Sequence
atgc intronic sequence ATGC exonic sequencegtattcattcttccaagtttgtaatgaattgctatccaccacaaattgcttctgaatcagaaagatgttgatatagGTGTTAAGGAGACCAAGAATTGGGGCAGGCTACAAGTTAATAGACATGATCACAGAGCCTTGCAGGCTGATACGTCGTTGTGAAGTCACTGCGATTCTCA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G36860.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA02G06720.2 (Glycine max), 3'ss of exon 9
--------------------------gtattcattcttccaagttt---gtaatgaattgctatccaccacaaattgcttctgaatcagaaagatgttgatatagGTGTTAAGGAGACCAAGAATTGGGGCAGGCTACAAGTTAATAGACATGATCACAGAGCCTTGCAGGCTGATACGTCGTTGTGAAGTCACTGCGATTCTCA
|||| || || || | | ||| || || | | | | || | | | | ||| | || | |||||||||||||| || || ||||| ||| || | ||||| ||||| || ||||||| |||||| | |||||||||||||| || || || ||
gtagggatctcttgtgaatttcagtcttattgatgattttaattctcatataaaatatctctgttgataaagcagtggcttttatttgtttctttgtaattccagATTTTAAGGAGACCAAGGATAGGAGCAGGATACCAGCTCATAGATATGATAACCGAGCCTTTTAGGCTGGTCCGTCGTTGTGAAGTGACAGCCATACTTG
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G19010.1 (Glycine max), 3'ss of exon 8
--------------------------gtattcattcttccaagttt---gtaatgaattgctatccaccacaaattgcttctgaatcagaaagatgttgatatagGTGTTAAGGAGACCAAGAATTGGGGCAGGCTACAAGTTAATAGACATGATCACAGAGCCTTGCAGGCTGATACGTCGTTGTGAAGTCACTGCGATTCTCA
|||| || || || | | ||| || || | | | | || | | | | ||| | || | |||||||||||||| || || ||||| ||| || | ||||| ||||| || ||||||| |||||| | |||||||||||||| || || || ||
gtagggatctcttgtgaatttcagtcttattgatgattttaattctcatataaaatatctctgttgataaagcagtggcttttatttgtttctttgtaattccagATTTTAAGGAGACCAAGGATAGGAGCAGGATACCAGCTCATAGATATGATAACTGAGCCTTTTAGGCTGGTCCGTCGTTGTGAAGTGACAGCCATACTTG
upper sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA16G25750.1 (Glycine max), 3'ss of exon 9
----------------------------gtattcattcttccaagtttgtaatgaattgctatccaccacaaattgcttctgaatcagaaagatgttgatatagGTGTTAAGGAGACCAAGAATTGGGGCAGGCTACAAGTTAATAGACATGATCACAGAGCCTTGCAGGCTGATACGTCGTTGTGAAGTCACTGCGATTCTCA
| | ||| | | ||| || | | | || | || | | | | ||| | || | |||||||||||||| || || ||||| ||| || | ||||| ||||| || ||||||| |||||| | |||||||||||||| || || || ||
gtagggatctcttgtgaatttcagtcttatgatgattttaattctcatataaaatatatcggttgatcaagcagtggcttttatttgtttctttgtaattccagATTTTAAGGAGACCAAGGATAGGAGCAGGATACCAGCTCATAGATATGATAACTGAGCCTTTTAGGCTGGTCCGTCGTTGTGAAGTGACAGCCATACTTGMapped 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|86086879|gb|DR382638.1|DR382638EST: TACCTGAAACTAGAGGACTTTGTTTGTCTGAAGAACAAACTGTCACCACG GTGTTAAGGAGACCAAGAATTGGGGCAGGCTACAAGTTAATAGACATGATC
genomic: TACCTGAAACTAGAGGACTTTGTTTGTCTGAAGAACAAACTGTCACCACGgtattcattc ... gttgatatagGTGTTAAGGAGACCAAGAATTGGGGCAGGCTACAAGTTAATAGACATGATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatgaattgctatccaccacaaattgcttctgaatcagaaagatgttgatatagGTGTTAAGGAGACCAAGAATTGGGGCAGGCTACAAGTTAATAGACATGATCACAGAGCCTTGCAGGCTGATACGTCGTTGTGAAGTCACTGCGATTCTCA
tgttgat putative branch site (score: 4)
ttgatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattcattcttccaagtttgtaatgaattgctatccaccacaaattgcttctgaatcagaaagatgttgatatagGTGTTAAGGAGACCAAGAATTGGGGCAGGCTACAAGTTAATAGACATGATCACAGAGCCTTGCAGGCTGATACGTCGTTGTGAAGTCACTGCGATTCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT