTTTGGATTGCTGGAAAAGAGTACACTCTTGCTCGTGTTCATTTTCTCT
|| | ||| || || |||| | | ||||| ||||| | | || || | | | || | |||| | | | |||| ||||||| ||| | || ||||||||||| || ||||| ||| |||||||||||||||||||||| || || || || || || || ||||| | |
gtatttttaaatcacttctcatttattttcaacttgcatgttaaataatgtctcttgaattttctccccgatttattattgcaatgtttactcaaattacgtgcagaatgcatatttaaacttttcaattgtatcaataatttacaatctgcacttgttgtccagGTACTGGAGGAAAATTTGGACTGGGAAGATGTGCAATGGTCGCAAGCTGGTGTTTGGATTGCTGGAAAGGAATATACCCTGGCACGGGTGCATTTCTTGT
upper sequence: AT5G08450.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA10G31960.1 (Glycine max), 3'ss of exon 11
---------------------------------------------------------------gttaacatttttctccaatttgactcttcttgttttgaaaattctt-tataaaacaaatgctgatgatgtgttgtggattttggaatggag---tagGTGTTGGAGGAGAATCTTGATTGGGAAGATGTACAGTGGTCACAAACTGGTGTTTGGATTGCTGGAAAAGAGTACACTCTTGCTCGTGTTCATTTTCTCT
| | || | |||| | |||| || | | ||| | | | |||| | | | | | ||| || | | | || | ||||||| ||| | || ||||||||||| || ||||| ||||| |||||||||||||||||||| || || || | || || || ||||| | |
gtatttttaaatcacttctcatttattttcaacttgcattttgaatgtctcttgaattttctccctgattcattattgcaatgttactcaaattacgtgcagaatgcatatttaaactttccaattgtatcataatttatattctgcacttgctgtccagTTACTGGAGGAAAATTTGGACTGGGAAGATGTGCAATGGTCGCAAACAGGTGTTTGGATTGCTGGAAAGGAATATACCTTGGCACGAGTGCATTTCTTGT
upper sequence: AT5G08450.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 10
--gttaacatttttctccaatttgactcttcttgt--tttgaaaattctttataaaacaaatgctgatgatgtgttgtggat---tttggaatggagtagGTGTTGGAGGAGAATCTTGATTGGGAAGATGTACAGTGGTCACAAACTGGTGTTTGGATTGCTGGAAAAGAGTACACTCTTGCTCGTGTTCATTTTCTCT
|| || | | || ||| || || || || || |||| | ||||| ||| | || |||| |||||||||||||| || ||||| ||||| |||||||| |||||||||||||| || |||||||| || || | |||||||| |||||||| || |
taccaaatatccaaatggtgatgagctattcacaaaacttaaatatgtgcctggtaatccattctgaatcagaaccttggatctttttttggttgaacagGTCTTGGAGGAGAATCTCGACTGGGAGGATGTGCAGTGGTCCCAAACTGGTGTTTGTATAGCTGGAAAGGAATATGCGCTTGCTCGAGTTCATTTCCTATMapped 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|124940803|gb|EL017219.1|EL017219EST: AAGCTTATGCGGTCTATCGGGTTTCCACTCCCAGCAGATCATATACGAAG GTGTTGGAGGAGAATCTTGATTGGGAAG
genomic: AAGCTTATGCGGTCTATCGGGTTTCCACTCCCAGCAGATCATAT-CGA-Ggttaacattt ... aatggagtagGTGTTGGAGGAGAATCTTGATTGGGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaattctttataaaacaaatgctgatgatgtgttgtggattttggaatggagtagGTGTTGGAGGAGAATCTTGATTGGGAAGATGTACAGTGGTCACAAACTGGTGTTTGGATTGCTGGAAAAGAGTACACTCTTGCTCGTGTTCATTTTCTCT
tgctgat putative branch site (score: 3)
tttataaaacaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaacatttttctccaatttgactcttcttgttttgaaaattctttataaaacaaatgctgatgatgtgttgtggattttggaatggagtagGTGTTGGAGGAGAATCTTGATTGGGAAGATGTACAGTGGTCACAAACTGGTGTTTGGATTGCTGGAAAAGAGTACACTCTTGCTCGTGTTCATTTTCTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA