Sequence
atgc intronic sequence ATGC exonic sequence...cctgcgtttgtatgatttaagatcaggagagaaaacaatgttctttggggattgtatggtttgtatcgtgcccctaatcttatgacttgggtcgcatcagATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCATGAGCGAAAGGCTGCAATGGCACAGGAAGCTGAGGCCTTCATTGCACTCCCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G11950.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G11950.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G05550.1 (Glycine max), 3'ss of exon 3
------cctgcgtttgtatgatttaagatcaggagagaaaacaatgttctttggggattgtatggtttgtatcgtgcccctaatcttatgacttgggtcgcatcagATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCATGAGCGAAAGGCTGCAATGGCACAGGAAGCTGAGGCCTTCATTGCACTCCCTG
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tatggttgttcttttttataatgacccctttgccatggaaataat--ttatagatgctttgatggagaaaatatgatcagtga----attgttgtaattttgacagATATCTGGTGAAACAGTAGGTGAAGTGAGGATTGTTTCAGATATGCACGAGCGTAAGGCTGCAATGGCACAAGAAGCTGATGCATTTGTTGCTCTCCCTG
upper sequence: AT5G11950.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G34510.1 (Glycine max), 3'ss of exon 3
cctgcgtttgtatgatttaagatcaggagagaaaacaatgttctttggggattg----tatggtttgtatcgtgcccctaatcttatgacttgg--gtcgcatcagATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCATGAGCGAAAGGCTGCAATGGCACAGGAAGCTGAGGCCTTCATTGCACTCCCTG
| | ||| | | | | | | ||| | || |||| | | |||| | | | || ||| |||| | ||| | |||||||||||||| | || || || |||||| ||||| |||| ||||||||||| || ||||||||||| || |||||||| || || || || |||||||
-----gatagtagtccctttgttatgaaaaaaaattatggtgctttcaatgtcgaaaatatgatcttttaattgttagtaag-ttataatttgcctattttgacagATATCTGGTGAACCAGTTGGTGAAGTAAGAATTGTTTCAGATATGCATGAGCGTAAAGCTGCAATGGCTCAAGAAGCTGATGCATTTATCGCCCTCCCTG
upper sequence: AT5G11950.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G11070.1 (Glycine max), 3'ss of exon 3
cctgcgtttgtatgatttaagatcaggagagaaa-acaatgttctt--tggggattgtatggtttgt--atcgtgcccctaatcttatgacttgg--gtcgcatcagATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCATGAGCGAAAGGCTGCAATGGCACAGGAAGCTGAGGCCTTCATTGCACTCCCTG
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-------gtagtccctttgtcatgaaaaaaaaattatggtgctttcaatgtggaaaatatgatcttttaatttttgcttgtaagttgtaatttgtctattttgacagATATCTGGTGAACCAGTTGGTGAAGTAAGAATTGTTTCAGATATGCATGAGCCTAAAGCTGCAATGGCTCAAGGAGCTGATGCATTTATTGCTCTCCCAG
upper sequence: AT5G11950.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0008g01040.t01 (Vitis vinifera), 3'ss of exon 3
------cctgcgtttgtatgatttaagatcaggagagaaaacaatgttctttggggattgtatggtttgtatcgtgcccctaatcttatgacttgggtcgcatcagATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCATGAGCGAAAGGCTGCAATGGCACAGGAAGCTGAGGCCTTCATTGCACTCCCTG
||| | | | | | | ||| | ||| | | || | || | | ||| || ||| ||| | | | ||||||||||| | ||||| ||||| |||||| |||| | |||||||||||||| || |||| |||||| || |||||||| || || ||||| || ||||
tagttccctatgatggaaagtacttcaatcttgtgagcagcttggagcatgtgaacaatggactactaatatattgt---taac---atgggtaaaatggtgacagATATCTGGCCAAACTGTTGGAGAAGTAAGAATTGTGTCGGACATGCATGAGCGGAAAGCTGAAATGGCTCAAGAAGCTGATGCTTTTATTGCTCTTCCTGMapped 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|125211916|gb|EL226870.1|EL226870EST: AATCATTCCCAAAGCTTTGATGCCAATTGAG ATATCTGGTGAGACTGTGGGAGATGTAAGA
genomic: AATCATTCCCAAAGCTTTGATGCCAATTGAGgtatgtatct ... gtcgcatcagATATCTGGTGAGACTGTGGGAGATGTAAGA
EST:
gi|125317571|gb|EL331656.1|EL331656EST: TGTACTTGGAATCATTCCCAAAGCTTTGATGCCAATTGAG ATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCAT
genomic: TGTACTTGGAATCATTCCCAAAGCTTTGATGCCAATTGAGgtatgtatct ... gtcgcatcagATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCAT
EST:
gi|125136641|gb|EL176671.1|EL176671EST: AATCATTCCCAAAGCTTTGATGCCAATTGAG ATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCATGAG
genomic: AATCATTCCCAAAGCTTTGATGCCAATTGAGgtatgtatct ... gtcgcatcagATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCATGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggggattgtatggtttgtatcgtgcccctaatcttatgacttgggtcgcatcagATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCATGAGCGAAAGGCTGCAATGGCACAGGAAGCTGAGGCCTTCATTGCACTCCCTG
ccctaat putative branch site (score: 3)
taatcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctgcgtttgtatgatttaagatcaggagagaaaacaatgttctttggggattgtatggtttgtatcgtgcccctaatcttatgacttgggtcgcatcagATATCTGGTGAGACTGTGGGAGATGTAAGAGTTGTTGCAGACATGCATGAGCGAAAGGCTGCAATGGCACAGGAAGCTGAGGCCTTCATTGCACTCCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - aagatca
- - - - - - - - - - - - - - - -aaaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccctaa